Oxford Index Search Results

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community x Molecular and Cell Biology x Biochemistry x clear all

community

Overview page. Subjects: Social Sciences — Arts and Humanities.

Many sociological and anthropological definitions exist, but most tend to privilege some combination of small-scale, relative boundedness, strong affective ties, traditionalism, and...

See overview in Oxford Index

Environmental shaping of codon usage and functional adaptation across microbial communities

Maša Roller, Vedran Lucić, István Nagy, Tina Perica and Kristian Vlahoviček.

in Nucleic Acids Research

October 2013; p ublished online August 2013 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6971 words.

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic...

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Short pyrosequencing reads suffice for accurate microbial community analysis

Zongzhi Liu, Catherine Lozupone, Micah Hamady, Frederic D. Bushman and Rob Knight.

in Nucleic Acids Research

September 2007; p ublished online September 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4663 words.

Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been...

Bayesian estimation of bacterial community composition from 454 sequencing data

Lu Cheng, Alan W. Walker and Jukka Corander.

in Nucleic Acids Research

July 2012; p ublished online February 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6811 words.

Estimating bacterial community composition from a mixed sample in different applied contexts is an important task for many microbiologists. The bacterial community composition is commonly...

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ASAP, a systematic annotation package for community analysis of genomes

Jeremy D. Glasner, Paul Liss, Guy Plunkett III, Aaron Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael Gilson, Bryan Biehl, Frederick R. Blattner and Nicole T. Perna.

in Nucleic Acids Research

January 2003; p ublished online January 2003 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3499 words.

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and...

The Mouse Genome Database (MGD): A community resource. Status and enhancements

Judith A. Blake, Janan T. Eppig, Joel E. Richardson and Muriel T. Davisson.

in Nucleic Acids Research

January 1998; p ublished online January 1998 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2647 words.

The Mouse Genome Database (MGD) is a comprehensive community database that integrates genetic, genomic and phenotypic information about the laboratory mouse. MGD provides detailed...

WikiPathways: building research communities on biological pathways

Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Martina Kutmon, Bruce R. Conklin, Chris T. Evelo and Alexander R. Pico.

in Nucleic Acids Research

January 2012; p ublished online November 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4351 words.

Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as...

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RhesusBase: a knowledgebase for the monkey research community

Shi-Jian Zhang, Chu-Jun Liu, Mingming Shi, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuang Yang, Ning Hou, Zhiqiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang and Chuan-Yun Li.

in Nucleic Acids Research

January 2013; p ublished online September 2012 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6962 words.

Although the rhesus macaque is a unique model for the translational study of human diseases, currently its use in biomedical research is still in its infant stage due to error-prone gene...

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VMD: a community annotation database for oomycetes and microbial genomes

Sucheta Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas and Brett M. Tyler.

in Nucleic Acids Research

January 2006; p ublished online January 2006 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1835 words.

The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two...

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Association between translation efficiency and horizontal gene transfer within microbial communities

Tamir Tuller, Yana Girshovich, Yael Sella, Avi Kreimer, Shiri Freilich, Martin Kupiec, Uri Gophna and Eytan Ruppin.

in Nucleic Acids Research

June 2011; p ublished online February 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 8491 words.

Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign...

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agriGO: a GO analysis toolkit for the agricultural community

Zhou Du, Xin Zhou, Yi Ling, Zhenhai Zhang and Zhen Su.

in Nucleic Acids Research

July 2010; p ublished online April 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3853 words.

Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated...

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MaizeGDB, the community database for maize genetics and genomics

Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried and Volker Brendel.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3474 words.

The Maize Genetics and Genomics Database (MaizeGDB) is a central repository for maize sequence, stock, phenotype, genotypic and karyotypic variation, and chromosomal mapping data. In...

RiceWiki: a wiki-based database for community curation of rice genes

Zhang Zhang, Jian Sang, Lina Ma, Gang Wu, Hao Wu, Dawei Huang, Dong Zou, Siqi Liu, Ang Li, Lili Hao, Ming Tian, Chao Xu, Xumin Wang, Jiayan Wu, Jingfa Xiao, Lin Dai, Ling-Ling Chen, Songnian Hu and Jun Yu.

in Nucleic Acids Research

January 2014; p ublished online October 2013 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3570 words.

Rice is the most important staple food for a large part of the world’s human population and also a key model organism for biological studies of crops as well as other related plants. Here...

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The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Céline Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang and Arek Kasprzyk.

in Nucleic Acids Research

July 2015; p ublished online April 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4395 words.

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access...

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LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

Lina Ma, Ang Li, Dong Zou, Xingjian Xu, Lin Xia, Jun Yu, Vladimir B. Bajic and Zhang Zhang.

in Nucleic Acids Research

January 2015; p ublished online November 2014 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3523 words.

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki...

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The FlyBase Database of the Drosophila Genome Projects and community literature

in Nucleic Acids Research

January 1999; p ublished online January 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3124 words.

The flybase drosophila genetics database and the public interfaces of the berkeley drosophila genome project (bdgp) and european drosophila genome project (edgp) are in the process of...

EcoliWiki: a wiki-based community resource for Escherichia coli

Brenley K. McIntosh, Daniel P. Renfro, Gwendowlyn S. Knapp, Chanchala R. Lairikyengbam, Nathan M. Liles, Lili Niu, Amanda M. Supak, Anand Venkatraman, Adrienne E. Zweifel, Deborah A. Siegele and James C. Hu.

in Nucleic Acids Research

January 2012; p ublished online November 2011 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3812 words.

EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information on laboratory strains of null...

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The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato and Gavin Sherlock.

in Nucleic Acids Research

January 2005; p ublished online January 2005 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2513 words.

The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research...

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Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

Shulei Sun, Jing Chen, Weizhong Li, Ilkay Altintas, Abel Lin, Steve Peltier, Karen Stocks, Eric E. Allen, Mark Ellisman, Jeffrey Grethe and John Wooley.

in Nucleic Acids Research

January 2011; p ublished online November 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2846 words.

The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that...

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Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data

Yijun Sun, Yunpeng Cai, Volker Mai, William Farmerie, Fahong Yu, Jian Li and Steve Goodison.

in Nucleic Acids Research

December 2010; p ublished online October 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 5533 words.

With the aid of next-generation sequencing technology, researchers can now obtain millions of microbial signature sequences for diverse applications ranging from human epidemiological...

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HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes

Samuel C. Forster, Hilary P. Browne, Nitin Kumar, Martin Hunt, Hubert Denise, Alex Mitchell, Robert D. Finn and Trevor D. Lawley.

in Nucleic Acids Research

January 2016; p ublished online November 2015 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 3483 words.

The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal...

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