@article{morawska_electrochemical_2018,
	title = {Electrochemical and spectroscopic studies of the interaction of antiviral drug {Tenofovir} with single and double stranded {DNA}},
	volume = {123},
	doi = {10.1016/j.bioelechem.2018.06.002},
	abstract = {In the present study, the electrochemical behavior of the antiviral drug tenofovir (tnf) on a boron-doped diamond electrode (BDDE) has been studied using square-wave voltammetry (SWV). The experimental conditions such as the supporting electrolyte composition and the SWV parameters were optimized. Under the optimized conditions, a simple and sensitive SWV procedure for tnf determination was developed in the concentration range of 5.0 × 10−6 to 1.0 × 10−4 mol L−1. The calculated limit of detection and limit of quantification were equal to 5.6 × 10−7 and 1.9 × 10−6 mol L−1, respectively. The biological significance of the developed method was demonstrated by a quantitative analysis of the pharmaceutical formulations Viread and Tenofovir disoproxil Teva. Moreover, both voltammetric and spectroscopic techniques were used to study the interaction between tnf and DNA. Changes in the electrochemical and spectroscopic behavior of tnf in the presence of DNA were used to calculate the binding constants of the formed complexes. The estimated values of Gibbs free energy revealed that the formation of the drug–DNA complexes was a spontaneous and favorable process. Moreover, for free and bound tenofovir, kinetic parameters such as heterogeneous rate constant, electron transfer coefficient, and diffusion coefficient were determined. © 2018},
	journal = {Bioelectrochemistry},
	author = {Morawska, K. and Popławski, T. and Ciesielski, W. and Smarzewska, S.},
	year = {2018},
	keywords = {Animals, Antiviral Agents, Boron, Boron doped diamond, DNA, Diamond, Electrochemical Techniques, Electrodes, Limit of Detection, Salmon, Spectrum Analysis, Tenofovir, Thermodynamics, Voltammetry, dsDNA, ssDNA},
	pages = {227--232},
}

@article{sakowski_detailed_2017,
	title = {A detailed experimental study of a {DNA} computer with two endonucleases},
	volume = {72},
	issn = {0939-5075},
	doi = {10.1515/znc-2016-0137},
	abstract = {Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.},
	language = {eng},
	number = {7-8},
	journal = {Zeitschrift Fur Naturforschung. C, Journal of Biosciences},
	author = {Sakowski, Sebastian and Krasiński, Tadeusz and Sarnik, Joanna and Blasiak, Janusz and Waldmajer, Jacek and Poplawski, Tomasz},
	month = jul,
	year = {2017},
	pmid = {28432850},
	keywords = {Automation, Base Sequence, Computers, Molecular, DNA, DNA Ligases, DNA computing, Deoxyribonucleases, Type II Site-Specific, Endonucleases, Models, Theoretical, Oligonucleotides, biomolecular computers, finite automata},
	pages = {303--313},
}

@article{szejk_comparative_2017,
	title = {A comparative study on the radioprotective potential of the polyphenolic glycoconjugates from medicinal plants of {Rosaceae} and {Asteraceae} families versus their aglycones},
	volume = {171},
	issn = {1873-2682},
	doi = {10.1016/j.jphotobiol.2017.04.027},
	abstract = {Radioprotective potential of the polyphenolic glycoconjugates, isolated from flowers of Sanguisorba officinalis L. (So) and Erigeron canadensis L. (Ec), and from leaves of Fragaria vesca L. (Fv) and Rubus plicatus Whe. Et N. E. (Rp) as well as their aglycones (SoA, EcA, FvA and RpA, respectively), against γ-radiation-induced lipid peroxidation in human plasma and DNA damage in lymphocytes, were investigated in vitro. These properties were assessed by measuring the concentration of thiobarbituric acid reactive substances (TBARS) and using the alkaline comet assay, and were compared to the protective effects of rutin (R) and quercetin (Q). Cytotoxicity of the glycoconjugates/aglycones towards L929 mouse fibroblasts and human lymphocytes were also measured. Plant products from S. officinalis, similar to Q, were able to reduce the most radiation-induced lipid peroxidation as well as DNA damage and extent of oxidative damage to the DNA basis. Contrary to the pure flavonoids, where Q was shown to be significantly more effective than its glycoside R, the results did not show more benefit with application of SoA/EcA over So/Ec in terms of lipid peroxidation inhibition. Moreover, glycoconjugates Ec and So showed much higher capacity in protecting lymphocytes against radiation-induced genotoxicity which may suggest that between the polyphenolic and polysaccharide parts exist some synergistic effects. There were no significant differences between Fv versus FvA or Rp versus RpA in terms of the provided radioprotection. Summarizing, plant glycoconjugates isolated by the multi-step method offered sufficient radioprotection. In addition, they possess many advantages, compared to the synthetic polyphenolic compounds or the plant extracts, such as water-solubility and minor toxicity.},
	language = {eng},
	journal = {Journal of Photochemistry and Photobiology. B, Biology},
	author = {Szejk, Magdalena and Poplawski, Tomasz and Czubatka-Bienkowska, Anna and Olejnik, Alicja Klaudia and Pawlaczyk-Graja, Izabela and Gancarz, Roman and Zbikowska, Halina Malgorzata},
	month = jun,
	year = {2017},
	pmid = {28475935},
	keywords = {Aglycone, Animals, Antioxidants, Asteraceae, Cell Line, Cell Survival, Comet Assay, DNA, DNA Damage, Erigeron canadensis, Gamma Rays, Glycoconjugates, Humans, Lipid Peroxidation, Mice, Plants, Medicinal, Polyphenolic glycoconjugate, Polyphenols, Quercetin, Radiation-Protective Agents, Radioprotector, Rosaceae, Rutin, Sanguisorba officinalis, comet assay, γ-Irradiation},
	pages = {50--57},
}

@article{pascual_bloodstream_2016,
	title = {Bloodstream infections caused by {Escherichia} coli producing {AmpC} β-lactamases: epidemiology and clinical features},
	volume = {35},
	issn = {1435-4373},
	shorttitle = {Bloodstream infections caused by {Escherichia} coli producing {AmpC} β-lactamases},
	doi = {10.1007/s10096-016-2752-3},
	abstract = {The aim of the study was to investigate the epidemiology and clinical features of bloodstream infections due to Escherichia coli producing AmpC β-lactamases (AmpC-Ec-BSI). In a multi-centre case-control study, all third-generation-cephalosporin-resistant Escherichia coli BSI (3GC-Ec-BSI) isolates were analysed. Acquired bla AmpC (bla ac-AmpC) detection was done by polymerase chain reaction (PCR) and sequencing. Chromosomal bla AmpC (bla c-AmpC) expression was quantified by real-time PCR. Cases were patients with AmpC-Ec-BSI. Controls were patients with cephalosporin-susceptible E. coli BSI, matched 1:1 by sex and age. Demographics, comorbidities, intrinsic and extrinsic risk factors for antimicrobial resistance, clinical presentation and outcomes were investigated. Among 841 E. coli BSI, 17 were caused by AmpC-Ec (2 \%). Eleven isolates (58.8 \%) had bla ac-AmpC and six were bla c-AmpC overproducers. The mean age of cases was 66.2 years and 71 \% were men. Cases were more frequently healthcare-related (82 vs. 52 \% controls, p {\textless} 0.05) and presented more intrinsic and extrinsic risk factors. At least one risk factor was present in 94.1 \% of cases vs. 41.7 \% of controls (p = 0.002). Severity and length of stay (LOS) were higher among cases (mean Pitt Score 2.6 vs. 0.38 in controls, p = 0.03; LOS 17.5 days vs. 6 in controls, p = 0.02). Inappropriate empirical therapy (IET) was administered to 70.6 \% of cases and 23.5 \% of controls (p {\textless} 0.003). No differences were found in terms of cure rate at the 14th day and mortality. Bloodstream infections due to AmpC-Ec (mostly plasmid-mediated) are infrequent in our area. AmpC-Ec-BSI affects mainly patients with intrinsic risk factors and those with previous antibiotic exposure. A high proportion received IET.},
	language = {eng},
	number = {12},
	journal = {European Journal of Clinical Microbiology \& Infectious Diseases: Official Publication of the European Society of Clinical Microbiology},
	author = {Pascual, V. and Alonso, N. and Simó, M. and Ortiz, G. and Garcia, M. C. and Xercavins, M. and Rivera, A. and Morera, M. A. and Miró, E. and Espejo, E. and Navarro, F. and Gurguí, M. and Pérez, J. and Rodríguez-Carballeira, M. and Garau, J. and Calbo, E.},
	year = {2016},
	pmid = {27549108},
	keywords = {Adult, Age Distribution, Aged, Aged, 80 and over, Anti-Bacterial Agents, Bacteremia, Bacterial Proteins, Case-Control Studies, DNA, Bacterial, Escherichia coli, Escherichia coli Infections, Female, Humans, Length of Stay, Male, Middle Aged, Polymerase Chain Reaction, Risk Factors, Sequence Analysis, DNA, Severity of Illness Index, Treatment Outcome, beta-Lactamases},
	pages = {1997--2003},
}

@article{afiahayati_metavelvet-sl:_2015,
	title = {{MetaVelvet}-{SL}: an extension of the {Velvet} assembler to a de novo metagenomic assembler utilizing supervised learning},
	volume = {22},
	issn = {1756-1663},
	shorttitle = {{MetaVelvet}-{SL}},
	doi = {10.1093/dnares/dsu041},
	abstract = {The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics have been developed. MetaVelvet is an extension of the single-genome assembler Velvet. It has been proved to generate assemblies with higher N50 scores and higher quality than single-genome assemblers such as Velvet and SOAPdenovo when applied to metagenomic sequence reads and is frequently used in this research community. One important open problem for MetaVelvet is its low accuracy and sensitivity in detecting chimeric nodes in the assembly (de Bruijn) graph, which prevents the generation of longer contigs and scaffolds. We have tackled this problem of classifying chimeric nodes using supervised machine learning to significantly improve the performance of MetaVelvet and developed a new tool, called MetaVelvet-SL. A Support Vector Machine is used for learning the classification model based on 94 features extracted from candidate nodes. In extensive experiments, MetaVelvet-SL outperformed the original MetaVelvet and other state-of-the-art metagenomic assemblers, IDBA-UD, Ray Meta and Omega, to reconstruct accurate longer assemblies with higher N50 scores for both simulated data sets and real data sets of human gut microbial sequences.},
	language = {eng},
	number = {1},
	journal = {DNA research: an international journal for rapid publication of reports on genes and genomes},
	author = {Afiahayati, null and Sato, Kengo and Sakakibara, Yasubumi},
	month = feb,
	year = {2015},
	pmid = {25431440},
	pmcid = {PMC4379979},
	keywords = {Genome, Humans, Metagenome, Metagenomic, Sequence Analysis, DNA, Software, Support Vector Machine, de novo assembler, microbial community, short read, supervised learning},
	pages = {69--77}
}

@article{chin_short_2015,
	title = {Short {Communication}: {Increase} of {HIV}-1 {K103N} {Transmitted} {Drug} {Resistance} and {Its} {Association} with {Efavirenz} {Use} in {South} {Korea}},
	volume = {31},
	issn = {1931-8405},
	shorttitle = {Short {Communication}},
	doi = {10.1089/AID.2014.0368},
	abstract = {Previous studies reported a relatively low prevalence of transmitted drug resistance (TDR) in South Korea ({\textless}5\%). A genotypic resistance test was performed on 131 treatment-naive HIV-1-infected individuals from February 2013 to February 2014. Eleven individuals (8.4\%) presented TDR, of whom eight had K103N, revealing a significant increase in K103N TDR compared to previous studies (p{\textless}0.001). Using phylogenetic analysis, we identified three distinct clustering pairs with genetic relativeness and a total of five independent strains among the eight K103N cases. Our findings suggest that multiple sources of K103N occurred, most likely as a consequence of increased efavirenz use in South Korea.},
	language = {eng},
	number = {6},
	journal = {AIDS research and human retroviruses},
	author = {Chin, Bum Sik and Shin, Hyoung-Shik and Kim, Gayeon and Wagner, Gabriel A. and Gianella, Sara and Smith, Davey M.},
	month = jun,
	year = {2015},
	pmid = {25826122},
	pmcid = {PMC4516954},
	keywords = {Adult, Anti-HIV Agents, Benzoxazines, Cluster Analysis, Drug Resistance, Viral, Genotype, HIV Infections, HIV Reverse Transcriptase, HIV-1, Humans, Incidence, Male, Molecular Sequence Data, Mutation, Missense, Phylogeny, Republic of Korea, Sequence Analysis, DNA},
	pages = {603--607},
}

@article{mehta_hiv_2015,
	title = {{HIV} {Transmission} {Networks} in the {San} {Diego}-{Tijuana} {Border} {Region}},
	volume = {2},
	issn = {2352-3964},
	doi = {10.1016/j.ebiom.2015.07.024},
	abstract = {BACKGROUND: HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego-Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sides of the border.
METHODS: We gathered sociodemographic, geographic, clinical, and viral sequence data from HIV infected individuals participating in ten studies in the San Diego-Tijuana border region. Phylogenetic and network analysis was performed to infer putative relationships between HIV sequences. Correlates of identified clusters were evaluated and spatiotemporal relationships were explored using Bayesian phylogeographic analysis.
FINDINGS: After quality filtering, 843 HIV sequences with associated demographic data and 263 background sequences from the region were analyzed, and 138 clusters were inferred (2-23 individuals). Overall, the rate of clustering did not differ by ethnicity, residence, or sex, but bisexuals were less likely to cluster than heterosexuals or men who have sex with men (p = 0.043), and individuals identifying as white (p ≤ 0.01) were more likely to cluster than other races. Clustering individuals were also 3.5 years younger than non-clustering individuals (p {\textless} 0.001). Although the sampled San Diego and Tijuana epidemics were phylogenetically compartmentalized, five clusters contained individuals residing on both sides of the border.
INTERPRETATION: This study sampled {\textasciitilde} 7\% of HIV infected individuals in the border region, and although the sampled networks on each side of the border were largely separate, there was evidence of persistent bidirectional cross-border transmissions that linked risk groups, thus highlighting the importance of the border region as a "melting pot" of risk groups.
FUNDING: NIH, VA, and Pendleton Foundation.},
	language = {eng},
	number = {10},
	journal = {EBioMedicine},
	author = {Mehta, Sanjay R. and Wertheim, Joel O. and Brouwer, Kimberly C. and Wagner, Karla D. and Chaillon, Antoine and Strathdee, Steffanie and Patterson, Thomas L. and Rangel, Maria G. and Vargas, Mlenka and Murrell, Ben and Garfein, Richard and Little, Susan J. and Smith, Davey M.},
	month = oct,
	year = {2015},
	pmid = {26629540},
	pmcid = {PMC4634195},
	keywords = {Adult, Bayes Theorem, California, Cluster Analysis, Drug Resistance, Viral, Emigration and Immigration, Female, Genome, Viral, HIV, HIV Infections, HIV-1, Humans, International border, Male, Mexico, Middle Aged, Mutation, Phylogeny, Phylogeography, Population Surveillance, Sequence Analysis, DNA, Socioeconomic Factors, Transmission network, Young Adult},
	pages = {1456--1463},
}

Website  doi  abstract   bibtex   

@article{
 title = {Oxidized Porous Silicon Nanostructures Enabling Electrokinetic Transport for Enhanced DNA Detection},
 type = {article},
 year = {2015},
 keywords = {DNA,electrokinetic focusing,electrophoresis,optical biosensors,porous silicon},
 pages = {6725-6732},
 volume = {25},
 websites = {https://doi.org/10.1002/adfm.201502859},
 id = {43455a25-f4f4-38af-9d54-48bfa609617b},
 created = {2019-01-20T05:28:08.465Z},
 accessed = {2019-01-19},
 file_attached = {false},
 profile_id = {dc1fdcdf-637d-32ee-a353-6a1d76918405},
 last_modified = {2019-01-27T01:48:18.288Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Vilensky},
 private_publication = {false},
 abstract = {Nanostructured porous silicon (PSi) is a promising material for the label?free detection of biomolecules, but it currently suffers from limited applicability due to poor sensitivity, typically in micromolar range. This work presents the design, operation concept, and characterization of a novel microfluidic device and assay that integrates an oxidized PSi optical biosensor with electrokinetic focusing for a highly sensitive label?free detection of nucleic acids. Under proper oxidation conditions, the delicate nanostructure of PSi can be preserved, while providing sufficient dielectric insulation for application of high voltages. This enables the use of signal enhancement techniques, which are based on electric fields. Here, the DNA target molecules are focused using an electric field within a finite and confined zone, and this highly concentrated analyte is delivered to an on?chip PSi Fabry?Pérot optical transducer, prefunctionalized with capture probes. Using reflective interferometric Fourier transform spectroscopy real?time monitoring, a 1000?fold improvement in limit of detection is demonstrated compared to a standard assay, using the same biosensor. Thus, a measured limit of detection of 1 ? 10?9 m is achieved without compromising specificity. The concepts presented herein can be readily applied to other ionic targets, paving way for the development of other highly sensitive chemical and biochemical assays.},
 bibtype = {article},
 author = {Rita, Vilensky and Moran, Bercovici and Ester, Segal},
 doi = {10.1002/adfm.201502859},
 journal = {Advanced Functional Materials},
 number = {43}
}

@article{noor_big_2015,
	title = {Big {Data}: the challenge for small research groups in the era of cancer genomics.},
	volume = {113},
	issn = {1532-1827 0007-0920},
	doi = {10.1038/bjc.2015.341},
	abstract = {In the past decade, cancer research has seen an increasing trend towards high-throughput techniques and translational approaches. The increasing availability  of assays that utilise smaller quantities of source material and produce higher  volumes of data output have resulted in the necessity for data storage solutions  beyond those previously used. Multifactorial data, both large in sample size and  heterogeneous in context, needs to be integrated in a standardised, cost-effective  and secure manner. This requires technical solutions and administrative support not  normally financially accounted for in small- to moderate-sized research groups. In  this review, we highlight the Big Data challenges faced by translational research  groups in the precision medicine era; an era in which the genomes of over 75,000  patients will be sequenced by the National Health Service over the next 3 years to  advance healthcare. In particular, we have looked at three main themes of data  management in relation to cancer research, namely (1) cancer ontology management,  (2) IT infrastructures that have been developed to support data management and (3)  the unique ethical challenges introduced by utilising Big Data in research.},
	language = {eng},
	number = {10},
	journal = {British journal of cancer},
	author = {Noor, Aisyah Mohd and Holmberg, Lars and Gillett, Cheryl and Grigoriadis, Anita},
	month = nov,
	year = {2015},
	pmid = {26492224},
	pmcid = {PMC4815885},
	keywords = {*Genomics, High-Throughput Nucleotide Sequencing, Humans, Information Storage and Retrieval/economics, Neoplasms/*genetics, Precision Medicine, Sequence Analysis, DNA},
	pages = {1405--1412},
}

@article{ kidd_influenza_2014,
  title = {Influenza viruses: update on epidemiology, clinical features, treatment and vaccination},
  volume = {20},
  issn = {1531-6971},
  shorttitle = {Influenza viruses},
  doi = {10.1097/MCP.0000000000000049},
  abstract = {PURPOSE OF REVIEW: In the last decade, sporadic and lethal human disease caused by zoonotic avian influenza viruses, and the seasonal activity of human H1N1 2009 pandemic type have driven intense epidemiological and laboratory studies into the virus life cycle. This article highlights major developments from mid-2012 to early 2014.
RECENT FINDINGS: Advances in molecular techniques and efficient rollout of diagnostic tests have enabled the rapid identification of clinical cases and detailed genetic sequencing of viral genomes. Studies have contributed widely to the understanding of how and when influenza viruses circulate, what determines their innate pathogenicity in particular hosts and whether host cofactors influence disease severity. Other imperatives include investigations into how influenza can be better prevented by vaccination, or treated with antiviral drugs.
SUMMARY: Avian influenza viruses present a continuous threat to human populations. There is a need for sustained surveillance and downstream research to evaluate the potential for future pandemics.},
  language = {eng},
  number = {3},
  journal = {Current Opinion in Pulmonary Medicine},
  author = {Kidd, Mike},
  month = {May},
  year = {2014},
  pmid = {24637227},
  keywords = {Animals, Antiviral Agents, DNA, Viral, Drug Resistance, Viral, Female, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H5N1 Subtype, Influenza A Virus, H7N9 Subtype, Influenza A virus, Influenza in Birds, Influenza, Human, Male, Pandemics, Poultry, Seasons, Sentinel Surveillance, Sequence Analysis, DNA, Viral Vaccines, Zanamivir},
  pages = {242--246}
}

Paper  abstract   bibtex   

@electronic{citeulike:13075038,
    abstract = {List of indexed keywords within the transdisciplinary set of domains which relate to the Integrated Natural Resources Modelling and Management ({INRMM}). In particular, the list of keywords maps the semantic tags in the {INRMM} Meta-information Database ({INRMM}-{MiD}). [\n] The {INRMM}-{MiD} records providing this list are accessible by the special tag: inrmm-list-of-tags ( {http://mfkp.org/INRMM}/tag/inrmm-list-of-tags ).},
    author = {{M.R.I.}},
    citeulike-article-id = {13075038},
    citeulike-linkout-0 = {http://mfkp.org/INRMM/tag/inrmm-list-of-tags},
    citeulike-linkout-1 = {http://www.citeulike.org/group/15400/tag/inrmm-list-of-tags},
    keywords = {database, dataset, dating, dddas, de-facto-standard, dead-wood, debris, debris-floods, debris-flows, deciduous, deciduous-forest, decision-making, decision-making-procedure, decision-support-system, decline, decline-effect, decline-symptomology, deep-reproducible-research, deep-uncertainty, definition, deforestation, degenerated-soil, deglaciation, degradation, degradation-velocity, dehesas, delonix-regia, democracy, dendrochronology, dendroctonus, dendroctonus-frontalis, dendroctonus-micans, dendroctonus-ponderosae, dendroctonus-pseudotsugae, dendroecology, dendrology, denmark, density-related-behaviour, deposition, derived-data, desalinisation, description, desertification, deserts, design-diversity, devil-in-details, diabetes, diabetes-mellitus, diagram-data, diameter-differentiation, dictionary, die-off, dieback, diesel, differentiation, digital-preservation, digital-society, dimensional-analysis, dimensionality-reduction, dimensionless, dioryctria-splendidella, diospyros-kaki, diospyros-spp, diospyros-virginiana, diplodia-pinea, diprion-pini, dipteryx-panamensis, direct-reciprocity, disaster-recovery, disaster-response, disasters, discharge, disciplinary-barrier, disconcerting-learning, discount-rate, disease, diseases, disjunction, dispersal, dispersal-limitation, dispersal-models, dissent, distance-analysis, distance-correlation, distilled-gin, distribution, distribution-limit, disturbance-ecology, disturbance-interactions, disturbances, diversity, django, dna, dna-fingerprinting, dobrogea, dodonaea-viscosa, dormancy, dormouse, inrmm-list-of-tags},
    month = feb,
    posted-at = {2014-02-28 14:09:03},
    priority = {2},
    title = {List of keywords of the {INRMM} meta-information database - part 10},
    url = {http://mfkp.org/INRMM/tag/inrmm-list-of-tags},
    year = {2014}
}

