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1. WormBase in 2022—data, processes, and tools for analyzing Caenorhabditis elegans

Author

Davis, Paul, Zarowiecki, Magdalena, Arnaboldi, Valerio, Becerra, Andrés, Cain, Scott, Chan, Juancarlos, Chen, Wen J, Cho, Jaehyoung, da Veiga Beltrame, Eduardo, Diamantakis, Stavros, Gao, Sibyl, Grigoriadis, Dionysis, Grove, Christian A, Harris, Todd W, Kishore, Ranjana, Le, Tuan, Lee, Raymond YN, Luypaert, Manuel, Müller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, Quinton-Tulloch, Mark, Raciti, Daniela, Rodgers, Faye H, Russell, Matthew, Schindelman, Gary, Singh, Archana, Stickland, Tim, Van Auken, Kimberly, Wang, Qinghua, Williams, Gary, Wright, Adam J, Yook, Karen, Berriman, Matt, Howe, Kevin L, Schedl, Tim, Stein, Lincoln, and Sternberg, Paul W

Subjects
Biological Sciences, Genetics, Human Genome, Generic health relevance, Animals, Caenorhabditis, Caenorhabditis elegans, Databases, Genetic, Genome, Genomics, Humans, Nematoda, Caenorhabditis elegans, annotation, caenorhabditis, community, curation, data, database, gene, health, human, literature, mining, model, nematode, platform, research, resource, software, tools, Developmental Biology, Biochemistry and cell biology
Abstract

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

Published
2022

2. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A, Alexander, Micheal, Anagnostopoulos, Anna V, Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M, Blake, Judith A, Blodgett, Olin, Bradford, Yvonne M, Bult, Carol J, Cain, Scott, Calvi, Brian R, Carbon, Seth, Chan, Juancarlos, Chen, Wen J, Cherry, J Michael, Cho, Jaehyoung, Christie, Karen R, Crosby, Madeline A, Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L, D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E, dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R, Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C, Gondwe, Felix, Goodman, Josh, Gramates, L Sian, Grove, Christian A, Hale, Paul, Harris, Todd, Hayman, G Thomas, Hill, David P, Howe, Douglas G, Howe, Kevin L, Hu, Yanhui, Jha, Sagar, Kadin, James A, Kaufman, Thomas C, Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E, Laulederkind, Stanley JF, Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A, Martin, Ryan, Marygold, Steven J, Matthews, Beverley, McAndrews, Monica S, Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Muller, Hans-Michael, Mungall, Christopher J, Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S, Nash, Robert S, Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E, Gelbart, Susan Russo, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R, Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M, and Smith, Cynthia L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.5 Resources and infrastructure (underpinning), Alleles, Animals, Caenorhabditis elegans, Databases, Genetic, Drosophila, Gene Ontology, Humans, Internet, Mice, Molecular Sequence Annotation, Rats, Saccharomycetales, Zebrafish, Alliance of Genome Resources Consortium, biocuration, data mining, gene expression, gene function, gene interaction, genome, knowledgebase, phenotype, variants, Developmental Biology, Biochemistry and cell biology
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein-protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2022

