Oxford Index Search Results

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community x Bioinformatics and Computational Biology 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

Tools for the SBML Community

Colin S. Gillespie, Darren J. Wilkinson, Carole J. Proctor, Daryl P. Shanley, Richard J. Boys and Thomas B. L. Kirkwood.

in Bioinformatics

March 2006; p ublished online January 2006 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1035 words.

Motivation: SBML is quickly becoming the standard format to exchange biochemical models. The tools presented in this paper are loosely-coupled, and are intended to be...

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Community gene annotation in practice

Jane E. Loveland, James G.R. Gilbert, Ed Griffiths and Jennifer L. Harrow.

in Database

P ublished online February 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology; Ecology and Conservation; Evolutionary Biology. 3946 words.

Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model...

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Toward community standards in the quest for orthologs

Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero, Adrian Altenhoff, Rolf Apweiler, Michael Ashburner, Judith Blake, Brigitte Boeckmann, Alan Bridge, Elspeth Bruford, Mike Cherry, Matthieu Conte, Durand Dannie, Ruchira Datta, Christophe Dessimoz, Jean-Baka Domelevo Entfellner, Ingo Ebersberger, Toni Gabaldón, Michael Galperin, Javier Herrero, Jacob Joseph, Tina Koestler, Evgenia Kriventseva, Odile Lecompte, Jack Leunissen, Suzanna Lewis, Benjamin Linard, Michael S. Livstone, Hui-Chun Lu, Maria Martin, Raja Mazumder, David Messina, Vincent Miele, Matthieu Muffato, Guy Perrière, Marco Punta, David Roos, Mathieu Rouard, Thomas Schmitt, Fabian Schreiber, Alan Silva, Kimmen Sjölander, Nives Škunca, Erik Sonnhammer, Eleanor Stanley, Radek Szklarczyk, Paul Thomas, Ikuo Uchiyama, Michiel Van Bel, Klaas Vandepoele, Albert J. Vilella, Andrew Yates and Evgeny Zdobnov.

in Bioinformatics

March 2012; p ublished online February 2012 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 3334 words.

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics...

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Canto: an online tool for community literature curation

Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver and Valerie Wood.

in Bioinformatics

June 2014; p ublished online February 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1223 words.

Motivation: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their...

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Apollo: a community resource for genome annotation editing

Ed Lee, Nomi Harris, Mark Gibson, Raymond Chetty and Suzanna Lewis.

in Bioinformatics

July 2009; p ublished online May 2009 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1397 words.

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the...

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GLay: community structure analysis of biological networks

Gang Su, Allan Kuchinsky, John H. Morris, David J. States and Fan Meng.

in Bioinformatics

December 2010; p ublished online November 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 2019 words.

Summary: GLay provides Cytoscape users an assorted collection of versatile community structure algorithms and graph layout functions for network clustering and structured...

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Phylogeny-based classification of microbial communities

Olga Tanaseichuk, James Borneman and Tao Jiang.

in Bioinformatics

February 2014; p ublished online December 2013 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5694 words.

Motivation: Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative...

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Bayesian mixture analysis for metagenomic community profiling

Sofia Morfopoulou and Vincent Plagnol.

in Bioinformatics

September 2015; p ublished online May 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7422 words.

Motivation: Deep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data...

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Identifying biologically relevant differences between metagenomic communities

Donovan H. Parks and Robert G. Beiko.

in Bioinformatics

March 2010; p ublished online February 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5623 words.

Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can...

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The Bio-Community Perl toolkit for microbial ecology

Florent E. Angly, Christopher J. Fields and Gene W. Tyson.

in Bioinformatics

January 2014; p ublished online March 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1083 words.

Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles...

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Ontodog: a web-based ontology community view generation tool

Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert and Yongqun He.

in Bioinformatics

May 2014; p ublished online January 2014 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1299 words.

Summary: Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users,...

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Alzforum and SWAN: the present and future of scientific web communities

Tim Clark and June Kinoshita.

in Briefings in Bioinformatics

May 2007; p ublished online May 2007 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4408 words.

Scientists drove the early development of the World Wide Web, primarily as a means for rapid communication, document sharing and data access. They have been far slower to adopt the web as a...

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An algorithm for designing minimal microbial communities with desired metabolic capacities

Alexander Eng and Elhanan Borenstein.

in Bioinformatics

July 2016; p ublished online February 2016 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7057 words.

Motivation: Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems’ optimization, suggest a promising route for...

Building biomedical web communities using a semantically aware content management system

Sudeshna Das, Lisa Girard, Tom Green, Louis Weitzman, Alister Lewis-Bowen and Tim Clark.

in Briefings in Bioinformatics

March 2009; p ublished online December 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4885 words.

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information...

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Payao: a community platform for SBML pathway model curation

Yukiko Matsuoka, Samik Ghosh, Norihiro Kikuchi and Hiroaki Kitano.

in Bioinformatics

May 2010; p ublished online April 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1663 words.

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and...

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SmashCommunity: a metagenomic annotation and analysis tool

Manimozhiyan Arumugam, Eoghan D. Harrington, Konrad U. Foerstner, Jeroen Raes and Peer Bork.

in Bioinformatics

December 2010; p ublished online October 2010 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1059 words.

Summary: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports...

A dynamic programming algorithm for binning microbial community profiles

Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman and Fengzhu Sun.

in Bioinformatics

June 2006; p ublished online March 2006 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5526 words.

Motivation: A number of community profiling approaches have been widely used to study the microbial community composition and its variations in environmental ecology. Automated...

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Modeling community-wide molecular networks of multicellular systems

Kakajan Komurov.

in Bioinformatics

March 2012; p ublished online December 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4538 words.

Motivation: Multicellular systems, such as tissues, are composed of different cell types that form a heterogeneous community. Behavior of these systems is determined by complex...

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spacodiR: structuring of phylogenetic diversity in ecological communities

Jonathan M. Eastman, C. E. Timothy Paine and Olivier J. Hardy.

in Bioinformatics

September 2011; p ublished online July 2011 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1438 words.

Motivation: spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and...

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Probe selection algorithms with applications in the analysis of microbial communities

James Borneman, Marek Chrobak, Gianluca Della Vedova, Andres Figueroa and Tao Jiang.

in Bioinformatics

June 2001; p ublished online June 2001 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 0 words.

We propose two efficient heuristics for minimizing the number of oligonucleotide probes needed for analyzing populations of ribosomal RNA gene (rDNA) clones by hybridization experiments...

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