@article{kalderimis_intermine:_2014,
	title = {{InterMine}: extensive web services for modern biology},
	volume = {42},
	issn = {1362-4962},
	shorttitle = {{InterMine}},
	doi = {10.1093/nar/gku301},
	abstract = {InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the web interface and can be re-used in many other applications: to find and filter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments, and for other statistical and analysis tools. Here we describe these features and discuss how they can be used separately or in combinations to support integrative and comparative analysis.},
	language = {eng},
	number = {Web Server issue},
	journal = {Nucleic Acids Research},
	author = {Kalderimis, Alex and Lyne, Rachel and Butano, Daniela and Contrino, Sergio and Lyne, Mike and Heimbach, Joshua and Hu, Fengyuan and Smith, Richard and Stěpán, Radek and Sullivan, Julie and Micklem, Gos},
	month = jul,
	year = {2014},
	pmid = {24753429},
	pmcid = {PMC4086141},
	keywords = {Animals, Chromosomes, Databases, Factual, Humans, Internet, Mice, Sequence Analysis, DNA, Software, User-Computer Interface},
	pages = {W468--472}
}

@book{el-metwally_next_2014,
	address = {New York},
	series = {{SpringerBriefs} in {Systems} {Biology}},
	title = {Next generation sequencing technologies and challenges in sequence assembly},
	isbn = {978-1-4939-0714-4},
	abstract = {The introduction of Next Generation Sequencing (NGS) technologies resulted in a major transformation in the way scientists extract genetic information from biological systems, revealing limitless insight about the genome, transcriptome and epigenome of any species. However, with NGS, came its own challenges that require continuous development in the sequencing technologies and bioinformatics analysis of the resultant raw data and assembly of the full length genome and transcriptome. Such developments lead to outstanding improvements of the performance and coverage of sequencing and improved quality for the assembled sequences, nevertheless, challenges such as sequencing errors, expensive processing and memory usage for assembly and sequencer specific errors remains major challenges in the field. This book aims to provide brief overviews the NGS field with special focus on the challenges facing the NGS field, including information on different experimental platforms, assembly algorithms and software tools, assembly error correction approaches and the correlated challenges.–},
	publisher = {Springer},
	author = {El-Metwally, Sara and Ouda, Osama M. and Helmy, Mohamed},
	year = {2014},
	keywords = {Base Sequence, DNA, Nucleotide sequence, Sequence Alignment, Sequence Analysis, Sequence alignment (Bioinformatics)},
}

Website  abstract   bibtex   

@article{
 title = {DNA binding dynamics and energetics of cobalt, nickel, and copper metallopeptides.},
 type = {article},
 year = {2014},
 identifiers = {[object Object]},
 keywords = {Amino Acid Sequence,Cluster Analysis,Cobalt,Cobalt: chemistry,Cobalt: metabolism,Copper,Copper: chemistry,DNA,DNA: chemistry,DNA: metabolism,Metalloproteases,Metalloproteases: chemistry,Metalloproteases: metabolism,Molecular Conformation,Molecular Dynamics Simulation,Nickel,Nickel: chemistry,Thermodynamics,Thymine,Thymine: chemistry},
 pages = {1252-9},
 volume = {9},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/24799395},
 month = {6},
 id = {498a55df-17e0-3f54-970a-30b0a4603aef},
 created = {2015-09-17T21:16:35.000Z},
 accessed = {2015-09-17},
 file_attached = {false},
 profile_id = {f6dc1d9a-3905-3337-924c-214414352692},
 last_modified = {2015-09-17T21:18:19.000Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {We present molecular dynamics (MD) and Quantum Theory of Atoms in Molecules (QTAIM) analysis of the DNA binding properties of three metallopeptides to the Drew-Dickerson dodecamer DNA: Co(II) -Gly(1) -Gly(2) -His, Ni(II) -Gly(1) -Gly(2) -His and Cu(II) -Gly(1) -Gly(2) -His. Fairly extensive MD simulations were run on each system until a stable binding mode for each ligand was sampled. Clustering analysis was used in an attempt to find representative structures for the most populated clusters sampled during the MD, and a QTAIM analysis was performed. Additionally, MM-PBSA analysis was performed to obtain approximate binding energies for each complex. The results suggest that stable DNA-metallopeptide complexes are formed with each of the three ligands, and that the most stable interaction is with Co(GGH), then Ni(GGH), and finally Cu(GGH). Bond Critical Points (BCP) information between the minor groove of the DNA and the metallopeptides shows an increase in electronic density between Gly(1) , the His residues, and the oxygen atoms of the thymine nucleotide. Overall, we present a detailed theoretical study of the specific interactions involved and the binding properties of each complex formed.},
 bibtype = {article},
 author = {Galindo-Murillo, Rodrigo and Cheatham 3rd, Thomas. E.},
 journal = {ChemMedChem},
 number = {6}
}

@article{adamsPhylogenyJuniperusUsing2013a,
  title = {Phylogeny of {{Juniperus}} Using {{nrDNA}} and Four {{cpDNA}} Regions},
  author = {Adams, R. P. and Schwarzbach, A. E.},
  year = {2013},
  volume = {95},
  pages = {179--187},
  abstract = {The Phylogeny of Juniperusis presented based on nrDNA (ITS), petN-psbM, trnS-trnG, trnD-trnT, trnL-trnF sequencing (4411 bp) utilizing all currently recognized species. The major clades of the phylogenetic tree were congruent with the previouslypublished phylogenetic tree of Mao et al. (2010) that had a subset of taxa of the current study. The lone species with serrate leaves in the eastern hemisphere, J. phoenicea, was found to be in a clade quite separated from the serrate junipers of North America. Juniperus phoeniceais referred to as 'pseudoserrate' to distinguish it from the semi-arid, serrate leaf junipers of the western hemisphere. Section Sabinais the most derived group and has radiated into niches in both the eastern and western hemispheres with approx. 60 species.},
  journal = {Phytologia},
  keywords = {*imported-from-citeulike-INRMM,~INRMM-MiD:c-13699749,forest-resources,juniperus-spp,phylogenetics,taxonomy},
  lccn = {INRMM-MiD:c-13699749},
  number = {2}
}

@article{tan_identification_2013,
	title = {Identification of a new cyclovirus in cerebrospinal fluid of patients with acute  central nervous system infections.},
	volume = {4},
	issn = {2150-7511},
	doi = {10.1128/mBio.00231-13},
	abstract = {Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4\% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58\%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.},
	language = {eng},
	number = {3},
	journal = {mBio},
	author = {Tan, Le Van and van Doorn, H. Rogier and Nghia, Ho Dang Trung and Chau, Tran Thi Hong and Tu, Le Thi Phuong and de Vries, Michel and Canuti, Marta and Deijs, Martin and Jebbink, Maarten F. and Baker, Stephen and Bryant, Juliet E. and Tham, Nguyen Thi and BKrong, Nguyen Thi Thuy Chinh and Boni, Maciej F. and Loi, Tran Quoc and Phuong, Le Thi and Verhoeven, Joost T. P. and Crusat, Martin and Jeeninga, Rienk E. and Schultsz, Constance and Chau, Nguyen Van Vinh and Hien, Tran Tinh and van der Hoek, Lia and Farrar, Jeremy and de Jong, Menno D.},
	month = jun,
	year = {2013},
	pmid = {23781068},
	pmcid = {PMC3684831},
	keywords = {Adolescent, Adult, Aged, Animals, Central Nervous System Infections/epidemiology/*virology, Child, Child, Preschool, Circoviridae Infections/epidemiology/*virology, Circoviridae/*classification/genetics/*isolation \& purification, Cluster Analysis, DNA, Viral/chemistry/genetics, Female, Genome, Viral, Humans, Infant, Male, Middle Aged, Molecular Sequence Data, Phylogeny, Prevalence, Prospective Studies, Sequence Analysis, DNA, Vietnam, Young Adult},
	pages = {e00231--00213},
}

@article{strain_new_2013,
	title = {New assays for monitoring residual {HIV} burden in effectively treated individuals},
	volume = {8},
	issn = {1746-6318},
	doi = {10.1097/COH.0b013e32835d811b},
	abstract = {PURPOSE OF REVIEW: Measurements of HIV burden have relied upon quantification of viral nucleic acids by real-time PCR (qPCR). To develop and test strategies for eradication, new methods are needed to better characterize residual cellular reservoirs in patients on suppressive antiretroviral therapy (ART). This review summarizes recent advances that may lead to clinically useful tests with improved sensitivity, reproducibility and throughput.
RECENT FINDINGS: HIV DNA remains the most sensitive measure of residual infection, but its low levels are difficult to differentiate from assay noise by qPCR. Digital PCR has begun to improve the precision of existing real-time assays, but there remains a need to distinguish replication-competent proviruses. Rapid technological progress in single-cell analysis is beginning to offer new approaches, notably CyTOF and microengraving, which could provide vastly more information about the composition of the latent reservoir.
SUMMARY: To investigate and assess therapies directed towards eradication, improved assays that simultaneously offer high sensitivity, precision and information content will be needed.},
	language = {eng},
	number = {2},
	journal = {Current opinion in HIV and AIDS},
	author = {Strain, Matthew C. and Richman, Douglas D.},
	month = mar,
	year = {2013},
	pmid = {23314907},
	pmcid = {PMC3754420},
	keywords = {Anti-HIV Agents, DNA, Viral, Drug Monitoring, HIV, HIV Infections, Humans, Proviruses, Viral Load},
	pages = {106--110},
}

Paper  Website  bibtex   

@article{
 title = {Genetics. Genealogy databases enable naming of anonymous DNA donors.},
 type = {article},
 year = {2013},
 identifiers = {[object Object]},
 keywords = {Anonymous Testing,Anonymous Testing: methods,DNA,DNA: genetics,Databases, Genetic,Genetic Markers,Genetic Privacy,Humans,Male,Names,Pedigree},
 pages = {262},
 volume = {339},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/23329025},
 month = {1},
 day = {18},
 id = {53f05a06-b98e-34c1-a2bc-7fec85b8fb59},
 created = {2017-06-19T13:39:20.325Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:39:20.470Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 bibtype = {article},
 author = {Bohannon, John},
 journal = {Science (New York, N.Y.)},
 number = {6117}
}

@article{cui_comparative_2013,
	title = {Comparative analysis of four oxidized guanine lesions from reactions of {DNA} with peroxynitrite, singlet oxygen, and γ-radiation},
	volume = {26},
	issn = {1520-5010},
	doi = {10.1021/tx300294d},
	abstract = {Oxidative damage to DNA has many origins, including irradiation, inflammation, and oxidative stress, but the chemistries are not the same. The most oxidizable base in DNA is 2-deoxyguanosine (dG), and the primary oxidation products are 8-oxodG and 2-amino-imidazolone. The latter rapidly converts to 2,2-diamino-oxazolone (Ox), and 8-oxodG is further oxidized to spiroiminodihydantoin (Sp) and guanidinohydantoin (Gh). In this study, we have examined the dose-response relationship for the formation of the above four products arising in calf thymus DNA exposed to gamma irradiation, photoactivated rose bengal, and two sources of peroxynitrite. In order to carry out these experiments, we developed a chromatographic system and synthesized isotopomeric internal standards to enable accurate and precise analysis based upon selected reaction monitoring mass spectrometry. 8-OxodG was the most abundant products in all cases, but its accumulation was highly dependent on the nature of the oxidizing agent and the subsequent conversion to Sp and Gh. Among the other oxidation products, Ox was the most abundant, and Sp was formed in significantly greater yield than Gh.},
	language = {eng},
	number = {2},
	journal = {Chemical Research in Toxicology},
	author = {Cui, Liang and Ye, Wenjie and Prestwich, Erin G. and Wishnok, John S. and Taghizadeh, Koli and Dedon, Peter C. and Tannenbaum, Steven R.},
	month = feb,
	year = {2013},
	pmid = {23140136},
	pmcid = {PMC3578445},
	note = {00026 },
	keywords = {Animals, Cattle, DNA, Deoxyguanosine, Gamma Rays, Guanidines, Guanine, Guanosine, Hydantoins, Oxidants, Oxidation-Reduction, Peroxynitrous Acid, Rose Bengal, Singlet oxygen, Spiro Compounds},
	pages = {195--202}
}

Website  abstract   bibtex   

@article{
 title = {Molecular recognition between DNA and a copper-based anticancer complex.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Antineoplastic Agents,Antineoplastic Agents: chemistry,Antineoplastic Agents: pharmacology,Copper,Copper: chemistry,DNA,DNA: chemistry,DNA: drug effects,Ligands,Molecular Dynamics Simulation,Organometallic Compounds,Organometallic Compounds: chemistry,Organometallic Compounds: pharmacology,Structure-Activity Relationship},
 pages = {15539-46},
 volume = {14},
 websites = {http://pubs.rsc.org/en/content/articlehtml/2012/cp/c2cp42185b},
 month = {11},
 publisher = {The Royal Society of Chemistry},
 day = {28},
 id = {71db2563-a07f-3450-9e24-c4f3c79f9787},
 created = {2013-04-01T20:34:59.000Z},
 accessed = {2013-04-01},
 file_attached = {false},
 profile_id = {f6dc1d9a-3905-3337-924c-214414352692},
 last_modified = {2015-08-21T05:42:19.000Z},
 read = {false},
 starred = {true},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Galindo-Murillo2012},
 language = {en},
 folder_ids = {49690701,49946861},
 abstract = {The aim of this work is to describe the specific recognition site between DNA and an anticancer copper complex by means of computational methods. Molecular dynamics were used to find the preferred site of binding between selected DNA chains and [Cu(2,2'-bipyridine)(acetylacetonate)(H(2)O)](+) (Cas). Full DFT optimizations of selected geometries extracted from simulations, followed by a topological analysis of electron density allowed us to define the specific interactions inside the recognition site. Cas links deoxyribose-phosphate by a coordination bond between metal and the phosphate group. There are several C-H···π, O···π(C) and O···π(N) interactions between the sugar group and the aromatic ligand of Cas. The results indicate that the adduct Cas-deoxyribose-phosphate may be an initial step toward the hydrolysis of DNA chains. Overall, this study provides insights into the initial step of the action mechanism of copper complexes as apoptosis-inducing agents and provides guidelines for the design of this kind of drugs.},
 bibtype = {article},
 author = {Galindo-Murillo, R. and Ruiz-Azuara, L. and Moreno-Esparza, R. and Cortés-Guzmán, F.},
 journal = {Physical chemistry chemical physics : PCCP},
 number = {44}
}

@article{
 title = {Metagenomes of the Picoalga Bathycoccus from the Chile coastal upwelling},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Chile,Chlorophyta,Chlorophyta: genetics,DNA,Metagenomics,Metagenomics: methods,Molecular Sequence Data,Oceans and Seas,RCC,SBR_Phyto_DIPO,Sequence Analysis},
 pages = {e39648},
 volume = {7},
 websites = {http://dx.plos.org/10.1371/journal.pone.0039648,http://figshare.com/articles/Metagenomes_of_the_Picoalga_Bathycoccus_from_the_Chile_Coastal_Upwelling/123702},
 month = {1},
 publisher = {Public Library of Science},
 editors = {[object Object]},
 id = {628d98fc-f70b-33e2-9b78-33543927cc62},
 created = {2015-11-02T11:41:37.000Z},
 accessed = {2014-11-27},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2015-11-02T11:41:37.000Z},
 tags = {2012,microb3,sbr_phyto_dipo},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.},
 bibtype = {article},
 author = {Vaulot, Daniel and Lepère, Cécile and Toulza, Eve and de la Iglesia, Rodrigo and Poulain, Julie and Gaboyer, Frédéric and Moreau, Hervé and Vandepoele, Klaas and Ulloa, Osvaldo and Gavory, Frederick and Piganeau, Gwenael},
 journal = {PLoS ONE},
 number = {6}
}

@article{choi_genetic_2012,
	title = {Genetic features of cerebrospinal fluid-derived subtype {B} {HIV}-1 tat},
	volume = {18},
	issn = {1538-2443},
	doi = {10.1007/s13365-011-0059-9},
	abstract = {Since HIV-1 Tat has been associated with neurocognitive dysfunction, we investigated 60 HIV-1 subtype B-infected individuals who were characterized for neurocognitive functioning and had paired CSF and blood plasma samples available. To avoid issues with repeated sampling, we generated population-based HIV-1 tat sequences from each compartment and evaluated these data using a battery of phylogenetic, statistical, and machine learning tools. These analyses identified position HXB2 5905 within the cysteine-rich domain of tat as a signature of CSF-derived HIV-1, and a higher number of mixed bases in CSF, as measure of diversity, was associated with HIV-associated neurocognitive disorder. Since identified mutations were synonymous, we evaluated the predicted secondary RNA structures, which showed that this mutation altered secondary structure. As a measure of divergence, the genetic distance between the blood and CSF-derived tat was inversely correlated with current and nadir CD4+ T cell counts. These data suggest that specific HIV-1 features of tat influence neurotropism and neurocognitive impairment.},
	language = {eng},
	number = {2},
	journal = {Journal of Neurovirology},
	author = {Choi, Jun Yong and Hightower, George K. and Wong, Joseph K. and Heaton, Robert and Woods, Steven and Grant, Igor and Marcotte, Thomas D. and Ellis, Ronald J. and Letendre, Scott L. and Collier, Ann C. and Marra, Christina M. and Clifford, David B. and Gelman, Benjamin B. and McArthur, Justin C. and Morgello, Susan and Simpson, David M. and McCutchan, J. Allen and Richman, Douglas D. and Smith, Davey M. and {Charter Group}},
	month = apr,
	year = {2012},
	pmid = {22528397},
	pmcid = {PMC3572198},
	keywords = {AIDS Dementia Complex, Adult, Artificial Intelligence, CD4 Lymphocyte Count, CD4-Positive T-Lymphocytes, Female, Genetic Heterogeneity, HIV-1, Humans, Male, Middle Aged, Mutation, Nucleic Acid Conformation, Protein Structure, Tertiary, RNA, Viral, Sequence Analysis, DNA, Viral Tropism, tat Gene Products, Human Immunodeficiency Virus},
	pages = {81--90},
}

@article{le_roex_novel_2012,
	title = {Novel {SNP} {Discovery} in {African} {Buffalo}, {Syncerus} caffer, using high-throughput {Sequencing}},
	volume = {7},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0048792},
	abstract = {The African buffalo, Syncerus caffer, is one of the most abundant and ecologically important species of megafauna in the savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9 animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× coverage over the mapped regions was obtained. Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of 2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43-54\% of the Bowtie SNPs and 57-58\% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly evolving house-keeping genes.},
	language = {eng},
	number = {11},
	journal = {PloS One},
	author = {le Roex, Nikki and Noyes, Harry and Brass, Andrew and Bradley, Daniel G. and Kemp, Steven J. and Kay, Suzanne and van Helden, Paul D. and Hoal, Eileen G.},
	year = {2012},
	pmid = {23144973},
	pmcid = {PMC3492240},
	note = {00008 },
	keywords = {Animals, Buffaloes, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Selection, Genetic, Sequence Analysis, DNA},
	pages = {e48792},
}

Paper  doi  abstract   bibtex   

@article{Pinheiro2012,
	title = {Synthetic genetic polymers capable of heredity and evolution.},
	volume = {336},
	issn = {1095-9203},
	url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1217622 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3362463&tool=pmcentrez&rendertype=abstract},
	doi = {10.1126/science.1217622},
	abstract = {Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown. With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage.},
	number = {6079},
	journal = {Science (New York, N.Y.)},
	author = {Pinheiro, Vitor B. and Taylor, Alexander I. and Cozens, Christopher and Abramov, Mikhail and Renders, Marleen and Zhang, Su and Chaput, John C. and Wengel, Jesper and Peak-Chew, S.-Y. Sew-Yeu S.-Y. and McLaughlin, Stephen H. and Herdewijn, Piet and Holliger, Philipp},
	month = apr,
	year = {2012},
	pmid = {22517858},
	note = {tex.ids= pinheiroSyntheticGeneticPolymers2012, pinheiroSyntheticGeneticPolymers2012a},
	keywords = {Aptamers, DNA, DNA-Directed DNA Polymerase, DNA-Directed DNA Polymerase: chemistry, DNA-Directed DNA Polymerase: genetics, DNA-Directed DNA Polymerase: metabolism, DNA: chemistry, DNA: genetics, Directed Molecular Evolution, Evolution, Genetic, Molecular, Molecular Mimicry, Nucleic Acids, Nucleic Acids: chemistry, Nucleic Acids: genetics, Nucleic Acids: metabolism, Nucleotide, Nucleotide: chemistry, Nucleotide: genetics, Nucleotide: metabolism, Polymers, Polymers: chemistry, Polymers: metabolism, RNA, RNA-Directed DNA Polymerase, RNA-Directed DNA Polymerase: chemistry, RNA-Directed DNA Polymerase: metabolism, RNA: chemistry, RNA: genetics, Reverse Transcription, Templates, Transcription},
	pages = {341--4},
}

Paper  Website  abstract   bibtex   

@article{
 title = {Impact of fertility transmission and other sociodemographic factors on reproductive success and coalescent trees},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Child,Computer Simulation,DNA,Demography,Female,Fertility,Fertility: genetics,Genetic,Humans,Male,Mitochondrial,Mitochondrial: genetics,Models,Pedigree,Reproduction,Reproduction: genetics,Selection,Socioeconomic Factors},
 pages = {121-131},
 volume = {94},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/22647505},
 month = {6},
 id = {a18e731f-a7b9-387b-855e-2c00bc595d5d},
 created = {2017-06-19T13:39:53.156Z},
 accessed = {2013-05-22},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:39:53.295Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 notes = {<m:note>        <m:bold>From Duplicate 2 ( </m:bold>                <m:bold>          </m:bold><m:bold><m:italic>Impact of fertility transmission and other sociodemographic factors on reproductive success and coalescent trees.</m:italic></m:bold><m:bold>        </m:bold>                <m:bold> - Brandenburg, Jean-Tristan; Austerlitz, Frédéric; Toupance, Bruno )<m:linebreak/>        </m:bold>        <m:linebreak/>        <m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {Fertility transmission (FT) is a phenomenon with a cultural and/or genetic basis, whereby a positive correlation exists between the number of offspring of an individual and that of his/her parents. Theoretical studies using a haploid individual-based model have shown that FT increases the variance and intergenerational correlation in reproductive success and results in an imbalance in the coalescent tree of sampled genes. This phenomenon has been documented in several demographic studies conducted on the correlation in fertility between generations, or through the reconstruction of the genealogical trees of mitochondrial DNA sequences. However, as mtDNA is a single locus, potentially subject to other forces (e.g. natural selection), it is of interest to extend the theory of FT to nuclear loci.We show that because random mating between individuals leads to a mixing of their fertility profiles, FT in these cases will have less influence on the variance and intergenerational correlation of reproductive success. This, in turn, results in less impact on the shape of the coalescent trees. Nevertheless, in the presence of FT, high heterogeneity in reproductive success and homogamy for family size will increase the imbalance in the coalescent tree. Thus, FT should be easier to detect when occurring in conjunction with these other factors.We also show the utility of analysing different kinds of loci (X-linked, Y-linked, mitochondrial and autosomal) to assess whether FT is matrilineal, patrilineal or biparental. Finally, we demonstrate that the shape of the coalescent tree depends upon population size, in contrast to the classical Kingman’s model.},
 bibtype = {article},
 author = {Brandenburg, Jean-Tristan and Austerlitz, Frédéric and Toupance, Bruno},
 journal = {Genetics research},
 number = {3}
}

