GMODWeb: a web framework for the generic model organism database (2008)
O'Connor, Brian D, Day, Allen, Cain, Scott, Arnaiz, Olivier, Sperling, Linda, Stein, Lincoln D
Abstract The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD...
Rogers, Anthony, Antoshechkin, Igor, Bieri, Tamberlyn, Blasiar, Darin, Bastiani, Carol, Canaran, Payan, ...
WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the...
Chen, Nansheng, Mah, Allan, Blacque, Oliver E, Chu, Jeffrey, Phgora, Kiran, Bakhoum, Mathieu W, ...
Abstract Background The recent availability of genome sequences of multiple related Caenorhabditis species has made it possible to identify, using comparative genomics, similarly transcribed genes in...
WormBase: new content and better access (2006)
Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, ...
WormBase (http://wormbase.org), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on...
WormBook: the online review of Caenorhabditis elegans biology (2006)
Girard, Lisa R., Fiedler, Tristan J., Harris, Todd W., Carvalho, Felicia, Antoshechkin, Igor, Han, Michael, ...
WormBook (www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in...
WormBase: better software, richer content (2006)
Schwarz, Erich M., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Canaran, Payan, ...
WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content....
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics (2005)
Chen, Nansheng, Harris, Todd W., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, ...
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year,...
WormBase: a multi-species resource for nematode biology and genomics (2004)
Harris, Todd W., Chen, Nansheng, Cunningham, Fiona, Tello-Ruiz, Marcela, Antoshechkin, Igor, Bastiani, Carol, ...
WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
WormBase: a cross-species database for comparative genomics (2003)
Harris, Todd W., Lee, Raymond, Schwarz, Erich, Bradnam, Keith, Lawson, Daniel, Chen, Wen, ...
WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant...
The Bioperl Toolkly Perl Modules (2002)
Steven E. Brenner, Stephen A. Chervitz, Chris Dagdigian, Georg Fuellen, Ian Korf, ...
Data Type by defining how a given modul wil behave without specifying the mechanism by which it achieves this end.
Workflow Management Software for Genome-Laboratory Informatics (1995)
Goodman Rozen Stein, Genome-laboratory Informatics, Nathan Goodman, Steve Rozen, Lincoln D. Stein
y automation becomes the modus operandi for genome laboratories, a software component whose primary function is workflow management will become a critical factor in managing operational complexity....
How to set up and maintain a World Wide Web site : the guide for information providers (1995)
0-201-63389-2
The SNP Consortium website: past, present and future
Thorisson, Gudmundur A., Stein, Lincoln D.
The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more...
WormBase: a cross-species database for comparative genomics
Harris, Todd W., Lee, Raymond, Schwarz, Erich, Bradnam, Keith, Lawson, Daniel, Chen, Wen, ...
WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant...
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
WormBase: a multi-species resource for nematode biology and genomics
Harris, Todd W., Chen, Nansheng, Cunningham, Fiona, Tello-Ruiz, Marcela, Antoshechkin, Igor, Bastiani, Carol, ...
WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the...
Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases
Stein, Lincoln D., Thierry-Mieg, Jean
Much of the world’s genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly...
WormBase as an Integrated Platform for the C. elegans ORFeome
Chen, Nansheng, Lawson, Daniel, Bradnam, Keith, Harris, Todd W., Stein, Lincoln D.
The ORFeome project has validated and corrected a large number of predicted gene models in the nematode C. elegans, and has provided an enormous resource for proteome-scale studies. To make the...
Identification of a nematode chemosensory gene family
Chen, Nansheng, Pai, Shraddha, Zhao, Zhongying, Mah, Allan, Newbury, Rebecca, Johnsen, Robert C., ...
Taking advantage of the recent availability of the whole genome sequence of Caenorhabditis briggsae, a closely related nematode to Caenorhabditis elegans, we have examined the chemosensory gene...
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
Chen, Nansheng, Harris, Todd W., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, ...
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year,...
WormBase: better software, richer content
Schwarz, Erich M., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Canaran, Payan, ...
WormBase (), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was...
The International HapMap Project Web site
Thorisson, Gudmundur A., Smith, Albert V., Krishnan, Lalitha, Stein, Lincoln D.
The HapMap Web site at http://www.hapmap.org is the primary portal to genotype data produced as part of the International Haplotype Map Project. In phase I of the project, >1.1 million SNPs were...
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans
Chen, Nansheng, Stein, Lincoln D.
We have systematically examined the correlation between transcriptional expression pattern and the physical layout of gene pairs in the genome of Caenorhabditis elegans using a public tissue-specific...
The SNP Consortium website: past, present and future
Thorisson, Gudmundur A., Stein, Lincoln D.