4. Harmonizing model organism data in the Alliance of Genome Resources

Author

Agapite, Julie, Albou, Laurent-Philippe, Aleksander, Suzanne A., Alexander, Micheal, Anagnostopoulos, Anna V., Antonazzo, Giulia, Argasinska, Joanna, Arnaboldi, Valerio, Attrill, Helen, Becerra, Andrés, Bello, Susan M., Blake, Judith A., Blodgett, Olin, Bradford, Yvonne M., Bult, Carol J., Cain, Scott, Calvi, Brian R., Carbon, Seth, Chan, Juancarlos, Chen, Wen J., Cherry, J. Michael, Cho, Jaehyoung, Christie, Karen R., Crosby, Madeline A., Davis, Paul, da Veiga Beltrame, Eduardo, De Pons, Jeffrey L., D’Eustachio, Peter, Diamantakis, Stavros, Dolan, Mary E., dos Santos, Gilberto, Douglass, Eric, Dunn, Barbara, Eagle, Anne, Ebert, Dustin, Engel, Stacia R., Fashena, David, Foley, Saoirse, Frazer, Ken, Gao, Sibyl, Gibson, Adam C., Gondwe, Felix, Goodman, Josh, Gramates, L. Sian, Grove, Christian A., Hale, Paul, Harris, Todd, Thomas Hayman, G., Hill, David P., Howe, Douglas G., Howe, Kevin L., Hu, Yanhui, Jha, Sagar, Kadin, James A., Kaufman, Thomas C., Kalita, Patrick, Karra, Kalpana, Kishore, Ranjana, Kwitek, Anne E., Laulederkind, Stanley J. F., Lee, Raymond, Longden, Ian, Luypaert, Manuel, MacPherson, Kevin A., Martin, Ryan, Marygold, Steven J., Matthews, Beverley, McAndrews, Monica S., Millburn, Gillian, Miyasato, Stuart, Motenko, Howie, Moxon, Sierra, Müller, Hans-Michael, Mungall, Christopher J., Muruganujan, Anushya, Mushayahama, Tremayne, Nalabolu, Harika S., Nash, Robert S., Ng, Patrick, Nuin, Paulo, Paddock, Holly, Paulini, Michael, Perrimon, Norbert, Pich, Christian, Quinton-Tulloch, Mark, Raciti, Daniela, Ramachandran, Sridhar, Richardson, Joel E., Russo Gelbart, Susan, Ruzicka, Leyla, Schaper, Kevin, Schindelman, Gary, Shimoyama, Mary, Simison, Matt, Shaw, David R., Shrivatsav, Ajay, Singer, Amy, Skrzypek, Marek, Smith, Constance M., Smith, Cynthia L., Smith, Jennifer R., Stein, Lincoln, Sternberg, Paul W., Tabone, Christopher J., Thomas, Paul D., Thorat, Ketaki, Thota, Jyothi, Toro, Sabrina, Tomczuk, Monika, Trovisco, Vitor, Tutaj, Marek A., Tutaj, Monika, Urbano, Jose-Maria, Van Auken, Kimberly, Van Slyke, Ceri E., Wang, Qinghua, Wang, Shur-Jen, Weng, Shuai, Westerfield, Monte, Williams, Gary, Wilming, Laurens G., Wong, Edith D., Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Zhou, Pinglei, and Zytkovicz, Mark

Subjects
Internet, Molecular Sequence Annotation, Rats, Mice, Gene Ontology, Databases, Genetic, Saccharomycetales, Genetics, Animals, Humans, Drosophila, Caenorhabditis elegans, Alleles, Zebrafish
Abstract

The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.

Published
2021

5. WormBase 2014: new views of curated biology

Author

Harris, Todd W., Baran, Joachim, Bieri, Tamberlyn, Cabunoc, Abigail, Chan, Juancarlos, Chen, Wen J., Davis, Paul, Done, James, Grove, Christian, Howe, Kevin, Kishore, Ranjana, Lee, Raymond, Li, Yuling, Muller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Paulini, Michael, Raciti, Daniela, Schindelman, Gary, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Wong, J. D., Yook, Karen, Schedl, Tim, Hodgkin, Jonathan, Berriman, Matthew, Kersey, Paul, Spieth, John, Stein, Lincoln, and Sternberg, Paul W.

Published
2014
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6. The L-type cyclin CYL-1 and the heat-shock-factor HSF-1 are required for heat-shock-induced protein expression in Caenorhabditis elegans

Author

Hajdu-Cronin, Yvonne M., Chen, Wen J., and Sternberg, Paul W.

Subjects
Caenorhabditis elegans -- Forecasts and trends, Proteins -- Analysis, Mutation (Biology), Market trend/market analysis, Biological sciences
Abstract