@article{gianella_sexual_2012,
	title = {Sexual transmission of predicted {CXCR4}-tropic {HIV}-1 likely originating from the source partner's seminal cells},
	volume = {434},
	issn = {1096-0341},
	doi = {10.1016/j.virol.2012.09.010},
	abstract = {We present a case of sexual transmission of HIV-1 predicted to have CXCR4-tropism during male-to-male sexual exposure. Phylogenetic analyses exclude cell-free virus in the seminal plasma of the source partner and possibly point to the seminal cells as the origin of the transmission event.},
	language = {eng},
	number = {1},
	journal = {Virology},
	author = {Gianella, Sara and Mehta, Sanjay R. and Young, Jason A. and Vargas, Milenka V. and Little, Susan J. and Richman, Douglas D. and Kosakovsky Pond, Sergei L. and Smith, Davey M.},
	month = dec,
	year = {2012},
	pmid = {23040890},
	pmcid = {PMC3485073},
	keywords = {Adult, Cluster Analysis, HIV Infections, HIV-1, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Viral, Receptors, CXCR4, Receptors, HIV, Semen, Sequence Analysis, DNA, Young Adult},
	pages = {2--4},
}

@article{naka_role_2012,
	title = {The role of physical barriers in the location of avian suture zones in the {Guiana} {Shield}, northern {Amazonia}},
	volume = {179},
	issn = {1537-5323},
	doi = {10.1086/664627},
	abstract = {Suture zones represent natural forums in which to examine the role of geography and ecology in the speciation process. Here, we conduct a comparative analysis designed to investigate the location of avian phylogeographic breaks and contact zones in the Guiana Shield, northern Amazonia. We use distributional and genetic data from 78 pairs of avian taxa to address whether phylogeographic breaks and contact zones are associated with contemporary landscape features. Using spatially explicit statistical models, we found that phylogeographic breaks and contact zones are not randomly distributed throughout the landscape. In general, geographic breaks cluster along physical barriers (rivers, nonforested habitats, and small mountain ranges), whereas contact zones aggregate where these barriers either break down or are easier to overcome, such as around rivers' headwaters. Our results indicate that although major Amazonian rivers are often key determinants of taxon boundaries, the "riverine barrier effect" is a synergistic consequence of the wide lower reaches of some rivers, coupled with nonriverine landscape features at the headwaters. Our data suggest that ancestral refugia are not necessary to explain current distribution patterns and that pairs of codistributed taxa do not seem to be the result of simultaneous diversification processes.},
	language = {eng},
	number = {4},
	journal = {The American Naturalist},
	author = {Naka, Luciano Nicolas and Bechtoldt, Catherine L. and Henriques, L. Magalli Pinto and Brumfield, Robb T.},
	month = apr,
	year = {2012},
	pmid = {22437185},
	keywords = {Animals, Birds, DNA, Mitochondrial, Genotype, Models, Genetic, NADH Dehydrogenase, Phenotype, Phylogeny, Phylogeography, Rivers, South America, Trees},
	pages = {E115--132}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S. vulgaris autosome.},
 type = {article},
 year = {2012},
 identifiers = {[object Object]},
 keywords = {Base Composition,Base Composition: genetics,Chromosomes, Artificial, Bacterial,Chromosomes, Artificial, Bacterial: genetics,Chromosomes, Plant,Chromosomes, Plant: genetics,DNA Transposable Elements,DNA Transposable Elements: genetics,Gene Expression Regulation, Plant,Genes, Plant,Genes, Plant: genetics,Genetic Linkage,Microsatellite Repeats,Microsatellite Repeats: genetics,Molecular Sequence Annotation,Molecular Sequence Data,Mutagenesis, Insertional,Mutagenesis, Insertional: genetics,Recombination, Genetic,Recombination, Genetic: genetics,Sequence Analysis, DNA,Silene,Silene: genetics},
 pages = {226},
 volume = {13},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3431222&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {013e0ebf-fc13-39ac-85ce-c35124ae223e},
 created = {2017-09-18T09:15:16.823Z},
 file_attached = {true},
 profile_id = {1c95d708-d42d-399e-b365-9d34fead1a19},
 last_modified = {2017-09-18T09:22:14.644Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Blavet2012},
 abstract = {BACKGROUND: The sex chromosomes of Silene latifolia are heteromorphic as in mammals, with females being homogametic (XX) and males heterogametic (XY). While recombination occurs along the entire X chromosome in females, recombination between the X and Y chromosomes in males is restricted to the pseudoautosomal region (PAR). In the few mammals so far studied, PARs are often characterized by elevated recombination and mutation rates and high GC content compared with the rest of the genome. However, PARs have not been studied in plants until now. In this paper we report the construction of a BAC library for S. latifolia and the first analysis of a > 100 kb fragment of a S. latifolia PAR that we compare to the homologous autosomal region in the closely related gynodioecious species S. vulgaris.

RESULTS: Six new sex-linked genes were identified in the S. latifolia PAR, together with numerous transposable elements. The same genes were found on the S. vulgaris autosomal segment, with no enlargement of the predicted coding sequences in S. latifolia. Intergenic regions were on average 1.6 times longer in S. latifolia than in S. vulgaris, mainly as a consequence of the insertion of transposable elements. The GC content did not differ significantly between the PAR region in S. latifolia and the corresponding autosomal region in S. vulgaris.

CONCLUSIONS: Our results demonstrate the usefulness of the BAC library developed here for the analysis of plant sex chromosomes and indicate that the PAR in the evolutionarily young S. latifolia sex chromosomes has diverged from the corresponding autosomal region in the gynodioecious S. vulgaris mainly with respect to the insertion of transposable elements. Gene order between the PAR and autosomal region investigated is conserved, and the PAR does not have the high GC content observed in evolutionarily much older mammalian sex chromosomes.},
 bibtype = {article},
 author = {Blavet, Nicolas and Blavet, Hana and Cegan, Radim and Zemp, Niklaus and Zdanska, Jana and Janoušek, Bohuslav and Hobza, Roman and Widmer, Alex},
 journal = {BMC genomics}
}

@article{ gkikopoulos_swi/snf_2011,
  title = {The {SWI}/{SNF} complex acts to constrain distribution of the centromeric histone variant {Cse}4},
  volume = {30},
  issn = {1460-2075},
  doi = {10.1038/emboj.2011.112},
  abstract = {In order to gain insight into the function of the Saccharomyces cerevisiae SWI/SNF complex, we have identified DNA sequences to which it is bound genomewide. One surprising observation is that the complex is enriched at the centromeres of each chromosome. Deletion of the gene encoding the Snf2 subunit of the complex was found to cause partial redistribution of the centromeric histone variant Cse4 to sites on chromosome arms. Cultures of snf2Δ yeast were found to progress through mitosis slowly. This was dependent on the mitotic checkpoint protein Mad2. In the absence of Mad2, defects in chromosome segregation were observed. In the absence of Snf2, chromatin organisation at centromeres is less distinct. In particular, hypersensitive sites flanking the Cse4 containing nucleosomes are less pronounced. Furthermore, SWI/SNF complex was found to be especially effective in the dissociation of Cse4 containing chromatin in vitro. This suggests a role for Snf2 in the maintenance of point centromeres involving the removal of Cse4 from ectopic sites.},
  language = {eng},
  number = {10},
  journal = {The EMBO journal},
  author = {Gkikopoulos, Triantaffyllos and Singh, Vijender and Tsui, Kyle and Awad, Salma and Renshaw, Matthew J. and Scholfield, Pieta and Barton, Geoffrey J. and Nislow, Corey and Tanaka, Tomoyuki U. and Owen-Hughes, Tom},
  month = {May},
  year = {2011},
  pmid = {21505420},
  pmcid = {PMC3098484},
  keywords = {Adenosine Triphosphatases, Binding Sites, Centromere, Chromatin Assembly and Disassembly, Chromosomal Proteins, Non-Histone, Chromosome Segregation, DAG, DNA, Fungal, DNA-Binding Proteins, Gene Deletion, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors},
  pages = {1919--1927}
}

@Article{Meder2011a,
  author          = {Meder, Benjamin and Haas, Jan and Keller, Andreas and Heid, Christiane and Just, Steffen and Borries, Anne and Boisguerin, Valesca and Scharfenberger-Schmeer, Maren and Stähler, Peer and Beier, Markus and Weichenhan, Dieter and Strom, Tim M and Pfeufer, Arne and Korn, Bernhard and Katus, Hugo A and Rottbauer, Wolfgang},
  title           = {Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies.},
  journal         = {Circulation. Cardiovascular genetics},
  year            = {2011},
  volume          = {4},
  pages           = {110--122},
  month           = apr,
  issn            = {1942-3268},
  abstract        = {Today, mutations in more than 30 different genes have been found to cause inherited cardiomyopathies, some associated with very poor prognosis. However, because of the genetic heterogeneity and limitations in throughput and scalability of current diagnostic tools up until now, it is hardly possible to genetically characterize patients with cardiomyopathy in a fast, comprehensive, and cost-efficient manner. We established an array-based subgenomic enrichment followed by next-generation sequencing to detect mutations in patients with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). With this approach, we show that the genomic region of interest can be enriched by a mean factor of 2169 compared with the coverage of the whole genome, resulting in high sequence coverage of selected disease genes and allowing us to define the genetic pathogenesis of cardiomyopathies in a single sequencing run. In 6 patients, we detected disease-causing mutations, 2 microdeletions, and 4 point mutations. Furthermore, we identified several novel nonsynonymous variants, which are predicted to be harmful, and hence, might be potential disease mutations or modifiers for DCM or HCM. The approach presented here allows for the first time a comprehensive genetic screening in patients with hereditary DCM or HCM in a fast and cost-efficient manner.},
  chemicals       = {Carrier Proteins, Codon, Nonsense, MYH7 protein, human, myosin-binding protein C, integrin-linked kinase, Protein-Serine-Threonine Kinases, Cardiac Myosins, Myosin Heavy Chains},
  citation-subset = {IM},
  completed       = {2011-08-10},
  country         = {United States},
  doi             = {10.1161/CIRCGENETICS.110.958322},
  issn-linking    = {1942-3268},
  issue           = {2},
  keywords        = {Adult; Base Sequence; Cardiac Myosins, genetics; Cardiomyopathy, Dilated, diagnosis, genetics; Cardiomyopathy, Hypertrophic, diagnosis, genetics; Carrier Proteins, genetics; Child; Codon, Nonsense; Female; Frameshift Mutation; Gene Deletion; Genetic Heterogeneity; Humans; Male; Middle Aged; Mutation, Missense; Myosin Heavy Chains, genetics; Point Mutation; Protein-Serine-Threonine Kinases, genetics; Sequence Analysis, DNA, methods},
  nlm-id          = {101489144},
  owner           = {NLM},
  pii             = {CIRCGENETICS.110.958322},
  pmid            = {21252143},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2013-11-21},
}

@article{kodama_rhizomicrobium_2011,
	title = {Rhizomicrobium electricum sp. nov., a facultatively anaerobic, fermentative, prosthecate bacterium isolated from a cellulose-fed microbial fuel cell},
	volume = {61},
	issn = {1466-5034},
	doi = {10.1099/ijs.0.023580-0},
	abstract = {A facultatively anaerobic, prosthecate bacterium, strain Mfc52(T), was isolated from a microbial fuel cell inoculated with soil and fed with cellulose as the sole fuel. Cells were Gram-negative, non-spore-forming, straight or slightly curved rods, and some of them had one or two polar prosthecae (stalks). Cells reproduced by binary fission or by budding from mother cells having prosthecae. Strain Mfc52(T) fermented various sugars and produced lactate, acetate and fumarate. Ferric iron, nitrate, oxygen and fumarate served as electron acceptors, while sulfate and malate did not. Nitrate was reduced to nitrite. The DNA G+C content was 64.7 mol\%. On the basis of 16S rRNA gene sequence phylogeny, strain Mfc52(T) was affiliated with the genus Rhizomicrobium in the class Alphaproteobacteria and most closely related to Rhizomicrobium palustre with a sequence similarity of 97 \%. Based on these physiological and phylogenetic characteristics, the name Rhizomicrobium electricum sp. nov. is proposed; the type strain is Mfc52(T) ( = JCM 15089(T)  = KCTC 5806(T)).},
	number = {Pt 8},
	journal = {International journal of systematic and evolutionary microbiology},
	author = {Kodama, Yumiko and Watanabe, Kazuya},
	month = aug,
	year = {2011},
	pmid = {20802060},
	keywords = {Alphaproteobacteria, Bacteria, Anaerobic, Base Composition, Bioelectric Energy Sources, Cellulose, DNA, Bacterial, DNA, Ribosomal, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S},
	pages = {1781--1785}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Novel Family of Carbohydrate-Binding Modules Revealed by the Genome Sequence of Spirochaeta thermophila DSM 6192},
 type = {article},
 year = {2011},
 identifiers = {[object Object]},
 keywords = {4-beta Xylanases,4-beta Xylanases: genetics,Amino Acid Sequence,Bacterial,Base Sequence,Carbohydrate Metabolism,Carbohydrates,Cell Surface,Cell Surface: chemistry,Cell Surface: genetics,Cell Surface: metabolism,Cellulase,Cellulase: genetics,Cellulose,Cellulose: metabolism,Cytophaga,Cytophaga: genetics,Cytophaga: metabolism,DNA,Endo-1,Genome,Glycoside Hydrolases,Glycoside Hydrolases: chemistry,Glycoside Hydrolases: genetics,Glycoside Hydrolases: metabolism,Phylogeny,Protein Binding,Protein Binding: genetics,Proteoglycans,Proteoglycans: metabolism,Receptors,Sequence Alignment,Sequence Analysis,Spirochaeta,Spirochaeta: genetics,Spirochaeta: metabolism,Transforming Growth Factor beta,Transforming Growth Factor beta: metabo},
 pages = {5483-5489},
 volume = {77},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3147429&tool=pmcentrez&rendertype=abstract},
 month = {6},
 day = {17},
 id = {58317be2-c703-3488-b075-8d91d488f7ff},
 created = {2014-02-24T16:38:28.000Z},
 accessed = {2014-02-07},
 file_attached = {true},
 profile_id = {5224208a-a292-315a-8304-ffd095bfd482},
 last_modified = {2017-03-15T14:05:40.435Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Angelov2011},
 private_publication = {false},
 abstract = {Spirochaeta thermophila is a thermophilic, free-living, and cellulolytic anaerobe. The genome sequence data for this organism have revealed a high density of genes encoding enzymes from more than 30 glycoside hydrolase (GH) families and a noncellulosomal enzyme system for (hemi)cellulose degradation. Functional screening of a fosmid library whose inserts were mapped on the S. thermophila genome sequence allowed the functional annotation of numerous GH open reading frames (ORFs). Seven different GH ORFs from the S. thermophila DSM 6192 genome, all putative β-glycanase ORFs according to sequence similarity analysis, contained a highly conserved novel GH-associated module of unknown function at their C terminus. Four of these GH enzymes were experimentally verified as xylanase, β-glucanase, β-glucanase/carboxymethylcellulase (CMCase), and CMCase. Binding experiments performed with the recombinantly expressed and purified GH-associated module showed that it represents a new carbohydrate-binding module (CBM) that binds to microcrystalline cellulose and is highly specific for this substrate. In the course of this work, the new CBM type was only detected in Spirochaeta, but recently we found sequences with detectable similarity to the module in the draft genomes of Cytophaga fermentans and Mahella australiensis, both of which are phylogenetically very distant from S. thermophila and noncellulolytic, yet inhabit similar environments. This suggests a possibly broad distribution of the module in nature.},
 bibtype = {article},
 author = {Angelov, A. and Loderer, C. and Pompei, S. and Liebl, W.},
 journal = {Applied and Environmental Microbiology},
 number = {15}
}

Paper  Website  abstract   bibtex   

@article{
 title = {The human genetic history of Oceania: near and remote views of dispersal.},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Chromosomes, Human, Y,Chromosomes, Human, Y: genetics,DNA, Mitochondrial,DNA, Mitochondrial: genetics,Demography,Emigration and Immigration,Female,Genetics, Population,Haplotypes,Haplotypes: genetics,History, Ancient,Humans,Linguistics,Male,Oceania,Oceanic Ancestry Group,Oceanic Ancestry Group: genetics,Oceanic Ancestry Group: history},
 pages = {R194-201},
 volume = {20},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20178767},
 month = {2},
 publisher = {Elsevier Ltd},
 day = {23},
 id = {f76953c5-ce52-39a2-89de-966bf4392257},
 created = {2017-06-19T13:46:17.041Z},
 accessed = {2012-10-24},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:17.274Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {The human history of Oceania is unique in the way that it encompasses both the first out-of-Africa expansion of modern humans to New Guinea and Australia as well as the last regional human occupation of Polynesia. Other anthropological peculiarities of Oceania include features like the extraordinarily rich linguistic diversity especially of New Guinea with about 1,000 often very distinct languages, the independent and early development of agriculture in the highlands of New Guinea about 10,000 years ago, or the long-term isolation of the entire region from the outside world, which lasted as long as until the 1930s for most of the interior of New Guinea. This review will provide an overview on the genetic aspects of human population history of Oceania and how some of the anthropological peculiarities are reflected in human genetic data. Due to current data availability it will mostly focus on insights from sex-specifically inherited mitochondrial DNA and Y-chromosomal DNA, whereas more genome-wide autosomal DNA data are soon expected to add additional details or may correct views obtained from these two, albeit highly complex, genetic loci.},
 bibtype = {article},
 author = {Kayser, Manfred},
 journal = {Current biology : CB},
 number = {4}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Ancient human genome sequence of an extinct Palaeo-Eskimo},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {*Cryopreservation,*Extinction,Ancient,Biological,DNA,Emigration and Immigration/history,Genetics,Genome,Genomics,Genotype,Greenland,Hair,History,Human/*genetics,Humans,Inuits/*genetics,Male,Phenotype,Phylogeny,Polymorphism,Population,Sequence Analysis,Siberia/ethnology,Single Nucleotide/genetics},
 pages = {757-762},
 volume = {463},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/20148029},
 month = {2},
 publisher = {Nature Publishing Group},
 day = {11},
 id = {060daa70-995e-34e1-bd6b-11e762367ce7},
 created = {2015-12-15T10:33:32.000Z},
 accessed = {2013-12-12},
 file_attached = {true},
 profile_id = {be57537b-17b1-39be-b233-ed67db2cc4b7},
 last_modified = {2017-03-15T00:24:05.134Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Rasmussen2010},
 source_type = {JOUR},
 folder_uuids = {07308178-ea07-4b21-b718-b83cdc9ecb43,b70a4f98-1546-4259-afbd-d9a8fe296e69,f7245de5-b312-4a59-ab6d-2dfb4344df71,e0d742db-83ed-4925-85ba-c0344307eca4},
 abstract = {We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.},
 bibtype = {article},
 author = {Rasmussen, M and Li, Y and Lindgreen, S and Pedersen, J S and Albrechtsen, A and Moltke, I and Metspalu, M and Metspalu, E and Kivisild, T and Gupta, R and Bertalan, M and Nielsen, K and Gilbert, M T and Wang, Y and Raghavan, M and Campos, P F and Kamp, H M and Wilson, A S and Gledhill, A and Tridico, S and Bunce, M and Lorenzen, E D and Binladen, J and Guo, X and Zhao, J and Zhang, X and Zhang, H and Li, Z and Chen, M and Orlando, L and Kristiansen, K and Bak, M and Tommerup, N and Bendixen, C and Pierre, T L and Gronnow, B and Meldgaard, M and Andreasen, C and Fedorova, S A and Osipova, L P and Higham, T F and Ramsey, C B and Hansen, T V and Nielsen, F C and Crawford, M H and Brunak, S and Sicheritz-Ponten, T and Villems, R and Nielsen, R and Krogh, A and Wang, J and Willerslev, E},
 journal = {Nature},
 number = {7282}
}

Website  abstract   bibtex   

@article{
 title = {Establishing , maintaining and modifying DNA methylation patterns in plants and animals},
 type = {article},
 year = {2010},
 identifiers = {[object Object]},
 keywords = {Animals,CpG Islands,DNA,DNA Methylation,DNA Methylation/ genetics/physiology,DNA Methylation: genetics,DNA Methylation: physiology,Epigenesis,Gametogenesis,Gametogenesis/genetics,Gametogenesis: genetics,Genetic,Histones,Histones/genetics/metabolism,Histones: genetics,Histones: metabolism,Models,Plant,Plant/genetics/metabolism,Plant: genetics,Plant: metabolism,Plants,Plants/genetics/metabolism,Plants: genetics,Plants: metabolism,RNA,Small Interfering,Small Interfering/genetics/metabolism,Small Interfering: genetics,Small Interfering: metabolism},
 pages = {204-220},
 volume = {11},
 websites = {http://dx.doi.org/10.1038/nrg2719},
 month = {3},
 publisher = {Nature Publishing Group},
 id = {e38badcf-b208-3875-995a-512806f6a978},
 created = {2017-10-14T10:53:30.488Z},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:30.488Z},
 read = {false},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Law2010a},
 source_type = {article},
 short_title = {Nat Rev Genet},
 private_publication = {false},
 abstract = {Cytosine DNA methylation is a stable epigenetic mark that is crucial for diverse biological processes, including gene and transposon silencing, imprinting and X chromosome inactivation. Recent findings in plants and animals have greatly increased our understanding of the pathways used to accurately target, maintain and modify patterns of DNA methylation and have revealed unanticipated mechanistic similarities between these organisms. Key roles have emerged for small RNAs, proteins with domains that bind methylated DNA and DNA glycosylases in these processes. Drawing on insights from both plants and animals should deepen our understanding of the regulation and biological significance of DNA methylation.},
 bibtype = {article},
 author = {Law, Julie A and Jacobsen, Steven E.},
 journal = {Nature Rev. Genet.},
 number = {MARCH}
}

@article{quintana-murci_strong_2010,
	title = {Strong maternal {Khoisan} contribution to the {South} {African} coloured population: a case of gender-biased admixture},
	volume = {86},
	issn = {1537-6605},
	shorttitle = {Strong maternal {Khoisan} contribution to the {South} {African} coloured population},
	doi = {10.1016/j.ajhg.2010.02.014},
	abstract = {The study of recently admixed populations provides unique tools for understanding recent population dynamics, socio-cultural factors associated with the founding of emerging populations, and the genetic basis of disease by means of admixture mapping. Historical records and recent autosomal data indicate that the South African Coloured population forms a unique highly admixed population, resulting from the encounter of different peoples from Africa, Europe, and Asia. However, little is known about the mode by which this admixed population was recently founded. Here we show, through detailed phylogeographic analyses of mitochondrial DNA and Y-chromosome variation in a large sample of South African Coloured individuals, that this population derives from at least five different parental populations (Khoisan, Bantus, Europeans, Indians, and Southeast Asians), who have differently contributed to the foundation of the South African Coloured. In addition, our analyses reveal extraordinarily unbalanced gender-specific contributions of the various population genetic components, the most striking being the massive maternal contribution of Khoisan peoples (more than 60\%) and the almost negligible maternal contribution of Europeans with respect to their paternal counterparts. The overall picture of gender-biased admixture depicted in this study indicates that the modern South African Coloured population results mainly from the early encounter of European and African males with autochthonous Khoisan females of the Cape of Good Hope around 350 years ago.},
	language = {eng},
	number = {4},
	journal = {American Journal of Human Genetics},
	author = {Quintana-Murci, Lluis and Harmant, Christine and Quach, Hélène and Balanovsky, Oleg and Zaporozhchenko, Valery and Bormans, Connie and van Helden, Paul D. and Hoal, Eileen G. and Behar, Doron M.},
	month = apr,
	year = {2010},
	pmid = {20346436},
	pmcid = {PMC2850426},
	note = {00056 },
	keywords = {African Continental Ancestry Group, Chromosomes, Human, Y, DNA, Mitochondrial, Female, Genetic Linkage, Genetics, Population, Humans, Male, Mothers, Polymorphism, Single Nucleotide, Sex Factors},
	pages = {611--620},
}