The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more...
WormBase: a cross-species database for comparative genomics
Harris, Todd W., Lee, Raymond, Schwarz, Erich, Bradnam, Keith, Lawson, Daniel, Chen, Wen, ...
WormBase (http://www.wormbase.org/) is a web-accessible central data repository for information about Caenorhabditis elegans and related nematodes. The past two years have seen a significant...
The Generic Genome Browser: A Building Block for a Model Organism System Database
Stein, Lincoln D., Mungall, Christopher, Shu, ShengQiang, Caudy, Michael, Mangone, Marco, Day, Allen, ...
The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser...
The Bioperl Toolkit: Perl Modules for the Life Sciences
Stajich, Jason E., Block, David, Boulez, Kris, Brenner, Steven E., Chervitz, Stephen A., Dagdigian, Chris, ...
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
WormBase: a multi-species resource for nematode biology and genomics
Harris, Todd W., Chen, Nansheng, Cunningham, Fiona, Tello-Ruiz, Marcela, Antoshechkin, Igor, Bastiani, Carol, ...
WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the...
Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases
Stein, Lincoln D., Thierry-Mieg, Jean
Much of the world’s genomic data are available to the community through networked databases that are accessed via Web interfaces. Although this paradigm provides browse-level access and has greatly...
WormBase as an Integrated Platform for the C. elegans ORFeome
Chen, Nansheng, Lawson, Daniel, Bradnam, Keith, Harris, Todd W., Stein, Lincoln D.
The ORFeome project has validated and corrected a large number of predicted gene models in the nematode C. elegans, and has provided an enormous resource for proteome-scale studies. To make the...
Identification of a nematode chemosensory gene family
Chen, Nansheng, Pai, Shraddha, Zhao, Zhongying, Mah, Allan, Newbury, Rebecca, Johnsen, Robert C., ...
Taking advantage of the recent availability of the whole genome sequence of Caenorhabditis briggsae, a closely related nematode to Caenorhabditis elegans, we have examined the chemosensory gene...
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
Chen, Nansheng, Harris, Todd W., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, ...
WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year,...
The International HapMap Project Web site
Thorisson, Gudmundur A., Smith, Albert V., Krishnan, Lalitha, Stein, Lincoln D.
The HapMap Web site at http://www.hapmap.org is the primary portal to genotype data produced as part of the International Haplotype Map Project. In phase I of the project, >1.1 million SNPs were...
WormBase: better software, richer content
Schwarz, Erich M., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Canaran, Payan, ...
WormBase (), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was...
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans
Chen, Nansheng, Stein, Lincoln D.
We have systematically examined the correlation between transcriptional expression pattern and the physical layout of gene pairs in the genome of Caenorhabditis elegans using a public tissue-specific...
Chen, Nansheng, Mah, Allan, Blacque, Oliver E, Chu, Jeffrey, Phgora, Kiran, Bakhoum, Mathieu W, ...
Comparative genomic analysis of three nematode species identifies 93 genes that encode putative components of the ciliated neurons in C. elegans and are subject to the same regulatory control.
WormBase: new content and better access
Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, ...
WormBase (), a model organism database for Caenorhabditis elegans and other related nematodes, continues to evolve and expand. Over the past year WormBase has added new data on C.elegans, including...
WormBook: the online review of Caenorhabditis elegans biology
Girard, Lisa R., Fiedler, Tristan J., Harris, Todd W., Carvalho, Felicia, Antoshechkin, Igor, Han, Michael, ...
WormBook () is an open-access, online collection of original, peer-reviewed chapters on the biology of Caenorhabditis elegans and related nematodes. Since WormBook was launched in June 2005 with 12...
Ilic, Katica, Kellogg, Elizabeth A., Jaiswal, Pankaj, Zapata, Felipe, Stevens, Peter F., Vincent, Leszek P., ...
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology....
Rogers, Anthony, Antoshechkin, Igor, Bieri, Tamberlyn, Blasiar, Darin, Bastiani, Carol, Canaran, Payan, ...
WormBase (www.wormbase.org) is the major publicly available database of information about Caenorhabditis elegans, an important system for basic biological and biomedical research. Derived from the...
Gallus GBrowse: a unified genomic database for the chicken
Schmidt, Carl J., Romanov, Michael, Ryder, Oliver, Magrini, Vincent, Hickenbotham, Matthew, Glasscock, Jarret, ...
Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource...
GMODWeb: a web framework for the generic model organism database
O'Connor, Brian D, Day, Allen, Cain, Scott, Arnaiz, Olivier, Sperling, Linda, Stein, Lincoln D
GMODWeb is a software framework designed to speed the development of websites for model organism databases.