@article{jogler_cultivation-independent_2010,
	title = {Cultivation-independent characterization of '{Candidatus} {Magnetobacterium} bavaricum' via ultrastructural, geochemical, ecological and metagenomic methods},
	volume = {12},
	issn = {1462-2920},
	doi = {10.1111/j.1462-2920.2010.02220.x},
	abstract = {'Candidatus Magnetobacterium bavaricum' is unusual among magnetotactic bacteria (MTB) in terms of cell size (8-10 µm long, 1.5-2 µm in diameter), cell architecture, magnetotactic behaviour and its distinct phylogenetic position in the deep-branching Nitrospira phylum. In the present study, improved magnetic enrichment techniques permitted high-resolution scanning electron microscopy and energy dispersive X-ray analysis, which revealed the intracellular organization of the magnetosome chains. Sulfur globule accumulation in the cytoplasm point towards a sulfur-oxidizing metabolism of 'Candidatus M. bavaricum'. Detailed analysis of 'Candidatus M. bavaricum' microhabitats revealed more complex distribution patterns than previously reported, with cells predominantly found in low oxygen concentration. No correlation to other geochemical parameters could be observed. In addition, the analysis of a metagenomic fosmid library revealed a 34 kb genomic fragment, which contains 33 genes, among them the complete rRNA gene operon of 'Candidatus M. bavaricum' as well as a gene encoding a putative type IV RubisCO large subunit.},
	number = {9},
	journal = {Environmental microbiology},
	author = {Jogler, C and Niebler, M and Lin, W and Kube, M and Wanner, G and Kolinko, S and Stief, P and Beck, A J and De Beer, D and Petersen, N and Pan, Y and Amann, R and Reinhardt, R and Schüler, D},
	month = sep,
	year = {2010},
	pmid = {20406295},
	keywords = {Amino Acid Sequence, Bacteria, DNA, Bacterial, Ecology, Geologic Sediments, Metagenomics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S, Ribulose-Bisphosphate Carboxylase, Sequence Analysis, DNA, Water Microbiology},
	pages = {2466--2478}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Light and molecular ions: the emergence of vacuum UV single-photon ionization in MS.},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Biofilms,DNA,DNA: analysis,Electrospray Ionization,Ions,Ions: chemistry,Mass,Mass Spectrometry,Mass Spectrometry: methods,Mass Spectrometry: trends,Matrix-Assisted Laser Desorpti,Optics and Photonics,Peptides,Peptides: analysis,Photochemistry,Spectrometry,Ultraviolet Rays,Vacuum},
 pages = {4174-82},
 volume = {81},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2716692&tool=pmcentrez&rendertype=abstract},
 month = {6},
 day = {1},
 id = {046ec04a-e4b9-350f-b4b4-28e111a82641},
 created = {2015-05-08T02:34:14.000Z},
 file_attached = {true},
 profile_id = {f8c267c4-4c39-31dc-80fa-3a9691373386},
 group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
 last_modified = {2015-05-08T11:19:56.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Thanks to recent technological advances and single-photon ionization's (SPI's) ability to detect all organics, the technique could become the long-sought universal soft ionization method. (To listen to a podcast about this feature, please go to the Analytical Chemistry Web site at pubs.acs.org/journal/ancham.).},
 bibtype = {article},
 author = {Hanley, Luke and Zimmermann, Ralf},
 journal = {Analytical chemistry},
 number = {11}
}

@article{zhou_atomically_2009,
	title = {Atomically monodispersed and fluorescent sub-nanometer gold clusters created by biomolecule-assisted etching of nanometer-sized gold particles and rods},
	volume = {15},
	issn = {1521-3765},
	doi = {10.1002/chem.200802743},
	abstract = {Atomically monodispersed gold clusters were synthesized by etching gold nanocrystals (particles and rods) with the assistance of biomolecules (amino acids, peptides, proteins, and DNA) under sonication in water. The resulting gold clusters were exclusively composed of eight atoms, as demonstrated by photoluminescence, optical absorption, electrospray ionization mass spectrometry, and transmission electron microscopy measurements. The gold clusters exhibited solvent-dependent photoluminescence properties when exposed to organic solvents, such as chloroform, tetrahydrofuran, or N,N-dimethylformamide, which was attributed to the rich surface properties of the clusters. This strategy, based on top-down etching, offers an approach to create metal clusters from nanomaterials, which show great potential applications in biological labeling/imaging and sensors that utilize photoluminescence properties as the response.},
	language = {eng},
	number = {19},
	journal = {Chemistry (Weinheim an der Bergstrasse, Germany)},
	author = {Zhou, Renjia and Shi, Minmin and Chen, Xiaoqiang and Wang, Mang and Chen, Hongzheng},
	year = {2009},
	pmid = {19301340},
	keywords = {Albumins, DNA, Glutathione, Histidine, Microscopy, Electron, Transmission, Photochemistry, Solvents, Sonication, Spectrometry, Mass, Electrospray Ionization, Water, fluorescence, gold, luminescence, nanoparticles},
	pages = {4944--4951}
}

Paper  Website  abstract   bibtex   

@article{
 title = {On the phylogenetic position of Myzostomida: can 77 genes get it wrong?},
 type = {article},
 year = {2009},
 identifiers = {[object Object]},
 keywords = {Animals,Annelida,Annelida: genetics,Bayes Theorem,DNA, Mitochondrial,DNA, Mitochondrial: genetics,Evolution, Molecular,Gene Library,Gene Order,Genes, Mitochondrial,Genetic Markers,Genome, Mitochondrial,Models, Genetic,Phylogeny,Ribosomal Proteins,Ribosomal Proteins: genetics,Sequence Analysis, DNA},
 pages = {150},
 volume = {9},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2716322&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {17bf19f7-06f0-3e91-b6d3-122cb32a370d},
 created = {2014-11-18T15:01:22.000Z},
 accessed = {2012-10-04},
 file_attached = {true},
 profile_id = {c6c6f844-18d2-32db-a619-2e915134a952},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Bleidorn2009},
 folder_uuids = {090e2126-2ea2-4873-99f4-533b24d0906f},
 abstract = {Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.},
 bibtype = {article},
 author = {Bleidorn, Christoph and Podsiadlowski, Lars and Zhong, Min and Eeckhaut, Igor and Hartmann, Stefanie and Halanych, Kenneth M and Tiedemann, Ralph},
 journal = {BMC evolutionary biology}
}

@article{dong_exploring_2008,
	title = {Exploring marine bacterial diversity in coastal {Georgia} salt marshes using {DNA} technology},
	volume = {70},
	abstract = {An important aspect of teaching biology is to expose students to the concept of biodiversity. For this purpose, bacteria are excellent examples. Prokaryotes were the first inhabitants on Earth, surviving and even thriving under very harsh conditions as new species continuously evolved. In fact, it is believed that there are more than 5 x 10{\textasciicircum}30 prokaryotes living on Earth today (Whitman et al., 1998). Our current knowledge of these tiny organisms is very limited, and less than 1\% of all bacterial species have been described (Horner-Devine et al., 2004). However, the prominent roles bacteria play in nature are not easy to overlook: Their functions range from providing essential nutrients to plants through nitrogen-fixation (such as for Rhizobium leguminosarum) to enhancement of nutrient absorption in animal intestines (such as for Escherichia coli). As a result, identifying unknown species of bacteria and extending our understanding of known ones are important tasks for 21st Century scientists.},
	journal = {The American Biology Teacher},
	author = {Dong, Yihe. and Guerrero, Stella. and Moran, Mary Ann.},
	year = {2008},
	keywords = {GCE, microbial ecology, salt marshes, diversity, bacteria, dna, education, molecular biology}
}

Website  abstract   bibtex   

@article{
 title = {Metal concentrations, sperm motility, and RNA/DNA ratio in two echinoderm species from a highly contaminated fjord (the Sørfjord, Norway).},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {Animals,Asterias,Asterias: chemistry,Asterias: drug effects,DNA,DNA: analysis,Environmental Monitoring,Geologic Sediments,Geologic Sediments: chemistry,Heavy,Heavy: analysis,Heavy: toxicity,Male,Metals,Norway,RNA,RNA: analysis,Reproducibility of Results,Sea Urchins,Sea Urchins: chemistry,Sea Urchins: drug effects,Species Specificity,Sperm Count,Sperm Motility,Sperm Motility: drug effects,Spermatozoa,Spermatozoa: chemistry,Spermatozoa: cytology,Spermatozoa: drug effects},
 pages = {1553-60},
 volume = {27},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/18260690},
 month = {7},
 id = {d47f88ce-2e6e-300b-9579-b07d257903e9},
 created = {2014-04-18T08:51:25.000Z},
 file_attached = {false},
 profile_id = {369e8c52-7e84-3c5c-98de-6d14376073ae},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Catarino2008},
 abstract = {The present study evaluated the effects of field metal contamination on sperm motility and the RNA/DNA ratio in echinoderms. Populations of Asterias rubens and Echinus acutus that occur naturally along a contamination gradient of sediments by cadmium, copper, lead, and zinc in a Norwegian fjord (the Sørfjord) were studied. Sperm motility, a measure of sperm quality, was quantified using a computer-assisted sperm analysis system. The RNA/DNA ratio, a measure of protein synthesis, was assessed by a one-dye (ethidium bromide)/one-enzyme (RNase), 96-well microplate fluorometric assay. Although both species accumulate metals at high concentrations, neither sperm motility parameters in A. rubens nor the RNA/DNA ratio in both species were affected. The Sørfjord is still one of the most metal-contaminated marine sites in Europe, but even so, populations of A. rubens and E. acutus are able to endure under these conditions.},
 bibtype = {article},
 author = {Catarino, Ana I and Cabral, Henrique N and Peeters, Kris and Pernet, Philippe and Punjabi, Usha and Dubois, Philippe},
 journal = {Environmental toxicology and chemistry / SETAC},
 number = {7}
}

@article{ weiner_complete_2008,
  title = {Complete genome sequence of the complex carbohydrate-degrading marine bacterium, {Saccharophagus} degradans strain 2-40 {T}},
  volume = {4},
  issn = {1553-7404},
  doi = {10.1371/journal.pgen.1000087},
  abstract = {The marine bacterium Saccharophagus degradans strain 2-40 (Sde 2-40) is emerging as a vanguard of a recently discovered group of marine and estuarine bacteria that recycles complex polysaccharides. We report its complete genome sequence, analysis of which identifies an unusually large number of enzymes that degrade {\textgreater}10 complex polysaccharides. Not only is this an extraordinary range of catabolic capability, many of the enzymes exhibit unusual architecture including novel combinations of catalytic and substrate-binding modules. We hypothesize that many of these features are adaptations that facilitate depolymerization of complex polysaccharides in the marine environment. This is the first sequenced genome of a marine bacterium that can degrade plant cell walls, an important component of the carbon cycle that is not well-characterized in the marine environment.},
  language = {eng},
  number = {5},
  journal = {PLoS genetics},
  author = {Weiner, Ronald M. and Taylor, Larry E. and Henrissat, Bernard and Hauser, Loren and Land, Miriam and Coutinho, Pedro M. and Rancurel, Corinne and Saunders, Elizabeth H. and Longmire, Atkinson G. and Zhang, Haitao and Bayer, Edward A. and Gilbert, Harry J. and Larimer, Frank and Zhulin, Igor B. and Ekborg, Nathan A. and Lamed, Raphael and Richardson, Paul M. and Borovok, Ilya and Hutcheson, Steven},
  month = {May},
  year = {2008},
  pmid = {18516288},
  pmcid = {PMC2386152},
  keywords = {Alteromonadaceae, Bacterial Proteins, Base Sequence, Chromosome Mapping, Genome, Bacterial, Glycoside Hydrolases, Molecular Sequence Data, Polysaccharides, Protein Transport, Seawater, Sequence Analysis, DNA, Signal Transduction, Substrate Specificity},
  pages = {e1000087}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Fluorescence intensity and lifetime imaging of free and micellar-encapsulated doxorubicin in living cells},
 type = {article},
 year = {2008},
 keywords = {FLIM,anisotropy,cancer,microscopy},
 pages = {49-56},
 volume = {4},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=000262668200006,papers://5b342310-4c1b-4925-bbf8-38f14091331d/Paper/p30},
 month = {1},
 city = {Univ Cambridge, Dept Chem Engn, Cambridge CB2 3RA, England},
 id = {6b62bd49-18d1-356b-a20d-d4fed8437694},
 created = {2016-04-27T13:36:22.000Z},
 file_attached = {true},
 profile_id = {9b1c14de-b75a-3e23-a406-ef006d6fed26},
 last_modified = {2017-03-25T02:42:51.878Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 source_type = {JOUR},
 folder_uuids = {6e034f54-5623-437a-811f-80d304e37fd9},
 abstract = {Frequency domain fluorescence lifetime imaging microscopy (FLIM) has been used in combination with laser scanning confocal microscopy to study the cellular uptake behavior of the antitumor drug doxorubicin (DOX) and micellar-encapsulated DOX (PLyAd-DOX). The endocytosis uptake process of PLyAd-DOX was monitored over 72 hours using confocal microscopy, with a maximum fluorescence recorded at incubation periods around 24 hours. The micellar structure was not found to release the encapsulated DOX during the time course of imaging. FLIM revealed single lifetime distributions of PLyAd-DOX during accumulation in the cytoplasm. The free DOX in contrast was observed both in the cytoplasm and the nuclear domain of the cell, showing bimodal lifetime distributions. There was a marked dependence of the measured free-DOX lifetime on concentration within the cell, in contrast to reference experiments in aqueous solution, where no such dependence was found. The results suggest the formation of macromolecular structures inside the living cells. (c) 2008 Elsevier Inc. All rights reserved.},
 bibtype = {article},
 author = {Dai, undefined and Yue, undefined and Eccleston, undefined and Swartling, undefined and Slater, undefined and Kaminski, undefined},
 journal = {Nanomedicine-Nanotechnology Biology And Medicine},
 number = {1}
}

Paper  doi  abstract   bibtex   

@article{foissac_astalavista:_2007,
	title = {{ASTALAVISTA}: dynamic and flexible analysis of alternative splicing events in custom gene datasets.},
	volume = {35},
	issn = {1362-4962},
	url = {http://nar.oxfordjournals.org/content/35/suppl_2/W297.abstract},
	doi = {10.1093/nar/gkm311},
	abstract = {In the process of establishing more and more complete annotations of eukaryotic genomes, a constantly growing number of alternative splicing (AS) events has been reported over the last decade. Consequently, the increasing transcript coverage also revealed the real complexity of some variations in the exon-intron structure between transcript variants and the need for computational tools to address 'complex' AS events. ASTALAVISTA (alternative splicing transcriptional landscape visualization tool) employs an intuitive and complete notation system to univocally identify such events. The method extracts AS events dynamically from custom gene annotations, classifies them into groups of common types and visualizes a comprehensive picture of the resulting AS landscape. Thus, ASTALAVISTA can characterize AS for whole transcriptome data from reference annotations (GENCODE, REFSEQ, ENSEMBL) as well as for genes selected by the user according to common functional/structural attributes of interest: http://genome.imim.es/astalavista.},
	number = {Web Server issue},
	journal = {Nucleic acids research},
	author = {Foissac, Sylvain and Sammeth, Michael},
	month = jul,
	year = {2007},
	pmid = {17485470},
	keywords = {Alternative Splicing, Alternative Splicing: genetics, Chromosome Mapping, Chromosome Mapping: methods, Computational Biology, Computational Biology: methods, DNA, DNA Probes, DNA Probes: genetics, DNA: methods, Databases, Genetic, Genome, Humans, Internet, Messenger, Messenger: metabolism, Oligonucleotide Array Sequence Analysis, Oligonucleotide Array Sequence Analysis: instrumen, Oligonucleotide Array Sequence Analysis: methods, RNA, RNA Splice Sites, RNA Splice Sites: genetics, Sequence Analysis, Software},
	pages = {297}
}

Paper  Website  abstract   bibtex   

@article{
 title = {High efficiency DNA extraction from bone by total demineralization.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Bone Demineralization Technique,Bone Demineralization Technique: methods,Bone and Bones,Bone and Bones: chemistry,DNA,DNA, Mitochondrial,DNA, Mitochondrial: genetics,DNA, Mitochondrial: isolation & purification,DNA: genetics,DNA: isolation & purification,Forensic Genetics,Forensic Genetics: methods,Humans,Microsatellite Repeats,Tooth,Tooth: chemistry},
 pages = {191-5},
 volume = {1},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/19083754},
 month = {6},
 id = {2aa68071-5255-311a-935f-14249638382d},
 created = {2012-12-06T09:12:59.000Z},
 accessed = {2010-08-18},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Loreille2007a},
 abstract = {In historical cases, missing persons' identification, mass disasters, and ancient DNA investigations, bone and teeth samples are often the only, and almost always the best, biological material available for DNA typing. This is because of the physical and chemical barrier that the protein:mineral matrix of bone poses to environmental deterioration and biological attack. Most bone extraction protocols utilized in the forensic community involve an incubation period of bone powder in extraction buffer for proteinase digestion, followed by the collection of the supernatant, and the disposal of large quantities of undissolved bone powder. Here we present an extremely efficient protocol for recovery of DNA by complete demineralization, resulting in full physical dissolution of the bone sample. This is performed in a manner that retains and concentrates all the reagent volume, for complete DNA recovery. For our study, we selected 14 challenging bone samples. The bones were extracted side-by-side with our new demineralization protocol and the standard extraction protocol in use at AFDIL. A real-time quantification assay based on the amplification of a 143 bp mtDNA fragment showed that this new demineralization protocol significantly enhances the quantity of DNA that can be extracted and amplified from degraded skeletal remains. We have used this technique to successfully recover authentic DNA sequences from extremely challenging samples that failed repeatedly using the standard protocol.},
 bibtype = {article},
 author = {Loreille, Odile M and Diegoli, Toni M and Irwin, Jodi a and Coble, Michael D and Parsons, Thomas J},
 journal = {Forensic science international. Genetics},
 number = {2}
}

@article{noviello_maintenance_2007,
	title = {Maintenance of {Nef}-mediated modulation of major histocompatibility complex class {I} and {CD4} after sexual transmission of human immunodeficiency virus type 1},
	volume = {81},
	issn = {0022-538X},
	doi = {10.1128/JVI.01793-06},
	abstract = {Viruses encounter changing selective pressures during transmission between hosts, including host-specific immune responses and potentially varying functional demands on specific proteins. The human immunodeficiency virus type 1 Nef protein performs several functions potentially important for successful infection, including immune escape via down-regulation of class I major histocompatibility complex (MHC-I) and direct enhancement of viral infectivity and replication. Nef is also a major target of the host cytotoxic T-lymphocyte (CTL) response. To examine the impact of changing selective pressures on Nef functions following sexual transmission, we analyzed genetic and functional changes in nef clones from six transmission events. Phylogenetic analyses indicated that the diversity of nef was similar in both sources and acutely infected recipients, the patterns of selection across transmission were variable, and regions of Nef associated with distinct functions evolved similarly in sources and recipients. These results weighed against the selection of specific Nef functions by transmission or during acute infection. Measurement of Nef function provided no evidence that the down-regulation of either CD4 or MHC-I was optimized by transmission or during acute infection, although rare nef clones from sources that were impaired in these activities were not detected in recipients. Nef-specific CTL activity was detected as early as 3 weeks after infection and appeared to be an evolutionary force driving the diversification of nef. Despite the change in selective pressure between the source and recipient immune systems and concomitant genetic diversity, the majority of Nef proteins maintained robust abilities to down-regulate MHC-I and CD4. These data suggest that both functions are important for the successful establishment of infection in a new host.},
	language = {eng},
	number = {9},
	journal = {Journal of Virology},
	author = {Noviello, C. M. and Pond, S. L. Kosakovsky and Lewis, M. J. and Richman, D. D. and Pillai, S. K. and Yang, O. O. and Little, S. J. and Smith, D. M. and Guatelli, J. C.},
	month = may,
	year = {2007},
	pmid = {17329339},
	pmcid = {PMC1900175},
	keywords = {Amino Acid Sequence, Base Sequence, Blotting, Western, CD4 Antigens, Evolution, Molecular, Flow Cytometry, Gene Expression Regulation, Viral, Gene Products, nef, Genes, MHC Class I, Genetic Variation, HIV Infections, HIV-1, Humans, Likelihood Functions, Models, Genetic, Molecular Sequence Data, Phylogeny, Selection, Genetic, Sequence Alignment, Sequence Analysis, DNA, T-Lymphocytes, Cytotoxic, nef Gene Products, Human Immunodeficiency Virus},
	pages = {4776--4786},
}

Paper  Website  abstract   bibtex   

@article{
 title = {Testing the adaptive selection of human mtDNA haplogroups: an experimental bioenergetics approach},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {*Haplotypes,Adenosine Triphosphate/biosynthesis,DNA, Mitochondrial/*genetics,Evolution,Humans,Oxidative Phosphorylation},
 pages = {e3-5},
 volume = {404},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17488234},
 edition = {2007/05/10},
 id = {cf7cb1bc-8107-3ab4-a306-d3b19e7fb20b},
 created = {2017-06-19T13:45:53.797Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:53.944Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Elson, Joanna L<m:linebreak/>Turnbull, Douglass M<m:linebreak/>Taylor, Robert W<m:linebreak/>United Kingdom Wellcome Trust<m:linebreak/>Comment<m:linebreak/>Research Support, Non-U.S. Gov't<m:linebreak/>England<m:linebreak/>The Biochemical journal<m:linebreak/>Bj20070524<m:linebreak/>Biochem J. 2007 Jun 1;404(2):e3-5.</m:note>},
 abstract = {The evolution of human mtDNA (mitochondrial DNA) has been characterized by the emergence of distinct haplogroups, which are associated with the major global ethnic groups and defined by the presence of specific mtDNA polymorphic variants. A recent analysis of complete mtDNA genome sequences has suggested that certain mtDNA haplogroups may have been positively selected as humans populated colder climates due to a decreased mitochondrial coupling efficiency, in turn leading to increased generation of heat instead of ATP synthesis by oxidative phosphorylation. If this is true, implying different evolutionary processes in different haplogroups, this could potentially void the usefulness of mtDNA as a genetic tool to study the timing of major events in evolutionary history. In this issue of the Biochemical Journal, Taku Amo and Martin Brand present experimental biochemical data to test this hypothesis. Measurements of the bioenergetic capacity of cybrid cells harbouring specific Arctic or tropical climate mtDNA haplogroups on a control nuclear background reveal no significant changes in coupling efficiency between the two groups, indicating that mtDNA remains a viable evolutionary tool to assess the timing of major events in the history of humans and other species.},
 bibtype = {article},
 author = {Elson, J L and Turnbull, D M and Taylor, R W},
 journal = {Biochem J},
 number = {2}
}

Paper  abstract   bibtex   

@article{
 title = {Characterization of chimeric Bacillus thuringiensis Vip3 toxins.},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Animals,Bacillus thuringiensis,Bacillus thuringiensis: genetics,Bacillus thuringiensis: metabolism,Bacterial Proteins,Bacterial Proteins: genetics,Bacterial Proteins: metabolism,Bacterial Proteins: pharmacology,Bombyx,Bombyx: drug effects,Insecticides,Insecticides: pharmacology,Molecular Sequence Data,Moths,Moths: drug effects,Pest Control, Biological,Plants, Genetically Modified,Recombinant Fusion Proteins,Recombinant Fusion Proteins: genetics,Recombinant Fusion Proteins: metabolism,Recombinant Fusion Proteins: pharmacology,Sequence Analysis, DNA,Spodoptera,Spodoptera: drug effects},
 pages = {956-61},
 volume = {73},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1800787&tool=pmcentrez&rendertype=abstract},
 month = {2},
 id = {3a447809-41eb-320a-9c91-36495351e3ef},
 created = {2012-02-03T19:19:34.000Z},
 accessed = {2011-11-03},
 file_attached = {true},
 profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
 group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
 last_modified = {2012-10-26T12:52:02.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Bacillus thuringiensis vegetative insecticidal proteins (Vip) are potential alternatives for B. thuringiensis endotoxins that are currently utilized in commercial transgenic insect-resistant crops. Screening a large number of B. thuringiensis isolates resulted in the cloning of vip3Ac1. Vip3Ac1 showed high insecticidal activity against the fall armyworm Spodoptera frugiperda and the cotton bollworm Helicoverpa zea but very low activity against the silkworm Bombyx mori. The host specificity of this Vip3 toxin was altered by sequence swapping with a previously identified toxin, Vip3Aa1. While both Vip3Aa1 and Vip3Ac1 showed no detectable toxicity against the European corn borer Ostrinia nubilalis, the chimeric protein Vip3AcAa, consisting of the N-terminal region of Vip3Ac1 and the C-terminal region of Vip3Aa1, became insecticidal to the European corn borer. In addition, the chimeric Vip3AcAa had increased toxicity to the fall armyworm. Furthermore, both Vip3Ac1 and Vip3AcAa are highly insecticidal to a strain of cabbage looper (Trichoplusia ni) that is highly resistant to the B. thuringiensis endotoxin Cry1Ac, thus experimentally showing for the first time the lack of cross-resistance between B. thuringiensis Cry1A proteins and Vip3A toxins. The results in this study demonstrated that vip3Ac1 and its chimeric vip3 genes can be excellent candidates for engineering a new generation of transgenic plants for insect pest control.},
 bibtype = {article},
 author = {Fang, Jun and Xu, Xiaoli and Wang, Ping and Zhao, Jian-Zhou and Shelton, Anthony M and Cheng, Jiaan and Feng, Ming-Guang and Shen, Zhicheng},
 journal = {Applied and environmental microbiology},
 number = {3}
}

Paper  doi  abstract   bibtex   

@article{bayles_biological_2007,
	title = {The biological role of death and lysis in biofilm development},
	volume = {5},
	issn = {1740-1534},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/17694072},
	doi = {10.1038/nrmicro1743},
	abstract = {Recent studies have revealed that the regulated death of bacterial cells is important for biofilm development. Following cell death, a sub-population of the dead bacteria lyse and release genomic DNA, which then has an essential role in intercellular adhesion and biofilm stability. This Opinion focuses on the role of regulated cell death and lysis in biofilm development and provides a functional comparison between bacterial programmed cell death and apoptosis. The hypothesis that the differential regulation of these processes during biofilm development contributes to the antibiotic tolerance of biofilm cells is also explored.},
	number = {9},
	urldate = {2009-04-12TZ},
	journal = {Nature Reviews. Microbiology},
	author = {Bayles, Kenneth W},
	month = sep,
	year = {2007},
	pmid = {17694072},
	keywords = {Anti-Bacterial Agents, Bacteria, Bacterial Adhesion, Bacterial Proteins, Bacteriolysis, Biofilms, DNA, Bacterial, Microbial Viability, Models, Biological},
	pages = {721--6}
}

Paper  abstract   bibtex   

@article{
 title = {Cycling of extracellular DNA in the soil environment},
 type = {article},
 year = {2007},
 identifiers = {[object Object]},
 keywords = {Agriculture,Bacteria,Cycle,DNA,Degradation,Environment,Extracellular,Gene transfer,Microorganisms,Natural transformation,Persistence,Recombinant,Soil,Transgenic plants},
 pages = {2977-2991},
 volume = {39},
 websites = {http://www.sciencedirect.com/science/article/pii/S0038071707002660},
 month = {12},
 id = {3382155d-2a85-3cf1-ac9f-8eb16336b9fc},
 created = {2012-01-05T13:07:03.000Z},
 file_attached = {true},
 profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
 group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
 last_modified = {2012-01-05T13:15:24.000Z},
 read = {true},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {JOUR},
 abstract = {Upon entering the soil environment, extracellular DNA is subjected to dynamic biological, physical, and chemical factors that determine its fate. This review concerns the fate of both recombinant and non-recombinant sources of DNA. A schematic of DNA cycling coupled with genetic transformation is presented to understand its behavior in soil. Extracellular DNA may persist through cation bridging onto soil minerals and humic substances, be enzymatically degraded and restricted by DNases of microbial origin, and/or enter the microbial DNA cycle through natural transformation of competent bacteria. Lateral gene transfer may disseminate DNA through the microbial community. An understanding of DNA cycling is fundamental to elucidating the fate of extracellular DNA in the soil environment.},
 bibtype = {article},
 author = {Levy-Booth, David J and Campbell, Rachel G and Gulden, Robert H and Hart, Miranda M and Powell, Jeff R and Klironomos, John N and Pauls, K Peter and Swanton, Clarence J and Trevors, Jack T and Dunfield, Kari E},
 journal = {Soil Biology and Biochemistry},
 number = {12}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus.},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Codon,Consensus Sequence,DNA Primers,DNA Primers: genetics,DNA, Algal,DNA, Algal: genetics,Databases, Nucleic Acid,Expressed Sequence Tags,Genetic Markers,Microsatellite Repeats,Microsatellite Repeats: genetics,Open Reading Frames,Phylogeny,Phytophthora,Phytophthora: genetics,Species Specificity,Transcription, Genetic},
 pages = {245},
 volume = {7},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1594578&tool=pmcentrez&rendertype=abstract},
 month = {1},
 id = {f0612254-194c-38b3-865d-113bae82d407},
 created = {2015-09-09T02:21:59.000Z},
 accessed = {2015-09-09},
 file_attached = {true},
 profile_id = {f95ef69b-8f96-32da-8de9-769c2acf0685},
 last_modified = {2015-09-09T02:22:11.000Z},
 read = {false},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 abstract = {BACKGROUND: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.

RESULTS: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.

CONCLUSION: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.},
 bibtype = {article},
 author = {Garnica, Diana P and Pinzón, Andrés M and Quesada-Ocampo, Lina M and Bernal, Adriana J and Barreto, Emiliano and Grünwald, Niklaus J and Restrepo, Silvia},
 journal = {BMC genomics}
}

Paper  Website  abstract   bibtex   

@article{
 title = {cDNA microarrays as a tool for identification of biomineralization proteins in the coccolithophorid Emiliania huxleyi (Haptophyta).},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Algae,Algae: genetics,Algae: growth & development,Algae: metabolism,Calcification, Physiologic,Culture Media,DNA, Complementary,Gene Expression Profiling,Gene Expression Regulation,Molecular Sequence Data,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Polymerase Chain Reaction,Proteins,Proteins: genetics,Proteins: metabolism,Sequence Analysis, DNA},
 pages = {5512-26},
 volume = {72},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/16885305},
 month = {8},
 id = {94e783d8-a466-3577-b3e2-a00b8777e72c},
 created = {2012-12-06T09:13:40.000Z},
 file_attached = {true},
 profile_id = {0b777e31-8c9d-39dd-97a3-3e054bd99cfe},
 group_id = {764582e8-5773-3a66-8d6b-9b40e4fb5a88},
 last_modified = {2017-03-14T17:27:14.020Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Quinn2006},
 abstract = {Marine unicellular coccolithophore algae produce species-specific calcite scales otherwise known as coccoliths. While the coccoliths and their elaborate architecture have attracted the attention of investigators from various scientific disciplines, our knowledge of the underpinnings of the process of biomineralization in this alga is still in its infancy. The processes of calcification and coccolithogenesis are highly regulated and likely to be complex, requiring coordinated expression of many genes and pathways. In this study, we have employed cDNA microarrays to investigate changes in gene expression associated with biomineralization in the most abundant coccolithophorid, Emiliania huxleyi. Expression profiling of cultures grown under calcifying and noncalcifying conditions has been carried out using cDNA microarrays corresponding to approximately 2,300 expressed sequence tags. A total of 127 significantly up- or down-regulated transcripts were identified using a P value of 0.01 and a change of >2.0-fold. Real-time reverse transcriptase PCR was used to test the overall validity of the microarray data, as well as the relevance of many of the proteins predicted to be associated with biomineralization, including a novel gamma-class carbonic anhydrase (A. R. Soto, H. Zheng, D. Shoemaker, J. Rodriguez, B. A. Read, and T. M. Wahlund, Appl. Environ. Microbiol. 72:5500-5511, 2006). Differentially regulated genes include those related to cellular metabolism, ion channels, transport proteins, vesicular trafficking, and cell signaling. The putative function of the vast majority of candidate transcripts could not be defined. Nonetheless, the data described herein represent profiles of the transcription changes associated with biomineralization-related pathways in E. huxleyi and have identified novel and potentially useful targets for more detailed analysis.},
 bibtype = {article},
 author = {Quinn, Patrick and Bowers, Robert M and Zhang, Xiaoyu and Wahlund, Thomas M and Fanelli, Michael a and Olszova, Daniela and Read, Betsy a},
 journal = {Applied and environmental microbiology},
 number = {8}
}

Paper  Website  abstract   bibtex   

@article{
 title = {New bounds and tractable instances for the transposition distance},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Algorithms,Chromosome Mapping,Chromosome Mapping: methods,DNA,DNA Mutational Analysis,DNA Mutational Analysis: methods,DNA Transposable Elements,DNA Transposable Elements: genetics,DNA: methods,Evolution,Linkage Disequilibrium,Linkage Disequilibrium: genetics,Molecular,Sequence Alignment,Sequence Alignment: methods,Sequence Analysis},
 pages = {380-394},
 volume = {3},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/17085847,http://www.computer.org/portal/web/csdl/doi/10.1109/tcbb.2006.56},
 month = {10},
 publisher = {Published by the IEEE CS, CI, and EMB Societies & the ACM},
 city = {Los Alamitos, CA, USA},
 id = {87436cd8-5b57-349e-bd20-d831b9b9a415},
 created = {2009-09-25T17:31:36.000Z},
 accessed = {2011-06-07},
 file_attached = {true},
 profile_id = {192e9f37-d4de-3f1f-95dc-8b4ae5980aa4},
 last_modified = {2013-04-22T09:24:01.000Z},
 tags = {genome rearrangements,sorting by transpositions},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 citation_key = {Labarre2006},
 source_type = {article},
 abstract = {The problem of sorting by transpositions asks for a sequence of adjacent interval exchanges that sorts a permutation and is of the shortest possible length. The distance of the permutation is defined as the length of such a sequence. Despite the apparently intuitive nature of this problem, introduced in 1995 by Bafna and Pevzner, the complexity of both finding an optimal sequence and computing the distance remains open today. In this paper, we establish connections between two different graph representations of permutations, which allows us to compute the distance of a few non-trivial classes of permutations in linear time and space, bypassing the use of any graph structure. By showing that every permutation can be obtained from one of these classes, we prove a new tight upper bound on the transposition distance. Finally, we give improved bounds on some other families of permutations and prove formulas for computing the exact distance of other classes of permutations, again in polynomial time.},
 bibtype = {article},
 author = {Labarre, Anthony},
 journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
 number = {4}
}

Website  abstract   bibtex   

@article{
 title = {Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis},
 type = {article},
 year = {2006},
 identifiers = {[object Object]},
 keywords = {Arabidopsis,Arabidopsis: genetics,Arabidopsis: metabolism,Chromosome Mapping,Chromosome Mapping: methods,DNA Methylation,DNA Modification Methylases,DNA Modification Methylases: genetics,DNA Modification Methylases: metabolism,DNA, Plant,DNA, Plant: genetics,DNA, Plant: metabolism,Gene Expression Profiling,Gene Expression Profiling: methods,Gene Expression Regulation, Plant,Gene Expression Regulation, Plant: genetics,Gene Silencing,Gene Silencing: physiology,Genes, Plant,Genes, Plant: genetics,Genome, Plant,Genome, Plant: genetics,Molecular Sequence Data,Oligonucleotide Array Sequence Analysis,Oligonucleotide Array Sequence Analysis: methods,Promoter Regions, Genetic,Promoter Regions, Genetic: genetics,RNA, Small Interfering,RNA, Small Interfering: genetics,Transcription, Genetic,Transcription, Genetic: genetics},
 pages = {1189-1201},
 volume = {126},
 websites = {http://www.sciencedirect.com/science/article/pii/S009286740601018X},
 month = {9},
 day = {22},
 id = {a586b1f4-e03b-3e35-9aab-938a0666a153},
 created = {2017-10-14T10:53:33.674Z},
 accessed = {2015-09-07},
 file_attached = {false},
 profile_id = {57cbaa4c-3609-3597-b91c-bd12e56638fb},
 group_id = {b97159aa-8fdc-3227-aa16-9de80bf090dd},
 last_modified = {2017-10-14T10:53:33.674Z},
 read = {false},
 starred = {true},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Zhang2006},
 private_publication = {false},
 abstract = {Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only ???5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation. ?? 2006 Elsevier Inc. All rights reserved.},
 bibtype = {article},
 author = {Zhang, Xiaoyu and Yazaki, Junshi and Sundaresan, Ambika and Cokus, Shawn and Chan, Simon W L and Chen, Huaming and Henderson, Ian R. and Shinn, Paul and Pellegrini, Matteo and Jacobsen, Steve E. and Ecker, Joseph R},
 journal = {Cell},
 number = {6}
}

Paper  doi  abstract   bibtex   

@article{ben-yehuda_defining_2005,
	title = {Defining a centromere-like element in {Bacillus} subtilis by {Identifying} the binding sites for the chromosome-anchoring protein {RacA}},
	volume = {17},
	issn = {1097-2765},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/15780934},
	doi = {10.1016/j.molcel.2005.02.023},
	abstract = {Chromosome segregation during sporulation in Bacillus subtilis involves the anchoring of sister chromosomes to opposite ends of the cell. Anchoring is mediated by RacA, which acts as a bridge between a centromere-like element in the vicinity of the origin of replication and the cell pole. To define this element we mapped RacA binding sites by performing chromatin immunoprecipitation in conjunction with gene microarray analysis. RacA preferentially bound to 25 regions spread over 612 kb across the origin portion of the chromosome. Computational and biochemical analysis identified a GC-rich, inverted 14 bp repeat as the recognition sequence. Experiments with single molecules of DNA demonstrated that RacA can condense nonspecific DNA dramatically against appreciable forces to form a highly stable protein-DNA complex. We propose that interactions between DNA bound RacA molecules cause the centromere-like element to fold up into a higher order complex that fastens the chromosome to the cell pole.},
	number = {6},
	urldate = {2009-03-12TZ},
	journal = {Molecular Cell},
	author = {Ben-Yehuda, Sigal and Fujita, Masya and Liu, Xiaole Shirley and Gorbatyuk, Boris and Skoko, Dunja and Yan, Jie and Marko, John F and Liu, Jun S and Eichenberger, Patrick and Rudner, David Z and Losick, Richard},
	month = mar,
	year = {2005},
	pmid = {15780934},
	keywords = {Bacillus subtilis, Bacterial Proteins, Binding Sites, Cell Division, Cell Polarity, Centromere, Chromatin Immunoprecipitation, Chromosomes, Bacterial, DNA, Bacterial, GC Rich Sequence, Gene Expression Regulation, Bacterial, Microarray Analysis, Protein Binding, Replication Origin, Spores, Bacterial},
	pages = {773--82}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Mitochondrial DNA and human evolution},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {*Evolution, Molecular,DNA, Mitochondrial/*genetics,Female,Gene Dosage,Genetics, Population,Genome, Human,Humans,Male,Mutation,Recombination, Genetic,Variation (Genetics)},
 pages = {165-183},
 volume = {6},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16124858},
 edition = {2005/08/30},
 id = {78b8c248-c7aa-3681-8264-3afe319ea038},
 created = {2017-06-19T13:45:30.752Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:30.877Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Pakendorf, Brigitte<m:linebreak/>Stoneking, Mark<m:linebreak/>Review<m:linebreak/>United States<m:linebreak/>Annual review of genomics and human genetics<m:linebreak/>Annu Rev Genomics Hum Genet. 2005;6:165-83.</m:note>},
 abstract = {Several unique properties of human mitochondrial DNA (mtDNA), including its high copy number, maternal inheritance, lack of recombination, and high mutation rate, have made it the molecule of choice for studies of human population history and evolution. Here we review the current state of knowledge concerning these properties, how mtDNA variation is studied, what we have learned, and what the future likely holds. We conclude that increasingly, mtDNA studies are (and should be) supplemented with analyses of the Y-chromosome and other nuclear DNA variation. Some serious issues need to be addressed concerning nuclear inserts, database quality, and the possible influence of selection on mtDNA variation. Nonetheless, mtDNA studies will continue to play an important role in such areas as examining socio-cultural influences on human genetic variation, ancient DNA, certain forensic DNA applications, and in tracing personal genetic history.},
 bibtype = {article},
 author = {Pakendorf, B and Stoneking, M},
 journal = {Annu Rev Genomics Hum Genet}
}

@article{
 title = {Long term feeding of Bt-corn--a ten-generation study with quails},
 type = {article},
 year = {2005},
 pages = {449-451},
 volume = {59},
 id = {9134b2c4-d0fe-3073-ac4f-506379f4a7c4},
 created = {2012-01-04T22:01:13.000Z},
 file_attached = {false},
 profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
 group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
 last_modified = {2012-01-05T12:54:46.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {A ten-generation experiment with growing and laying quails were carried out to test diets with 40 (starter) or 50% (grower, layer) isogenic or transgenic (Bt 176) corn. Feeding of diets containing genetically-modified corn did not significantly influence health and performance of quails nor did it affect DNA-transfer and quality of meat and eggs of quails compared with the isogenic counterpart.},
 bibtype = {article},
 author = {Flachowsky, G and Halle, I and Aulrich, K},
 journal = {Arch Anim Nutr},
 number = {6}
}

Paper  Website  abstract   bibtex   

@article{
 title = {mtDNA variation in Inuit populations of Greenland and Canada: Migration history and population structure},
 type = {article},
 year = {2005},
 identifiers = {[object Object]},
 keywords = {21st Century,Ancient,Canada,DNA,DNA Mutational Analysis,Emigration and Immigration,Emigration and Immigration: history,Genetic Variation,Genetic Variation: genetics,Genetics,Greenland,Haplotypes,Haplotypes: genetics,History,Humans,Inuits,Inuits: genetics,Inuits: history,Locus Control Region,Locus Control Region: genetics,Mitochondrial,Mitochondrial: genetics,Mitochondrial: history,Phylogeny,Population,Population: methods},
 pages = {123-34},
 volume = {130},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/16353217},
 month = {5},
 id = {29ab58a7-77e9-3137-8de2-374f853ab484},
 created = {2017-06-19T13:42:00.230Z},
 accessed = {2012-10-24},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:00.585Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.},
 bibtype = {article},
 author = {Helgason, Agnar and Pálsson, Gísli and Pedersen, Henning Sloth and Angulalik, Emily and Gunnarsdóttir, Ellen Dröfn and Yngvadóttir, Bryndís and Stefánsson, Kári and Palsson, G and Gunnarsdottir, E D and Yngvadottir, B and Stefansson, K},
 journal = {American journal of physical anthropology},
 number = {1}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence.},
 type = {article},
 year = {2004},
 identifiers = {[object Object]},
 keywords = {Americas,Americas: epidemiology,Anthropology, Physical,Biological Evolution,Chromosomes, Human, Y,Chromosomes, Human, Y: genetics,DNA, Mitochondrial,DNA, Mitochondrial: genetics,DNA, Mitochondrial: history,Demography,Emigration and Immigration,Emigration and Immigration: history,Genetic Variation,Genetics, Population,Haplotypes,Haplotypes: genetics,History, Ancient,History, Early Modern 1451-1600,Humans,Indians, North American,Indians, North American: genetics,Indians, North American: history,Siberia,Siberia: ethnology},
 pages = {420-39},
 volume = {16},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/15214060},
 id = {6115f219-4d19-3554-a306-d8479c2786a2},
 created = {2017-06-19T13:41:23.972Z},
 accessed = {2012-10-24},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:24.152Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {A number of important insights into the peopling of the New World have been gained through molecular genetic studies of Siberian and Native American populations. While there is no complete agreement on the interpretation of the mitochondrial DNA (mtDNA) and Y chromosome (NRY) data from these groups, several generalizations can be made. To begin with, the primary migration of ancestral Asians expanded from south-central Siberia into the New World and gave rise to ancestral Amerindians. The initial migration seems to have occurred between 20,000-15,000 calendar years before present (cal BP), i.e., before the emergence of Clovis lithic sites (13,350-12,895 cal BP) in North America. Because an interior route through northern North America was unavailable for human passage until 12,550 cal BP, after the last glacial maximum (LGM), these ancestral groups must have used a coastal route to reach South America by 14,675 cal BP, the date of the Monte Verde site in southern Chile. The initial migration appears to have brought mtDNA haplogroups A-D and NRY haplogroups P-M45a and Q-242/Q-M3 to the New World, with these genetic lineages becoming widespread in the Americas. A second expansion that perhaps coincided with the opening of the ice-free corridor probably brought mtDNA haplogroup X and NRY haplogroups P-M45b, C-M130, and R1a1-M17 to North and Central America. Finally, populations that formerly inhabited Beringia expanded into northern North America after the LGM, and gave rise to Eskimo-Aleuts and Na-Dené Indians.},
 bibtype = {article},
 author = {Schurr, Theodore G and Sherry, Stephen T},
 journal = {American journal of human biology : the official journal of the Human Biology Council},
 number = {4}
}

Paper  doi  abstract   bibtex   

@article{bahatyrova_native_2004,
	title = {The native architecture of a photosynthetic membrane},
	volume = {430},
	copyright = {© 2004 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v430/n7003/abs/nature02823.html},
	doi = {10.1038/nature02823},
	abstract = {In photosynthesis, the harvesting of solar energy and its subsequent conversion into a stable charge separation are dependent upon an interconnected macromolecular network of membrane-associated chlorophyll–protein complexes. Although the detailed structure of each complex has been determined, the size and organization of this network are unknown. Here we show the use of atomic force microscopy to directly reveal a native bacterial photosynthetic membrane. This first view of any multi-component membrane shows the relative positions and associations of the photosynthetic complexes and reveals crucial new features of the organization of the network: we found that the membrane is divided into specialized domains each with a different network organization and in which one type of complex predominates. Two types of organization were found for the peripheral light-harvesting LH2 complex. In the first, groups of 10–20 molecules of LH2 form light-capture domains that interconnect linear arrays of dimers of core reaction centre (RC)–light-harvesting 1 (RC–LH1–PufX) complexes; in the second they were found outside these arrays in larger clusters. The LH1 complex is ideally positioned to function as an energy collection hub, temporarily storing it before transfer to the RC where photochemistry occurs: the elegant economy of the photosynthetic membrane is demonstrated by the close packing of these linear arrays, which are often only separated by narrow 'energy conduits' of LH2 just two or three complexes wide.},
	language = {en},
	number = {7003},
	urldate = {2013-03-16TZ},
	journal = {Nature},
	author = {Bahatyrova, Svetlana and Frese, Raoul N. and Siebert, C. Alistair and Olsen, John D. and van der Werf, Kees O. and van Grondelle, Rienk and Niederman, Robert A. and Bullough, Per A. and Otto, Cees and Hunter, C. Neil},
	month = aug,
	year = {2004},
	keywords = {Biotechnology, Cell Cycle, Computational Biology, DNA, Ecology, Evolution, Genomics, Marine Biology, Metabolomics, Molecular Biology, Nanotechnology, Proteomics, RNA, Signal Transduction, astronomy, astrophysics, biochemistry, bioinformatics, biology, cancer, cell signalling, climate change, development, developmental biology, drug discovery, earth science, environmental science, evolutionary biology, functional genomics, genetics, geophysics, immunology, interdisciplinary science, life, materials science, medical research, medicine, molecular interactions, nature, neurobiology, neuroscience, palaeobiology, pharmacology, physics, quantum physics, science, science news, science policy, structural biology, systems biology, transcriptomics},
	pages = {1058--1062}
}

Paper  bibtex   

@article{
 title = {Human evolution: pedigrees for all humanity},
 type = {article},
 year = {2004},
 identifiers = {[object Object]},
 keywords = {*Computer Simulation,*Pedigree,*Phylogeny,DNA, Mitochondrial/genetics,Emigration and Immigration,Female,Geography,Humans,Male,Population Density,Population Dynamics,Time Factors},
 pages = {518-519},
 volume = {431},
 id = {957c97e0-a5aa-3a7b-9483-683f94d98525},
 created = {2017-06-19T13:44:31.700Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:31.793Z},
 tags = {04/12/23},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Comment<m:linebreak/>News</m:note>},
 bibtype = {article},
 author = {Hein, J},
 journal = {Nature},
 number = {7008}
}

@article{royer_conservation_2003,
	title = {Conservation of total synaptic weight through balanced synaptic depression and potentiation},
	volume = {422},
	issn = {0028-0836},
	doi = {10.1038/nature01530},
	abstract = {Memory is believed to depend on activity-dependent changes in the strength of synapses. In part, this view is based on evidence that the efficacy of synapses can be enhanced or depressed depending on the timing of pre- and postsynaptic activity. However, when such plastic synapses are incorporated into neural network models, stability problems may develop because the potentiation or depression of synapses increases the likelihood that they will be further strengthened or weakened. Here we report biological evidence for a homeostatic mechanism that reconciles the apparently opposite requirements of plasticity and stability. We show that, in intercalated neurons of the amygdala, activity-dependent potentiation or depression of particular glutamatergic inputs leads to opposite changes in the strength of inputs ending at other dendritic sites. As a result, little change in total synaptic weight occurs, even though the relative strength of inputs is modified. Furthermore, hetero- but not homosynaptic alterations are blocked by intracellular dialysis of drugs that prevent Ca2+ release from intracellular stores. Thus, in intercalated neurons at least, inverse heterosynaptic plasticity tends to compensate for homosynaptic long-term potentiation and depression, thus stabilizing total synaptic weight.},
	language = {eng},
	number = {6931},
	journal = {Nature},
	author = {Royer, Sébastien and Paré, Denis},
	month = apr,
	year = {2003},
	pmid = {12673250},
	keywords = {Amygdala, Animals, Calcium, DNA, Excitatory Postsynaptic Potentials, Guinea Pigs, Long-Term Potentiation, Membrane Potentials, Neuronal Plasticity, Neuroscience, RNA, Signal Transduction, Synapses, astronomy, astrophysics, biochemistry, bioinformatics, biology, biotechnology, cancer, cell cycle, cell signalling, climate change, computational biology, development, developmental biology, drug discovery, earth science, ecology, environmental science, evolution, evolutionary biology, functional genomics, genetics, genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, memory, metabolomics, molecular biology, molecular interactions, nanotechnology, nature, neurobiology, palaeobiology, pharmacology, physics, proteomics, quantum physics, science, science news, science policy, structural biology, systems biology, transcriptomics},
	pages = {518--522}
}

Paper  abstract   bibtex   

@article{
 title = {Identification of multiple loci for Alzheimer disease in a consanguineous Israeli-Arab community},
 type = {article},
 year = {2003},
 identifiers = {[object Object]},
 keywords = {Aged,Aged, 80 and over,Alleles,Alzheimer Disease/*genetics,Arabs,Chromosome Mapping,Chromosomes, Human, Pair 10,Chromosomes, Human, Pair 12,Chromosomes, Human, Pair 2,Chromosomes, Human, Pair 9,Consanguinity,Dementia, Vascular/*genetics,Female,Gene Frequency,Genetic Markers,Genome, Human,Genotype,Heterozygote,Homozygote,Human,Israel,Linkage (Genetics),Lod Score,Male,Models, Genetic,Sequence Analysis, DNA,Support, Non-U.S. Gov't,Support, U.S. Gov't, P.H.S.},
 pages = {415-422},
 volume = {12},
 id = {cf9eab61-8a7f-38db-bc5f-f874a28d4f14},
 created = {2017-06-19T13:42:46.336Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:46.466Z},
 tags = {04/01/19},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article</m:note>},
 abstract = {We have observed an unusually high prevalence of dementia of the Alzheimer type (DAT) in Wadi Ara, an inbred Arab community in northern Israel comprising approximately 850 persons over the age of 60 years. Family studies revealed that more than one-third of the DAT cases are members of one hamula (tribal group) within Wadi Ara. To map chromosomal loci contributing to DAT susceptibility, we conducted a 10 cM scan in a series of five cases and five controls selected from this hamula. Markers from 18 chromosomal regions showed significant allelic association with DAT (P<0.05). Locations on chromosomes 2, 9 and 10 remained significant after testing additional affected and non-demented individuals. Significant associations were also observed for markers on chromosome 12 which overlap with a locus implicated in previous genome scans. Analysis of allele frequency distributions for 12 markers spanning 20 cM on chromosome 9 narrowed the possible location of an DAT susceptibility gene to a 13 cM interval between D9S157 and D9S259 (most significant result: P = 2.3 x 10(-7)). Analysis of 14 markers spanning 24 cM on chromosome 12 narrowed the possible location to a 14 cM interval distal to the LRP1 locus (most significant result: P = 1.3 x 10(-6)). Evidence for linkage on chromosome 9 stemmed primarily from excess homozygosity of marker alleles in cases compared with controls, suggesting that the gene at this location behaves in either a recessive or additive fashion. The unique characteristics of this community together with the emergent human genome data should allow for the rapid identification of DAT genes in these candidate regions.},
 bibtype = {article},
 author = {Farrer, L A and Bowirrat, A and Friedland, R P and Waraska, K and Korczyn, A D and Baldwin, C T},
 journal = {Hum Mol Genet},
 number = {4}
}

@article{Weber2002,
  title = {Building an Asynchronous Web-Based Tool for Machine Learning Classification.},
  author = {Weber, Griffin and Vinterbo, Staal and {Ohno-Machado}, Lucila},
  year = {2002},
  journal = {JAMIA},
  volume = {Suppl. S},
  pages = {869--73},
  abstract = {Various unsupervised and supervised learning methods including support vector machines, classification trees, linear discriminant analysis and nearest neighbor classifiers have been used to classify high-throughput gene expression data. Simpler and more widely accepted statistical tools have not yet been used for this purpose, hence proper comparisons between classification methods have not been conducted. We developed free software that implements logistic regression with stepwise variable selection as a quick and simple method for initial exploration of important genetic markers in disease classification. To implement the algorithm and allow our collaborators in remote locations to evaluate and compare its results against those of other methods, we developed a user-friendly asynchronous web-based application with a minimal amount of programming using free, downloadable software tools. With this program, we show that classification using logistic regression can perform as well as other more sophisticated algorithms, and it has the advantages of being easy to interpret and reproduce. By making the tool freely and easily available, we hope to promote the comparison of classification methods. In addition, we believe our web application can be used as a model for other bioinformatics laboratories that need to develop web-based analysis tools in a short amount of time and on a limited budget.},
  copyright = {All rights reserved},
  pii = {D020001919},
  pubmedid = {12463949},
  keywords = {12463949,Algorithms,Anonymous Testing,Artificial Intelligence,Carcinoma,Child,Comparative Study,Computerized,Confidentiality,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,Sarcoma,Small Cell,Software,U.S. Gov't},
  file = {/Users/staal/Documents/Zotero/storage/26TPF5RW/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/FRPABBPG/amia02-weber.pdf;/Users/staal/Documents/Zotero/storage/GME7HZA7/amia02-weber.pdf}
}

@article{Ohno-Machado2002,
  title = {Comparing Imperfect Measurements with the {{Bland-Altman}} Technique: Application in Gene Expression Analysis.},
  author = {{Ohno-Machado}, Lucila and Vinterbo, Staal and Dreiseitl, Stephen and Jenssen, Tor-Kristian and Kuo, Winston},
  year = {2002},
  journal = {JAMIA},
  volume = {Suppl. S},
  pages = {572--6},
  abstract = {Several problems in medicine and biology involve the comparison of two measurements made on the same set of cases. The problem differs from a calibration problem because no gold standard can be identified. Testing the null hypothesis of no relationship using measures of association is not optimal since the measurements are made on the same cases, and therefore correlation coefficients will tend to be significant. The descriptive Bland-Altman method can be used in exploratory analysis of this problem, allowing the visualization of gross systematic differences between the two sets of measurements. We utilize the method on three sets of matched observations and demonstrate its usefulness in detecting systematic variations between two measurement technologies to assess gene expression.},
  copyright = {All rights reserved},
  pii = {1833},
  pubmedid = {12463888},
  keywords = {12463888,Algorithms,Anonymous Testing,Artificial Intelligence,Bias (Epidemiology),Carcinoma,Child,Comparative Study,Computational Biology,Computerized,Confidentiality,Data Interpretation,Databases,Diagnosis,Differential,Disclosure,DNA,Gene Expression,Gene Expression Profiling,Gene Expression Regulation,Genetic Markers,Humans,Internet,Logistic Models,Lung Neoplasms,Medical Records Systems,Messenger,Multivariate Analysis,Neoplasm,Neoplasms,Neoplastic,Neural Networks (Computer),Non-U.S. Gov't,Oligonucleotide Array Sequence Analysis,P.H.S.,Privacy,Research Support,Rhabdomyosarcoma,RNA,Sarcoma,Small Cell,Software,Statistical,U.S. Gov't}
}

@article{breitbart_genomic_2002,
	title = {Genomic analysis of uncultured marine viral communities},
	volume = {99},
	issn = {0027-8424},
	doi = {10.1073/pnas.202488399},
	abstract = {Viruses are the most common biological entities in the oceans by an order of magnitude. However, very little is known about their diversity. Here we report a genomic analysis of two uncultured marine viral communities. Over 65\% of the sequences were not significantly similar to previously reported sequences, suggesting that much of the diversity is previously uncharacterized. The most common significant hits among the known sequences were to viruses. The viral hits included sequences from all of the major families of dsDNA tailed phages, as well as some algal viruses. Several independent mathematical models based on the observed number of contigs predicted that the most abundant viral genome comprised 2-3\% of the total population in both communities, which was estimated to contain between 374 and 7,114 viral types. Overall, diversity of the viral communities was extremely high. The results also showed that it would be possible to sequence the entire genome of an uncultured marine viral community.},
	language = {eng},
	number = {22},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Breitbart, Mya and Salamon, Peter and Andresen, Bjarne and Mahaffy, Joseph M. and Segall, Anca M. and Mead, David and Azam, Farooq and Rohwer, Forest},
	month = oct,
	year = {2002},
	pmid = {12384570},
	pmcid = {PMC137870},
	keywords = {Bacteriophages, Base Sequence, DNA Viruses, DNA, Viral, Genetic Variation, Models, Genetic, Molecular Sequence Data, Phycodnaviridae, Seawater},
	pages = {14250--14255}
}

Website  bibtex   

@article{
 title = {Tangled roots? Genetics meets genealogy},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Commerce,*Genetics, Medical,*Genetics, Population,*Pedigree,DNA, Mitochondrial/genetics,DNA/genetics,Databases, Nucleic Acid,Entrepreneurship,Female,Genetic Markers,Haplotypes,Human,Male,Microsatellite Repeats,Mutation,Y Chromosome},
 pages = {1634-5.},
 volume = {295},
 websites = {http://www.sciencemag.org/cgi/content/full/295/5560/1634,http://www.sciencemag.org/cgi/content/summary/295/5560/1634},
 id = {5413eefd-137b-32c7-9b0e-fdde2b23ddcd},
 created = {2017-06-19T13:45:53.457Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:45:53.540Z},
 tags = {02/04/26},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>News</m:note>},
 bibtype = {article},
 author = {Brown, K},
 journal = {Science},
 number = {5560}
}

Paper  Website  abstract   bibtex   

@article{
 title = {MALDI-TOF mass spectrometry of bacteria.},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {Bacteria,Bacteria: chemistry,Bacteria: pathogenicity,Bacterial Proteins,Bacterial Proteins: chemistry,Biological Markers,DNA, Bacterial,DNA, Bacterial: chemistry,Humans,Proteome,RNA, Bacterial,RNA, Bacterial: chemistry,Spectrometry, Mass, Matrix-Assisted Laser Desorpti},
 pages = {172-94},
 volume = {20},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11835305},
 id = {f31df6a4-342a-385b-8ac1-aa233eed78e7},
 created = {2014-05-31T04:14:15.000Z},
 accessed = {2013-05-21},
 file_attached = {true},
 profile_id = {9edae5ec-3a23-3830-8934-2c27bef6ccbe},
 group_id = {63e349d6-2c70-3938-9e67-2f6483f6cbab},
 last_modified = {2014-11-19T06:02:36.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {The development of MALDI-TOF mass spectrometry methods for the characterization of bacteria is reviewed and discussed. The general use of MALDI for the characterization of large biomolecules led directly to obvious applications involving the analysis of isolated bacterial proteins. More surprising was the observation that MALDI-TOF mass spectrometry could be applied directly to crude cellular fractions or cellular suspensions and that the resulting data from such complex mixtures could provide evidence for chemotaxonomic classification. Versatility and the rapidity of analysis led to the rapid development of a number of MALDI-TOF methods involving bacteria. Examples of some of the applications covered in this review are the analysis of bacterial RNA and DNA, the detection of recombinant proteins, the characterization of targeted or unknown proteins, bacterial proteomics, the detection of virulence markers, and the very rapid characterization of bacteria at the genus, species, and strain level. The demonstrated capability of taxonomic classification at the strain level, using unprocessed cells, opens the possibility that MALDI-TOF and similar mass spectrometry approaches may contribute significantly to fulfilling emerging needs for the development of near real-time methods for the characterization of bacteria.},
 bibtype = {article},
 author = {Lay, J O},
 journal = {Mass spectrometry reviews},
 number = {4}
}

Paper  abstract   bibtex   

@article{
 title = {Association between BRCA1 and BRCA2 mutations and cancer phenotype in Spanish breast/ovarian cancer families: implications for genetic testing},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Genes,*Genetic Screening/economics,*Mutation,Age of Onset,Breast Neoplasms,Breast Neoplasms/epidemiology/*genetics,Cohort Studies,Comparative Study,Cost-Benefit Analysis,DNA,DNA Mutational Analysis,Exons/genetics,Female,Frameshift Mutation,Gene Frequency,Genetic Predisposition to Disease,Hereditary/epidemiology/*gen,Human,Male,Male/epidemiology/*genetics,Neoplasm/genetics,Neoplastic Syndromes,Non-U.S. Gov't,Ovarian Neoplasms/epidemiology/genetics,Portugal/epidemiology,Prevalence,RNA Splicing/genetics,Sequence Deletion,Spain/epidemiology,Support,brca1,brca2,characterising the complete spectrum,fami-,in a sufficient number,is best done by,kind are limited and,lies,logistic regression model,of mutations,of phenotypically fully characterised,probabilistic models of this,restricted},
 pages = {466-471},
 volume = {97},
 id = {d2ed78a6-6da6-33ab-a4c3-83e7a858f69b},
 created = {2017-06-19T13:41:59.712Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:59.856Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>        <m:bold>From Duplicate 1 ( </m:bold>                <m:bold>          </m:bold><m:bold><m:italic>Association between BRCA1 and BRCA2 mutations and cancer phenotype in Spanish breast/ovarian cancer families: implications for genetic testing</m:italic></m:bold><m:bold>        </m:bold>                <m:bold> - de la Hoya, M; Osorio, A; Godino, J; Sulleiro, S; Tosar, A; Perez-Segura, P; Fernandez, C; Rodriguez, R; Diaz-Rubio, E; Benitez, J; Devilee, P; Caldes, T )<m:linebreak/>        </m:bold>        <m:linebreak/>eng<m:linebreak/>Journal Article<m:linebreak/>        <m:linebreak/>      </m:note>},
 abstract = {Index cases from a clinically relevant cohort of 102 Spanish families with at least 3 cases of breast and/or ovarian cancer (at least 1 case diagnosed before age 50) in the same lineage were screened for germline mutations in the entire coding sequence and intron boundaries of the breast cancer susceptibility genes BRCA1 and BRCA2. Overall, the prevalence of mutations was 43% in female breast/ovarian cancer families, 15% in female breast cancer families and 100% in male breast cancer families. Three recurrent mutations (185delAG, 589delCT and A1708E) explained 63% of BRCA1-related families. Early age at diagnosis of breast cancer, ovarian cancer, bilateral breast cancer, concomitant breast/ovarian cancer in a single patient and prostate cancer but not unilateral breast cancer were associated with BRCA1 and BRCA2 mutations. Male breast cancer was associated with BRCA2 mutations. The presence of male breast cancer was the only cancer phenotype that distinguished BRCA2- from BRCA1-related families. We have developed a logistic regression model for predicting the probability of harbouring a mutation in either BRCA1 or BRCA2 as a function of the cancer phenotype present in the family. The predictive positive and negative values of this model were 77.4% and 79%, respectively (probability cutoff of 30%). The findings of our work may be a useful tool for increasing the cost-effectiveness of genetic testing in familial cancer clinics.},
 bibtype = {article},
 author = {Hoya, Miguel De la and Osorio, Ana and Godino, Javier and Sulleiro, Sara and Tosar, Alicia and Perez-Segura, Pedro and Fernandez, Christina and de la Hoya, M and Rodriguez, R and Diaz-Rubio, E and Benitez, J and Devilee, P and Caldes, T},
 journal = {Int J Cancer},
 number = {4}
}

Paper  abstract   bibtex   

@article{
 title = {Detecting recombination in TT virus: a phylogenetic approach},
 type = {article},
 year = {2002},
 identifiers = {[object Object]},
 keywords = {*Phylogeny,*Recombination, Genetic,DNA, Viral/genetics,Evolution, Molecular,Support, Non-U.S. Gov't,Transfusion-Transmitted Virus/*genetics,Variation (Genetics),Viral Proteins/genetics},
 pages = {563-572},
 volume = {55},
 id = {07b0de60-3014-3ec3-b731-f0bdc6769cc5},
 created = {2017-06-19T13:44:32.858Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:33.014Z},
 tags = {03/05/15},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article</m:note>},
 abstract = {TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic clustering indicates that DNA sequence analysis is biased by homoplasy (i.e., genetic variability not originated by descent), indicative of either hypermutation or recombination. Statistical analysis shows that the significant excess of homoplasy is due to frequent recombination among closely related strains. Recombination events imply that the transmission of TTV is not clonal and provide the necessary basis to explain (i) the high degree of genetic divergence between TTV isolates, (ii) the lack of population structure on a world scale, and (iii) the number of highly divergent strains that seems typical of this virus. We show that recombination phenomena can be detected by phylogenetic analyses in very short sequences when a sufficiently large data set is available.},
 bibtype = {article},
 author = {Manni, F and Rotola, A and Caselli, E and Bertorelle, G and Di Luca, D},
 journal = {J Mol Evol},
 number = {5}
}

@article{
 title = {Involvement of a cytochrome P450 monooxygenase in thaxtomin A biosynthesis by Streptomyces acidiscabies},
 type = {article},
 year = {2002},
 keywords = {Amino Acid Sequence,Cytochrome P-450 Enzyme System,DNA, Bacterial,Escherichia coli,Indoles,Models, Molecular,Molecular Sequence Data,Piperazines,Sequence Homology, Amino Acid,Streptomyces,Streptomyces acidiscabies,Support, U.S. Gov't, Non-P.H.S.,adenylation,article,biosynthesis,catalysis,controlled study,cyclization,cytochrome P450,enzyme purification,esterification,gene product,hemoprotein,herbicide,high performance liquid chromatography,hydroxylation,methylation,molecular cloning,nonhuman,nuclear magnetic resonance spectroscopy,priority journal,reaction analysis,sequence analysis,sequence homology,thaxtomin A,unclassified drug,unspecific monooxygenase},
 pages = {2019-2029},
 volume = {184},
 id = {c32a38c2-6d3c-3187-aaf0-25bec11fbaee},
 created = {2012-01-05T13:05:41.000Z},
 file_attached = {false},
 profile_id = {1a467167-0a41-3583-a6a3-034c31031332},
 group_id = {0e532975-1a47-38a4-ace8-4fe5968bcd72},
 last_modified = {2015-03-05T16:01:49.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {The biosynthesis of the thaxtomin cyclic dipeptide phytotoxins proceeds nonribosomally via the thiotemplate mechanism. Acyladenylation, thioesterification, N-methylation, and cyclization of two amino acid substrates are catalyzed by the txtAB-encoded thaxtomin synthetase. Nucleotide sequence analysis of the region 3? of txtAB in Streptomyces acidiscabies 84.104 identified an open reading frame (ORF) encoding a homolog of the P450 monooxygenase gene family. It was proposed that thaxtomin A phenylalanyl hydroxylation was catalyzed by the monooxygenase homolog. The ORF was mutated in S. acidiscabies 84.104 by using an integrative gene disruption construct, and culture filtrate extracts of the mutant were assayed for the presence of dehydroxy derivatives of thaxtomin A. Reversed-phase high-performance liquid chromatography (HPLC) and HPLC-mass spectrometry indicated that the major component in culture filtrate extracts of the mutant was less polar and smaller than thaxtomin A. Comparisons of electrospray mass spectra as well as 1H- and 13C-nuclear magnetic resonance spectra of the purified compound with those previously reported for thaxtomins confirmed the structure of the compound as 12,15-N-dimethylcyclo-(L-4-nitrotryptophyl-L-phenylalanyl), the didehydroxy analog of thaxtomin A. The ORF, designated txtC, was cloned and the recombinant six-His-tagged fusion protein produced in Escherichia coli and purified from cell extracts. TxtC produced in E. coli exhibited spectral properties similar to those of cytochrome P450-type hemoproteins that have undergone conversion to the catalytically inactive P420 form. Based on these properties and the high similarity of TxtC to other well-characterized P450 enzymes, we conclude that txtC encodes a cytochrome P450-type monooxygenase required for postcyclization hydroxylation of the cyclic dipeptide.},
 bibtype = {article},
 author = {Healy, F G and Krasnoff, S B and Wach, M and Gibson, D M and Loria, R},
 journal = {Journal of Bacteriology},
 number = {7}
}

Website  abstract   bibtex   

@article{
 title = {Single molecule detection of double-stranded DNA in poly(methylmethacrylate) and polycarbonate microfluidic devices.},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Bacteriophage lambda,Bacteriophage lambda: chemistry,DNA, Viral,DNA, Viral: analysis,Electrophoresis, Capillary,Electrophoresis, Capillary: instrumentation,Equipment Design,Fluorescent Dyes,Fluorescent Dyes: analysis,Fluorescent Dyes: chemistry,Fluorometry,Fluorometry: instrumentation,Intercalating Agents,Intercalating Agents: analysis,Intercalating Agents: chemistry,Lasers,Microchemistry,Microchemistry: instrumentation,Molecular Weight,Polycarboxylate Cement,Polycarboxylate Cement: chemistry,Polymethyl Methacrylate,Polymethyl Methacrylate: chemistry,Quinolines,Quinolines: analysis,Quinolines: chemistry,Rheology,Sensitivity and Specificity,Thiazoles,Thiazoles: analysis,Thiazoles: chemistry,Time Factors},
 pages = {3939-48},
 volume = {22},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11700724},
 month = {10},
 id = {a6442936-70ae-3027-b44b-cf57e559a3fe},
 created = {2016-06-24T20:49:59.000Z},
 file_attached = {false},
 profile_id = {954a987f-819f-3985-95a4-2991e0cf0552},
 group_id = {8440dcff-74cc-3783-aef7-fe2749cfc7ef},
 last_modified = {2016-06-24T20:49:59.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 citation_key = {Wabuyele2001},
 abstract = {Single photon burst techniques were used to detect double-stranded DNA molecules in poly(methylmethacrylate) (PM MA) and polycarbonate (PC) microfluidic devices. A confocal epi-illumination detection system was constructed to monitor the fluorescence signature from single DNA molecules that were multiply labeled with the mono-intercalating dye, TOPRO-5, which possessed an absorption maximum at 765 nm allowing excitation with a solid-state diode laser and fluorescence monitoring in the near-infrared (IR). Near-IR excitation minimized autofluorescence produced from the polymer substrate, which was found to be significantly greater when excitation was provided in the visible range (488 nm). A solution containing lambda-DNA (48.5 kbp) was electrokinetically transported through the microfluidic devices at different applied voltages and solution pH values to investigate the effects of polymer substrate on the transport rate and detection efficiency of single molecular events. By applying an autocorrelation analysis to the data, we were able to obtain the molecular transit time of the individual molecules as they passed through the 7 microm laser beam. It was observed that the applied voltage for both devices affected the transport rate. However, solution pH did not alter the transit time for PM MA-based devices since the electroosmotic flow of PMMA was independent of solution pH. In addition, efforts were directed toward optimizing the sampling efficiency (number of molecules passing through the probe volume) by using either hydrodynamically focused flows from a sheath generated by electrokinetic pumping from side channels or reducing the channel width of the microfluidic device. Due to the low electroosmotic flows generated by both PMMA and PC, tight focusing of the sample stream was not possible. However, in PMMA devices, flow gating was observed by applying field strengths > -120 V/cm to the sheath flow channels. By narrowing the microchannel width, the number of molecular events detected per unit time was found to be four times higher in channels with 10 microm widths compared to those of 50 microm, indicating improved sampling efficiency for the narrower channels without significantly deteriorating detection efficiency. Attempts were made to do single molecule sizing of lambda-DNA, M13 (7.2 kbp) and pUC19 (2.7 kbp) using photon burst detection. While the average number of photons for each DNA type were different, the standard deviations were large due to the Gaussian intensity profile of the excitation beam. To demonstrate the sensitivity of single molecule analysis in the near-IR using polymer microfluidic devices, the near-IR chromophore, NN382, wasanalyzed using ourconfocal imager. A detection efficiency of 94% for single NN382 molecules was observed in the PC devices.},
 bibtype = {article},
 author = {Wabuyele, M B and Ford, S M and Stryjewski, W and Barrow, J and Soper, S a},
 journal = {Electrophoresis},
 number = {18}
}

Paper  abstract   bibtex   

@article{
 title = {Molecular genetic alterations on chromosomes 11 and 22 in ependymomas},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {Adolescent,Adult,Aged,Alleles,Base Sequence,Brain Neoplasms,Brain Neoplasms: genetics,Child,Chromosome Deletion,Chromosomes,DNA,DNA Primers,DNA Primers: chemistry,Ependymoma,Ependymoma: genetics,Ependymoma: pathology,Female,Genes,Human,Humans,Infant,Loss of Heterozygosity,Male,Microsatellite Repeats,Middle Aged,Mutation,Neoplasm Proteins,Neoplasm Proteins: genetics,Neurofibromatosis 2,Neurofibromatosis 2: genetics,Newborn,Pair 11,Pair 11: genetics,Pair 22,Pair 22: genetics,Polymerase Chain Reaction,Preschool,Proto-Oncogene Proteins,Sequence Analysis,Spinal Cord Neoplasms,Spinal Cord Neoplasms: genetics},
 pages = {803-8},
 volume = {91},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11275983},
 month = {3},
 day = {15},
 id = {7d56c6a1-5e17-379e-ab86-667dcf2ce1cd},
 created = {2013-08-05T21:04:27.000Z},
 file_attached = {true},
 profile_id = {8c4ca2d5-86de-3b5d-86be-8408415f34e0},
 group_id = {a484ae4c-fcac-3c7e-9ac3-3fad0df719a2},
 last_modified = {2014-12-29T19:36:50.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Ependymomas arise from the ependymal cells at different locations throughout the brain and spinal cord. These tumors have a broad age distribution with a range from less than 1 year to more than 80 years. In some intramedullary spinal ependymomas, mutations in the neurofibromatosis 2 (NF2) gene and loss of heterozygosity (LOH) on chromosome arm 22q have been described. Cytogenetic studies have also identified alterations involving chromosome arm 11q, including rearrangements at 11q13, in ependymomas. We analyzed 21 intramedullary spinal, 14 ventricular, 11 filum terminale and 6 intracerebral ependymomas for mutations in the MEN1 gene, which is located at 11q13, and mutations in the NF2 gene, which is located at 22q12, as well as for LOH on 11q and 22q. NF2 mutations were found in 6 tumors, all of which were intramedullary spinal and all of which displayed LOH 22q. Allelic loss on 22q was found in 20 cases and was significantly more frequent in intramedullary spinal ependymomas than in tumors in other locations. LOH 11q was found in 7 patients and exhibited a highly significant inverse association with LOH 22q (p<0.001). A hemizygous MEN1 mutation was identified in 3 tumors, all of which were recurrences from the same patient. Interestingly, the initial tumor corresponded to WHO grade II and displayed LOH 11q but not yet a MEN1 mutation. In 2 subsequent recurrences, the tumor had progressed to anaplastic ependymoma (WHO grade III) and exhibited a nonsense mutation in exon 10 of MEN1 (W471X) in conjunction with LOH 11q. This suggests that loss of wild-type MEN1 may be involved in the malignant progression of a subset of ependymomas. To conclude, our findings provide evidence for different genetic pathways involved in ependymoma formation and progression, which may allow to define genetically and clinically distinct tumor entities.},
 bibtype = {article},
 author = {Lamszus, K and Lachenmayer, L and Heinemann, U and Kluwe, L and Finckh, U and Höppner, W and Stavrou, D and Fillbrandt, R and Westphal, M},
 journal = {International journal of cancer},
 number = {6}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Modern African ape populations as genetic and demographic models of the last common ancestor of humans, chimpanzees, and gorillas},
 type = {article},
 year = {2001},
 identifiers = {[object Object]},
 keywords = {*Phylogeny,*Variation (Genetics),Africa,Animals,Cell Nucleus/genetics,DNA, Mitochondrial/genetics,Evolution, Molecular,Genetics, Population,Gorilla gorilla/*genetics,Humans,Pan troglodytes/*genetics,Research Support, U.S. Gov't, Non-P.H.S.},
 pages = {475-480},
 volume = {92},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11948214},
 id = {1feeff1b-7fe6-3f48-81c1-5b91c1b4bf58},
 created = {2017-06-19T13:43:49.239Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:49.377Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0022-1503 (Print)<m:linebreak/>Journal Article</m:note>},
 abstract = {In order to fully understand human evolutionary history through the use of molecular data, it is essential to include our closest relatives as a comparison. We provide here estimates of nucleotide diversity and effective population size of modern African ape species using data from several independent noncoding nuclear loci, and use these estimates to make predictions about the nature of the ancestral population that eventually gave rise to the living species of African apes, including humans. Chimpanzees, bonobos, and gorillas possess two to three times more nucleotide diversity than modern humans. We hypothesize that the last common ancestor (LCA) of these species had an effective population size more similar to modern apes than modern humans. In addition, estimated dates for the divergence of the Homo, Pan, and Gorilla lineages suggest that the LCA may have had stronger geographic structuring to its mtDNA than its nuclear DNA, perhaps indicative of strong female philopatry or a dispersal system analogous to gorillas, where females disperse only short distances from their natal group. Synthesizing different classes of data, and the inferences drawn from them, allows us to predict some of the genetic and demographic properties of the LCA of humans, chimpanzees, and gorillas.},
 bibtype = {article},
 author = {Jensen-Seaman, M I and Deinard, A S and Kidd, K K},
 journal = {J Hered},
 number = {6}
}

Paper  doi  abstract   bibtex   

@article{puig_tandem_2001,
	title = {The tandem affinity purification ({TAP}) method: a general procedure of protein complex purification},
	volume = {24},
	issn = {1046-2023},
	shorttitle = {The tandem affinity purification ({TAP}) method},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11403571},
	doi = {10.1006/meth.2001.1183},
	abstract = {Identification of components present in biological complexes requires their purification to near homogeneity. Methods of purification vary from protein to protein, making it impossible to design a general purification strategy valid for all cases. We have developed the tandem affinity purification (TAP) method as a tool that allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the TAP tag, either N- or C-terminally, to the target protein of interest. Starting from a relatively small number of cells, active macromolecular complexes can be isolated and used for multiple applications. Variations of the method to specifically purify complexes containing two given components or to subtract undesired complexes can easily be implemented. The TAP method was initially developed in yeast but can be successfully adapted to various organisms. Its simplicity, high yield, and wide applicability make the TAP method a very useful procedure for protein purification and proteome exploration.},
	number = {3},
	urldate = {2009-12-02TZ},
	journal = {Methods (San Diego, Calif.)},
	author = {Puig, O and Caspary, F and Rigaut, G and Rutz, B and Bouveret, E and Bragado-Nilsson, E and Wilm, M and Séraphin, B},
	month = jul,
	year = {2001},
	pmid = {11403571},
	keywords = {Bacterial Proteins, Blotting, Western, DNA, Bacterial, Fungal Proteins, Genetic Vectors, Methods, Mutation, Polymerase Chain Reaction, Proteins, Proteome, Ribonucleases, Ribonucleoproteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Staphylococcus aureus},
	pages = {218--229}
}

@article{
 title = {Anti-mitotic properties of indirubin-3'-monoxime, a CDK/GSK-3 inhibitor: induction of endoreplication following prophase arrest},
 type = {article},
 year = {2001},
 keywords = {Apoptosis,Cancer Cells,Cell Cycle,Chemical Inhibitors,Cyclin Dependent Kinases,DNA,GSK 3 beta,Medicine,Mitosis,SBR_Phyto,Sodium Butyrate,Staurosporine,cancer,cyclin dependent kinase,glycogen synthase kinase,indirubin,kinase inhibitor},
 pages = {3786-3797},
 volume = {20},
 id = {c9dc259f-0b13-31c1-be0d-47ecc0c4560d},
 created = {2015-11-02T11:41:39.000Z},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2016-06-16T13:23:04.000Z},
 tags = {2001,sbr_phyto},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {Jun 28 2001},
 bibtype = {article},
 author = {Damiens, Eve and Baratte, Blandine and Marie, Dominique and Eisenbrand, G and Meijer, Laurent},
 journal = {Oncogene},
 number = {29}
}

Paper  Website  abstract   bibtex   

@article{
 title = {Does a retrograde response in human aging and longevity exist?},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Adult,Aged,Aged, 80 and over,Aging,DNA, Mitochondrial,DNA, Mitochondrial: analysis,Female,Genotype,Humans,Longevity,Male,Middle Aged,Tyrosine 3-Monooxygenase,Tyrosine 3-Monooxygenase: genetics},
 pages = {795-801},
 volume = {35},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/11053670},
 month = {9},
 id = {d9ad0689-1d6d-302d-9e8d-3da14821f4c1},
 created = {2017-06-19T13:41:38.867Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:41:39.005Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {The retrograde response (RR) is a compensatory mechanism by which mutant strains of yeast are able to cope with mitochondrial DNA (mtDNA) impairments by up-regulating the expression of the stress-responder nuclear genes and significantly increasing lifespan. Starting from the observation that both mtDNA variability and Tyrosine hydroxylase (THO, stress-responder gene) variability are correlated with human longevity, we asked ourselves whether mechanisms similar to RR may exist in humans. As a first investigative step we have analyzed the distribution of the mtDNA inherited variants (haplogroups) according to THO genotypes in three sample groups of increasing ages (20-49 years; 50-80 years; centenarians). We found that the mtDNA haplogroups and the THO genotypes are associated randomly in the first group, while in the second group, and particularly in the centenarians, a non-random association is observed between the mtDNA and nuclear DNA variability. Moreover, in centenarians the U haplogroup is over-represented (p=0.012) in subjects carrying the THO genotype unfavorable to longevity. On the whole these findings are in line with the hypothesis that longevity requires particular interactions between mtDNA and nuclear DNA and do not exclude the possibility that an RR has been maintained throughout evolution and it is present in higher organisms.},
 bibtype = {article},
 author = {De Benedictis, G and Carrieri, G and Garasto, S and Rose, G and Varcasia, O and Bonafè, M and Franceschi, C and Jazwinski, S M},
 journal = {Experimental gerontology},
 number = {6-7}
}

Paper  Website  abstract   bibtex   

@article{
 title = {New estimates of intergenerational time intervals for the calculation of age and origins of mutations.},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Adolescent,Adult,Age Factors,Aged,Cohort Studies,DNA,Family,Female,Genetics,Humans,Male,Marriage,Maternal Age,Middle Aged,Mitochondrial,Mitochondrial: genetics,Mutation,Mutation: genetics,Parity,Paternal Age,Pedigree,Population,Quebec,Registries,Reproducibility of Results,X Chromosome,X Chromosome: genetics,Y Chromosome,Y Chromosome: genetics},
 pages = {651-8},
 volume = {66},
 websites = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1288116&tool=pmcentrez&rendertype=abstract},
 month = {2},
 id = {0ec560fa-3c57-3ad3-b56e-48901f694978},
 created = {2017-06-19T13:46:39.367Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:39.498Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Intergenerational time intervals are frequently used in human population-genetics studies concerned with the ages and origins of mutations. In most cases, mean intervals of 20 or 25 years are used, regardless of the demographic characteristics of the population under study. Although these characteristics may vary from prehistoric to historical times, we suggest that this value is probably too low, and that the ages of some mutations may have been underestimated. Analyses were performed by using the BALSAC Population Register (Quebec, Canada), from which several intergenerational comparisons can be made. Family reconstitutions were used to measure interval lengths and variations in descending lineages. Various parameters were considered, such as spouse age at marriage, parental age, and reproduction levels. Mother-child and father-child intervals were compared. Intergenerational male and female intervals were also analyzed in 100 extended ascending genealogies. Results showed that a mean value of 30 years is a better estimate of intergenerational intervals than 20 or 25 years. As marked differences between male and female interval length were observed, specific values are proposed for mtDNA, autosomal, X-chromosomal, and Y-chromosomal loci. The applicability of these results for age estimates of mutations is discussed.},
 bibtype = {article},
 author = {Tremblay, Marc and Vézina, Hélene},
 journal = {American journal of human genetics},
 number = {2}
}

Website  bibtex   

@article{
 title = {Genetic homogeneity of Icelanders},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {*Genetics, Population,Alleles,DNA, Mitochondrial/genetics,Female,Genetic Markers,Heterozygote,Homozygote,Human,Iceland,Male,Variation (Genetics)},
 pages = {395.},
 volume = {26},
 websites = {http://www.nature.com/cgi-taf/dynapage.taf?file=/ncb/genetics/v26/n4/full/ng1200_395b.html,http://www.nature.com/cgi-taf/dynapage.taf?file=/ncb/genetics/v26/n4/abs/ng1200_395b.html},
 id = {678add07-7f52-32f4-95f2-aa5951181c54},
 created = {2017-06-19T13:44:10.899Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:44:11.002Z},
 tags = {01/12/13},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Comment<m:linebreak/>Letter</m:note>},
 bibtype = {article},
 author = {Gulcher, J and Helgason, A and Stefansson, K},
 journal = {Nat Genet},
 number = {4}
}

Paper  abstract   bibtex   

@article{
 title = {The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data},
 type = {article},
 year = {2000},
 identifiers = {[object Object]},
 keywords = {Africa,Alleles,Alu Elements/genetics,Asia,Bias (Epidemiology),Chromosomes, Human/*genetics,Comparative Study,DNA Restriction Enzymes/metabolism,DNA, Mitochondrial/*genetics,Europe,Female,Gene Frequency/genetics,Human,Long Interspersed Nucleotide Elements/genetics,Male,Mutation/genetics,Phylogeny,Polymorphism (Genetics)/genetics,Support, U.S. Gov't, Non-P.H.S.,Support, U.S. Gov't, P.H.S.,Tandem Repeat Sequences/genetics,Variation (Genetics)/*genetics,Y Chromosome/*genetics},
 pages = {979-988},
 volume = {66},
 id = {de837c67-d8dc-3fe3-b1d6-21d7236de12f},
 created = {2017-06-19T13:43:25.760Z},
 file_attached = {true},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:25.903Z},
 tags = {03/05/16},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article</m:note>},
 abstract = {We report a comparison of worldwide genetic variation among 255 individuals by using autosomal, mitochondrial, and Y-chromosome polymorphisms. Variation is assessed by use of 30 autosomal restriction-site polymorphisms (RSPs), 60 autosomal short-tandem-repeat polymorphisms (STRPs), 13 Alu-insertion polymorphisms and one LINE-1 element, 611 bp of mitochondrial control-region sequence, and 10 Y-chromosome polymorphisms. Analysis of these data reveals substantial congruity among this diverse array of genetic systems. With the exception of the autosomal RSPs, in which an ascertainment bias exists, all systems show greater gene diversity in Africans than in either Europeans or Asians. Africans also have the largest total number of alleles, as well as the largest number of unique alleles, for most systems. GST values are 11%-18% for the autosomal systems and are two to three times higher for the mtDNA sequence and Y-chromosome RSPs. This difference is expected because of the lower effective population size of mtDNA and Y chromosomes. A lower value is seen for Y-chromosome STRs, reflecting a relative lack of continental population structure, as a result of rapid mutation and genetic drift. Africa has higher GST values than does either Europe or Asia for all systems except the Y-chromosome STRs and Alus. All systems except the Y-chromosome STRs show less variation between populations within continents than between continents. These results are reassuring in their consistency and offer broad support for an African origin of modern human populations.},
 bibtype = {article},
 author = {Jorde, L B and Watkins, W S and Bamshad, M J and Dixon, M E and Ricker, C E and Seielstad, M T and Batzer, M A},
 journal = {Am J Hum Genet},
 number = {3}
}

Paper  bibtex   

@article{weiner_is_1999,
	title = {Is self-regulation enough today?: {Evaluating} the recombinant {DNA} controversy},
	volume = {9},
	issn = {0748-383X},
	shorttitle = {Is self-regulation enough today?},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/10787474},
	number = {2},
	urldate = {2011-03-17},
	journal = {Health Matrix (Cleveland, Ohio: 1991)},
	author = {Weiner, C},
	year = {1999},
	pmid = {10787474},
	keywords = {DNA, Recombinant, Genetic Engineering, Government Regulation, Guidelines as Topic, Humans, National Institutes of Health (U.S.), Research, United States},
	pages = {289--302},
	file = {9HealthMatrix289.pdf:files/14355/9HealthMatrix289.pdf:application/pdf}
}

@article{
 title = {Which of our genes makes us human?},
 type = {article},
 year = {1998},
 keywords = {*Chromosomes, Human,*Genome,*Genome, Human,*Human Characteristics,*Sequence Analysis, DNA,Animal,Chromosome Mapping,Gene Expression,Human,Mutation,Pan troglodytes/genetics,Pongidae/*genetics,Sialic Acids/chemistry/physiology,Species Specificity},
 pages = {1432-1434},
 volume = {281},
 id = {85b008be-1b1d-3c94-bd62-2d641fa111cc},
 created = {2017-06-19T13:42:20.922Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:21.018Z},
 tags = {03/11/21},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>News</m:note>},
 bibtype = {article},
 author = {Gibbons, A},
 journal = {Science},
 number = {5382}
}

Website  bibtex   

@article{
 title = {Mitochondrial genotype associated with French Caucasian centenarians},
 type = {article},
 year = {1998},
 identifiers = {[object Object]},
 keywords = {Aged,Aged, 80 and over,DNA, Mitochondrial/*genetics,European Continental Ancestry Group/*genetics,France,Genotype,Humans},
 pages = {349},
 volume = {44},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9813436},
 id = {9603332d-82b1-3ee7-b245-6330a50e4dd1},
 created = {2017-06-19T13:43:39.834Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:40.185Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0304-324x<m:linebreak/>Letter</m:note>},
 bibtype = {article},
 author = {Ivanova, R and Lepage, V and Charron, D and Schachter, F},
 journal = {Gerontology},
 number = {6}
}

Website  abstract   bibtex   

@article{
 title = {Mitochondrial aging: open questions},
 type = {article},
 year = {1998},
 identifiers = {[object Object]},
 keywords = {Aging/*physiology,Animals,Antioxidants/metabolism,DNA, Mitochondrial/genetics,Humans,Life Expectancy,Longevity,Mammals,Mitochondria/*metabolism,Mutation,Oxidants/metabolism,Oxidative Phosphorylation,Research Support, U.S. Gov't, P.H.S.},
 pages = {118-127},
 volume = {854},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9928425},
 id = {ee9849b4-dbd9-3294-a5fe-31fd5a3bf139},
 created = {2017-06-19T13:43:14.144Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:43:14.247Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>0077-8923<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Interest in the role of mitochondria in aging has intensified in recent years. This focus on mitochondria originated in part from the free radical theory of aging, which argues that oxidative damage plays a key role in degenerative senescence. Among the numerous mechanisms known to generate oxidants, leakage of the superoxide anion and hydrogen peroxide from the mitochondrial electron transport chain are of particular interest, due to the correlation between species-specific metabolic rate ("rate of living") and life span. Phenomenological studies of mitochondrial function long ago noted a decline in mitochondrial function with age, and on-going research continues to add to this body of knowledge. The extranuclear somatic mutation theory of aging proposes that the accumulation of mutations in the mitochondrial genome may be responsible in part for the mitochondrial phenomenology of aging. Recent studies of mitochondrial DNA (mtDNA) deletions have shown that they increase with age in humans and other mammals. Currently, there exist numerous important and fundamental questions surrounding mitochondria and aging. Among these are (1) How important are mitochondrial oxidants in determining overall cellular oxidative stress? (2) What are the mechanisms of mitochondrial oxidant generation? (3) How are lesions and mutations in mtDNA formed? (4) How important are mtDNA lesions and mutations in causing mitochondrial dysfunction? (5) How are mitochondria regulated, and how does this regulation change during aging? (6) What are the dynamics of mitochondrial turnover? (7) What is the relationship between mitochondrial damage and lipofuscinogenesis? (8) What are the relationships among mitochondria, apopotosis, and aging? and (9) How can mitochondrial function (ATP generation and the establishment of a membrane potential) and dysfunction (oxidant generation) be modulated and degenerative senescence thereby treated?},
 bibtype = {article},
 author = {Beckman, K B and Ames, B N},
 journal = {Ann N Y Acad Sci}
}

Paper  abstract   bibtex   

@article{meisenzahl_isolation_1997,
	title = {Isolation and characterization of a xylose-dependent promoter from {Caulobacter} crescentus},
	volume = {179},
	issn = {0021-9193},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/9006009},
	abstract = {An inducible promoter is a useful tool for the controlled expression of a given gene. Accordingly, we identified, cloned, and sequenced a chromosomal locus, xylX, from Caulobacter crescentus which is required for growth on xylose as the sole carbon source and showed that transcription from a single site is dependent on the presence of xylose in the growth medium. P(xylX) promoter activity was determined as a function of the composition of the growth medium both in single copy and on a plasmid using different reporter genes. One hundred micromolar exogenously added xylose was required for maximal induction of P(xylX) in a strain that is unable to metabolize xylose. P(xylX) activity was induced immediately after the addition of xylose and repressed almost completely when xylose was removed from the growth medium. In addition to the strong transcriptional control, the expression of xylX is also regulated on the translational level.},
	number = {3},
	urldate = {2009-05-03TZ},
	journal = {Journal of Bacteriology},
	author = {Meisenzahl, A C and Shapiro, L and Jenal, U},
	month = feb,
	year = {1997},
	pmid = {9006009},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Base Sequence, Caulobacter crescentus, Chromosome Mapping, Chromosomes, Bacterial, Cloning, Molecular, Flagella, Gene Expression Regulation, Bacterial, Genes, Bacterial, Genes, Reporter, Kinetics, Molecular Sequence Data, Promoter Regions, Genetic, Sequence Analysis, DNA, Xylose},
	pages = {592--600}
}

@article{
 title = {Facts and artifacts of ancient DNA},
 type = {article},
 year = {1997},
 identifiers = {[object Object]},
 keywords = {*Artifacts,*Fossils,Animal,Base Sequence,Bone and Bones/chemistry,DNA, Mitochondrial/chemistry,DNA/*chemistry,Germany,Hominidae/genetics,Human},
 pages = {1-3.},
 volume = {90},
 id = {cd69f7f5-a62f-39d8-b674-3e6e0a4bc8ef},
 created = {2017-06-19T13:42:45.640Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:45.742Z},
 tags = {03/03/18},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Comment<m:linebreak/>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 bibtype = {article},
 author = {Lindahl, T},
 journal = {Cell},
 number = {1}
}

@article{
 title = {The genetical archaeology of the human genome},
 type = {article},
 year = {1996},
 identifiers = {[object Object]},
 keywords = {*Gene Pool,*Genome, Human,DNA, Mitochondrial/genetics,Evolution, Molecular,Female,Human,Male,Models, Genetic,Phylogeny,Support, Non-U.S. Gov't,Variation (Genetics)/*genetics},
 pages = {135-140},
 volume = {14},
 id = {da42c725-f648-32fa-a720-c48d07c5c47c},
 created = {2017-06-19T13:46:05.495Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:46:05.676Z},
 tags = {03/09/17},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>Journal Article<m:linebreak/>Review<m:linebreak/>Review, Tutorial</m:note>},
 abstract = {Palaentology and archaeology are disciplines that traditionally deal with the reconstruction of human origins and history. Recently, however, molecular genetics has come to make increasing contributions to this area. In particular, several data sets indicate that variation of the human gene pool originated in Africa within the last 200,000 years. Furthermore, the study of DNA sequences allows the detection of expansions in population size. Here we briefly summarize and exemplify how DNA sequences can be used to reconstruct the history of populations.},
 bibtype = {article},
 author = {von Haeseler, A and Sajantila, A and Paabo, S},
 journal = {Nat Genet},
 number = {2}
}

@article{
 title = {Parthenogenesis and apospory in the Laminariales: A flow cytometry analysis},
 type = {article},
 year = {1996},
 keywords = {CELL-WALL,CULTURE,DNA,GENETICS,JAPONICA,LIFE-HISTORY,PHAEOPHYTA,SACCHARINA,SBR_Phyto,SEAWEEDS,SPOROPHYTES},
 pages = {369-380},
 volume = {31},
 id = {b1cac542-699e-33d5-b6c6-d73c1d9d1e03},
 created = {2015-11-02T11:41:35.000Z},
 file_attached = {false},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 group_id = {98cf6291-ef58-3f8a-a4b6-c8754044662f},
 last_modified = {2016-06-16T13:22:52.000Z},
 tags = {1996,sbr_phyto},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 abstract = {Tissue explants and unisexual cultures of Macrocystis pyrifera, Laminaria saccharina and L. Digitata regenerated into various forms, including gametophyte-like filaments, callus-like structures. Stipe-like structures and either abnormal or normal sporophytes. The ploidy of the various forms of growth was assessed using flow cytometry analysis of isolated nuclei. Unisexual cultures of female gametophytes of L. Digitata gave rise to abnormal parthenogenetic sporophytes, with nuclei exhibiting 2C, 4C and 8C ploidy levels. Aposporous gametophyte-like filaments grown from the tissue explants of M. Pyrifera developed into abnormal sporophytes and both forms were diploid. Development of stipe medullary explants of L. Saccharina led to the complete regeneration of functional sporophytes, involving the outgrowth of aposporous gametophytes. The regenerated sporophytes were either diploid or tetraploid but only diploid sporophytes were found to be fertile. The developmental and biotechnological significance of these results is discussed.},
 bibtype = {article},
 author = {Gall, E A and Asensi, A and Marie, D and Kloareg, B},
 journal = {European Journal of Phycology},
 number = {4}
}

Paper  abstract   bibtex   

@article{greene_spo0a_1996,
	title = {The {Spo}0A protein of {Bacillus} subtilis inhibits transcription of the {abrB} gene without preventing binding of the polymerase to the promoter},
	volume = {271},
	issn = {0021-9258},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/8626703},
	abstract = {Repression of transcription of the abrB gene is essential to expression of many of the postexponential genes in Bacillus. The repression is due to the activity of the response regulator protein Spo0A. We have used in vitro transcription and DNase I and hydroxyl radical footprinting to explore the mechanism of transcription inhibition. Spo0A binds to specific DNA sequences (0A boxes), and two such boxes are found downstream of the tandem promoters for the abrB gene. The data indicate that both RNA polymerase and Spo0A bind simultaneously to a DNA fragment containing the promoters and the 0A boxes. The Spo0A prevents the polymerase from inducing DNA strand denaturation at the promoter for the abrB gene.},
	number = {19},
	urldate = {2009-05-03TZ},
	journal = {The Journal of Biological Chemistry},
	author = {Greene, E A and Spiegelman, G B},
	month = may,
	year = {1996},
	pmid = {8626703},
	keywords = {Bacillus subtilis, Bacterial Proteins, Base Sequence, Binding Sites, DNA Footprinting, DNA, Bacterial, DNA-Binding Proteins, DNA-Directed RNA Polymerases, Deoxyribonuclease I, Escherichia coli, Gene Expression Regulation, Bacterial, Genes, Bacterial, Hydroxyl Radical, Kinetics, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Factors, Transcription, Genetic},
	pages = {11455--11461}
}

Paper  abstract   bibtex   

@article{gilbert_protein_1995,
	title = {Protein {Hpn}: cloning and characterization of a histidine-rich metal-binding polypeptide in {Helicobacter} pylori and {Helicobacter} mustelae},
	volume = {63},
	issn = {0019-9567},
	shorttitle = {Protein {Hpn}},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/7790085},
	abstract = {Helicobacter pylori is a human gastrointestinal pathogen involved in gastritis, duodenal ulcers, and gastric neoplasia. This microorganism produces large amounts of a urease which, like all known ureases, has nickel in the active site. We have identified a protein in clinical isolates of H. pylori and an identical protein in the ferret pathogen Helicobacter mustelae that strongly binds Ni2+ and Zn2+. This protein has been named Hpn to emphasize its origins in H. pylori and its affinity for nickel. The encoding hpn gene, cloned and expressed in Escherichia coli ER1793, has an open reading frame (180 bp) that specifies a protein with a calculated molecular mass of 7,077 Da and with the same amino-terminal sequence as that of wild-type Hpn. The deduced sequence of Hpn consists of 60 amino acids, of which 28 (47\%) are histidines. The hpn gene does not map with the urease gene cluster on the H. pylori chromosome. An Hpn-negative, isogenic H. pylori strain, generated by hpn gene deletion and grown on blood agar, had the same urease activity that wild-type cells did. Thus, the role of Hpn in helicobacters is unknown.},
	number = {7},
	urldate = {2009-11-20TZ},
	journal = {Infection and Immunity},
	author = {Gilbert, J V and Ramakrishna, J and Sunderman, F W and Wright, A and Plaut, A G},
	month = jul,
	year = {1995},
	pmid = {7790085},
	keywords = {Amino Acid Sequence, Base Sequence, Cloning, Molecular, DNA, Bacterial, Genes, Bacterial, Helicobacter, Helicobacter pylori, Molecular Sequence Data, Nickel, Oligonucleotide Probes, Proteins, Restriction Mapping, Urease},
	pages = {2682--2688}
}

Website  bibtex   

@article{
 title = {A G-to-T transversion at the +5 position of intron 1 in the glutaryl CoA dehydrogenase gene is associated with the Island Lake variant of glutaric acidemia type I},
 type = {article},
 year = {1995},
 identifiers = {[object Object]},
 keywords = {*Mutation,*Oxidoreductases Acting on CH-CH Group Donors,Amino Acid Sequence,Asian Continental Ancestry Group,Base Sequence,Glutaryl-CoA Dehydrogenase,Humans,Molecular Sequence Data,Ontario,Oxidoreductases/*deficiency/*genetics,RNA Splicing,Sequence Analysis, DNA},
 pages = {493-495},
 volume = {4},
 websites = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7795610},
 edition = {1995/03/01},
 id = {e03e62c1-77f2-37cd-a817-712990bad7e9},
 created = {2017-06-19T13:42:46.803Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:46.913Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 language = {eng},
 notes = {<m:note>Greenberg, C R<m:linebreak/>Reimer, D<m:linebreak/>Singal, R<m:linebreak/>Triggs-Raine, B<m:linebreak/>Chudley, A E<m:linebreak/>Dilling, L A<m:linebreak/>Philipps, S<m:linebreak/>Haworth, J C<m:linebreak/>Seargeant, L E<m:linebreak/>Goodman, S I<m:linebreak/>Research Support, Non-U.S. Gov't<m:linebreak/>England<m:linebreak/>Human molecular genetics<m:linebreak/>Hum Mol Genet. 1995 Mar;4(3):493-5.</m:note>},
 bibtype = {article},
 author = {Greenberg, C R and Reimer, D and Singal, R and Triggs-Raine, B and Chudley, A E and Dilling, L A and Philipps, S and Haworth, J C and Seargeant, L E and Goodman, S I},
 journal = {Hum Mol Genet},
 number = {3}
}

@article{
 title = {Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data},
 type = {article},
 year = {1995},
 identifiers = {[object Object]},
 keywords = {*Evolution,*Genetics, Population,*Polymorphism (Genetics),Africa,Asia,Base Sequence,DNA, Mitochondrial/*genetics,Europe,Human,Molecular Sequence Data,Support, Non-U.S. Gov't,Support, U.S. Gov't, Non-P.H.S.,Support, U.S. Gov't, P.H.S.,Variation (Genetics)},
 pages = {523-38.},
 volume = {57},
 id = {c8fcd55c-4113-3c06-a1da-02b7e95168c7},
 created = {2017-06-19T13:42:45.605Z},
 file_attached = {false},
 profile_id = {de68dde1-2ff3-3a4e-a214-ef424d0c7646},
 group_id = {b2078731-0913-33b9-8902-a53629a24e83},
 last_modified = {2017-06-19T13:42:45.719Z},
 tags = {02/02/18},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 notes = {<m:note>eng<m:linebreak/>Journal Article</m:note>},
 abstract = {To test hypotheses about the origin of modern humans, we analyzed mtDNA sequences, 30 nuclear restriction-site polymorphisms (RSPs), and 30 tetranucleotide short tandem repeat (STR) polymorphisms in 243 Africans, Asians, and Europeans. An evolutionary tree based on mtDNA displays deep African branches, indicating greater genetic diversity for African populations. This finding, which is consistent with previous mtDNA analyses, has been interpreted as evidence for an African origin of modern humans. Both sets of nuclear polymorphisms, as well as a third set of trinucleotide polymorphisms, are highly consistent with one another but fail to show deep branches for African populations. These results, which represent the first direct comparison of mtDNA and nuclear genetic data in major continental populations, undermine the genetic evidence for an African origin of modern humans.},
 bibtype = {article},
 author = {Jorde, L B and Bamshad, M J and Watkins, W S and Zenger, R and Fraley, A E and Krakowiak, P A and Carpenter, K D and Soodyall, H and Jenkins, T and Rogers, A R},
 journal = {Am J Hum Genet},
 number = {3}
}

@article{
 title = {The Origin of Land Plants - Phylogenetic-Relationships among Charophytes, Bryophytes, and Vascular Plants Inferred from Complete Small-Subunit Ribosomal-Rna Gene-Sequences},
 type = {article},
 year = {1995},
 identifiers = {[object Object]},
 keywords = {18s ribosomal rna,bryophyta,charophyceae,chlorophyceae,chloroplast tufa gene,coding region,complete nucleotide sequence,dna,evolution,green algae,molecular clock,parsimony,phylogeny,ribonucleic acid,secondary structure,selaginella,sequence analysis,trees},
 pages = {74-84},
 volume = {41},
 id = {6e719b17-0608-3d3f-83b1-b0de2f51b9d8},
 created = {2011-05-20T17:26:09.000Z},
 file_attached = {false},
 profile_id = {b6c31fe8-61c6-3818-89a8-62873f3171f3},
 group_id = {7bdcaa0c-1528-351f-a09a-f8da52223946},
 last_modified = {2011-05-20T17:26:09.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Complete nuclear-encoded small-subunit 18S rRNA (=SSU rRNA) gene sequences were determined for the prasinophyte green alga Mantoniella squamata; the charophycean green algae Chara foetida, Coleochaete scutata, Klebsormidium flaccidum, and Mougeotia scalaris; the bryophytes Marchantia polymorpha, Fossombronia pusilla, and Funaria hygrometrica; and the lycopod Selaginella galleottii to get a better insight into the sequential evolution from green algae to land plants. The sequences were aligned with several previously published SSU rRNA sequences from chlorophytic and charophytic algae as well as from land plants to infer the evolutionary relationships for major evolutionary lineages within the Chlorobionta by distance matrix, maximum parsimony, and maximum likelihood analyses. Phylogenetic trees created by the different methods consistently placed the Charophyceae on the branch leading to the land plants. The Charophyceae were shown to be polyphyletic with the Charales (''charalean'' algae) diverging earlier than the Coleochaetales, Klebsormidiales, Chlorokybales, and Zygnematales (''charophycean'' algae) which branch from a point closer to the land plants in most analyses. Maximum parsimony and maximum likelihood analyses imply a successive evolution from ''charophycean'' algae, particularly Coleochaetales, to bryophytes, lycopods, and seed plants. In contrast, distance matrix methods group the bryophytes together with the ''charophycean'' algae, suggesting a separate evolution of these organisms compared with the club moss and the seed plants.},
 bibtype = {article},
 author = {Kranz, H D and Miks, D and Siegler, M L and Capesius, I and Sensen, C W and Huss, V A R},
 journal = {Journal of Molecular Evolution},
 number = {1}
}

@article{
 title = {The life cycle of Phaeocystis (Prymnesiophyceae): evidence and hypotheses},
 type = {article},
 year = {1994},
 keywords = {#PHAEOCYSTIS,DNA,LIFE CYCLE,SIZE SBR_Phyto},
 pages = {23-29},
 volume = {5},
 id = {0d81a1db-17a8-3969-96ed-76601829e924},
 created = {2014-12-04T15:29:39.000Z},
 file_attached = {true},
 profile_id = {9e8929f8-811d-3561-b42b-6003aef71c7c},
 last_modified = {2015-11-11T08:50:40.000Z},
 read = {true},
 starred = {false},
 authored = {true},
 confirmed = {true},
 hidden = {false},
 source_type = {Journal Article},
 bibtype = {article},
 author = {Rousseau, V and Vaulot, D and Casotti, R and Cariou, V and Lenz, J and Gunkel, J and Baumann, M E M},
 journal = {Journal of Marine Systems}
}

@article{
 title = {Transfer-Rna Genes in the Mitochondrial Genome from a Liverwort, Marchantia-Polymorpha - the Absence of Chloroplast-Like Transfer-Rnas},
 type = {article},
 year = {1992},
 identifiers = {[object Object]},
 keywords = {dna,maize,methionine transfer rna,nucleotide sequence,organization},
 pages = {3773-3777},
 volume = {20},
 id = {5d61099c-c2ba-3093-b010-5cad4d29f8f5},
 created = {2011-05-20T17:26:09.000Z},
 file_attached = {false},
 profile_id = {b6c31fe8-61c6-3818-89a8-62873f3171f3},
 group_id = {7bdcaa0c-1528-351f-a09a-f8da52223946},
 last_modified = {2011-05-20T17:26:09.000Z},
 read = {false},
 starred = {false},
 authored = {false},
 confirmed = {true},
 hidden = {false},
 abstract = {Twenty-nine genes for 27 species of tRNAs were deduced from the complete nucleotide sequence of the mitochondrial genome from a liverwort, Marchantia Polymorpha. One to three species of tRNA genes corresponded to each of 20 amino acids including three species for leucine and arginine, two species for serine and glycine, and one for the rest of the amino acids. Interestingly, all tRNA genes were located in the semicircle of the liverwort mitochondrial genome except for the trnY and trnR genes. The region containing these tRNA genes was originally duplicated, and two trnR genes have diverged from each other. On the other hand, trnY and trnfM are present as two identical copies. The G:U and U:N wobbling between the first nucleotide of the anticodon and the third nucleotide of the codon permit the 27 tRNA identified species to translate almost all codons. However, at least two additional tRNA genes, trnI-GAU for AUY codon and trnT-UGU for ACR codon, are required to read all codons used in the liverwort mitochondrial genome. All of the identified tRNA genes are 'native' in liverwort mitochondria, not 'chloroplast-like' tRNAs as are found in the mitochondria of higher plants. This result implies that the tRNA gene transfer from chloroplast to mitochondrial genome in higher plants has occurred after the divergence from bryophytes.},
 bibtype = {article},
 author = {Oda, K and Yamato, K and Ohta, E and Nakamura, Y and Takemura, M and Nozato, N and Akashi, K and Ohyama, K},
 journal = {Nucleic Acids Research},
 number = {14}
}

@article{excoffier_analysis_1992,
	title = {Analysis of molecular variance inferred from metric distances among {DNA} haplotypes: application to human mitochondrial {DNA} restriction data},
	volume = {131},
	issn = {0016-6731},
	shorttitle = {Analysis of molecular variance inferred from metric distances among {DNA} haplotypes},
	abstract = {We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.},
	language = {eng},
	number = {2},
	journal = {Genetics},
	author = {Excoffier, L. and Smouse, P. E. and Quattro, J. M.},
	month = jun,
	year = {1992},
	pmid = {1644282},
	pmcid = {PMC1205020},
	keywords = {Analysis of Variance, DNA, Mitochondrial, Ethnic Groups, Gene Frequency, Haplotypes, Humans, Models, Genetic, Restriction Mapping, genetic variation},
	pages = {479--491}
}

Paper  abstract   bibtex   

@article{mitchell_identification_1990,
	title = {Identification of genes affecting production of the adhesion organelle of {Caulobacter} crescentus {CB}2},
	volume = {172},
	issn = {0021-9193},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/2168382},
	abstract = {Transposon (Tn5) mutagenesis was used to identify regions in the genome involved with production, regulation, or attachment to the cell surface of the adhesive holdfast of the freshwater bacterium Caulobacter crescentus CB2. A total of 12,000 independently selected transposon insertion mutants were screened for defects in adhesion to cellulose acetate; 77 mutants were detected and examined by Southern blot hybridization mapping methods and pulsed-field gel electrophoresis. Ten unique sites of Tn5 insertion affecting holdfast function were identified that were clustered in four regions of the genome. Representative mutants of the 10 Tn5 insertion sites were examined by a variety of methods for differences in their phenotype leading to the loss of adhesiveness. Four phenotypes were identified: no holdfast production, production of a smaller or an altered holdfast, production of a holdfast that was unable to remain attached to the cell, and a fourth category in which a possible alteration of the stalk was related to impaired adhesion of the cell. With the possible exception of the last class, no pleiotropic mutants (those with multiple defects in the polar region of the cell) were detected among the adhesion-defective mutants. This was unexpected, since holdfast deficiency is often a characteristic of pleiotropic mutants obtained when selecting for loss of other polar structures. Overall, the evidence suggests that we have identified regions containing structural genes for the holdfast, genes involved with proper attachment or positioning on the caulobacter surface, and possibly regions that regulate the levels of holdfast production.},
	number = {9},
	urldate = {2009-05-03TZ},
	journal = {Journal of Bacteriology},
	author = {Mitchell, D and Smit, J},
	month = sep,
	year = {1990},
	pmid = {2168382},
	keywords = {Bacterial Adhesion, Blotting, Southern, DNA Transposable Elements, DNA, Bacterial, Gene Library, Genes, Bacterial, Gram-Negative Bacteria, Mutation, Organelles, Phenotype, Plasmids, Restriction Mapping},
	pages = {5425--5431}
}

Paper  doi  bibtex   

@article{shapiro_differentiation_1976,
	title = {Differentiation in the {Caulobacter} cell cycle},
	volume = {30},
	issn = {0066-4227},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/185940},
	doi = {10.1146/annurev.mi.30.100176.002113},
	urldate = {2009-05-03TZ},
	journal = {Annual Review of Microbiology},
	author = {Shapiro, L},
	year = {1976},
	pmid = {185940},
	keywords = {Bacteria, Bacteriophages, Carbohydrate Metabolism, Cell Division, Cell Wall, Cyclic GMP, DNA, Bacterial, Enzyme Repression, Flagella, Morphogenesis, Mutation, Nucleotides, Cyclic, Protein Biosynthesis, Transcription, Genetic, Transduction, Genetic},
	pages = {377--407}
}

Paper  abstract   bibtex   

@article{haars_stalk_1974,
	title = {Stalk formation and its inhibition in {Caulobacter} crescentus},
	volume = {120},
	issn = {0021-9193},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/4436259},
	abstract = {Estimates of average rates of stalk formation over several generations of growth in Caulobacter crescentus showed that long-stalked Sk1 mutant and phosphate-starved wild-type cultures produce stalk material at about twice the rate of wild-type C. crescentus grown with adequate nutrients. Thus, the long stalks of Sk1 or phosphate-starved caulobacters are not merely a function of their longer doubling times. Inhibition of cell division of Sk1 418 with mitomycin C (MC) caused production of cellular filaments and resulted in inhibition of stalk formation. There was no appreciable decrease in total cell mass or in rates of ribonucleic acid and protein synthesis in the MC-treated cultures as compared with controls, but stalk formation, which is normally dependent on these processes, was severely retarded. Average stalk lengths in MC-treated Sk1 cultures were 30\% of those found in control cultures. MC-produced cellular filaments were also subjected to deoxyribonucleic acid analysis and ultrastructural examination. The deoxyribonucleic acid content of MC-treated bacteria was about 50 to 60\% that of untreated bacteria. Hydroxyurea also was found to produce some cellular filaments and shorter stalks, but with accompanying decreases in growth rate and yield.},
	number = {3},
	urldate = {2009-05-03TZ},
	journal = {Journal of Bacteriology},
	author = {Haars, E G and Schmidt, J M},
	month = dec,
	year = {1974},
	pmid = {4436259},
	keywords = {Adenosine Triphosphate, Bacteria, Bacterial Proteins, Carbon Radioisotopes, Cell Division, DNA, Bacterial, Hydroxyurea, Leucine, Mitomycins, Morphogenesis, Mutation, Phosphates, RNA, Bacterial, Thymidine, Tritium, Uridine},
	pages = {1409--1416}
}