In a screen for suppressors of activated GOA-1 (G[[alpha].sub.0]) under the control of the hsp-16.2 heat-shock promoter, we identified three genetic loci that affected heat-shock-induced GOA-1 expression. The cyl-1 mutants are essentially wild type in appearance, while hsf-1 and sup-45 mutants have egg-laying defects. The hsf-1 mutation also causes a temperature-sensitive developmental arrest, and hsf-1 mutants have decreased life span. Western analysis indicated that mutations in all three loci suppressed the activated GOA-1 transgene by decreasing its expression. Heat-shock-induced expression of hsp-16.2 mRNA was reduced in cyl-1 mutants and virtually eliminated in hsf-1 and sup-45 mutants, as compared to wild-type expression. The mutations could also suppress other transgenes under heat-shock control. cyl-1 and sup-45, but not hsf-1, mutations suppressed a defect caused by a transgene not under heat-shock control, suggesting a role in general transcription or a post-transcriptional aspect of gene expression. hsf-1 encodes the C elegans homolog of the human heat-shock factor HSF1, and cyl-1 encodes a cyclin most similar to cyclin L. We believe HSF-1 acts in heat-shock-inducible transcription and CYL-1 acts more generally in gene expression.

Published
2004

7. WormBase 2012: more genomes, more data, new website

Author

Yook, Karen, Harris, Todd W., Bieri, Tamberlyn, Cabunoc, Abigail, Chan, Juancarlos, Chen, Wen J., Davis, Paul, de la Cruz, Norie, Duong, Adrian, Fang, Ruihua, Ganesan, Uma, Grove, Christian, Howe, Kevin, Kadam, Snehalata, Kishore, Ranjana, Lee, Raymond, Li, Yuling, Muller, Hans-Michael, Nakamura, Cecilia, Nash, Bill, Ozersky, Philip, Paulini, Michael, Raciti, Daniela, Rangarajan, Arun, Schindelman, Gary, Shi, Xiaoqi, Schwarz, Erich M., Ann Tuli, Mary, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Hodgkin, Jonathan, Berriman, Matthew, Durbin, Richard, Kersey, Paul, Spieth, John, Stein, Lincoln, and Sternberg, Paul W.

Published
2012
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8. WormBase: a comprehensive resource for nematode research

Author

Harris, Todd W., Antoshechkin, Igor, Bieri, Tamberlyn, Blasiar, Darin, Chan, Juancarlos, Chen, Wen J., De La Cruz, Norie, Davis, Paul, Duesbury, Margaret, Fang, Ruihua, Fernandes, Jolene, Han, Michael, Kishore, Ranjana, Lee, Raymond, Müller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Petcherski, Andrei, Rangarajan, Arun, Rogers, Anthony, Schindelman, Gary, Schwarz, Erich M., Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Yook, Karen, Durbin, Richard, Stein, Lincoln D., Spieth, John, and Sternberg, Paul W.

Published
2010
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9. Antagonism between G(sub.o)alpha and G (sub.q)alpha in Caenorhabditis elegans: The RGS protein EAT-16 is necessary for G(sub.o)alpha signaling and regulates G (sub.q)alpha activity

Author

Hajdu-Cronin, Yvonne M., Chen, Wen J., Patikoglou, Georgia, Koelle, Michael R., and Sternberg, Paul W.

Subjects
Caenorhabditis elegans -- Genetic aspects, Cellular signal transduction -- Genetic aspects, Biological sciences
Abstract

Antagonism between G(sub.o)alpha and G(sub.q)alpha in Caenorhabditis elegans is discussed in light of the finding that EAT-16, an RGS protein, regulates G(sub.q)alpha activity and is necessary for G(sub.o)alpha signaling. Research based on a molecular genetic approach in C. elegans was undertaken to look into the cellular role of the heterotrimeric G. protein G(sub.o) and it is proposed that a major role of G(sub.o) in the cell is antagonizing signaling by G(sub.q).

Published
1999

10. WormBase 2007

Author

Rogers, Anthony, Antoshechkin, Igor, Bieri, Tamberlyn, Blasiar, Darin, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Wen J., Davis, Paul, Fernandes, Jolene, Fiedler, Tristan J., Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Petcherski, Andrei, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Yook, Karen, Durbin, Richard, Stein, Lincoln D., Spieth, John, and Sternberg, Paul W.

Published
2008

11. WormBase: new content and better access

Author

Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Petcherski, Andrei, Rangarajan, Arun, Rogers, Anthony, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Durbin, Richard, Stein, Lincoln D., Sternberg, Paul W., and Spieth, John

Published
2007

12. WormBase: better software, richer content

Author

Schwarz, Erich M., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Harris, Todd W., Kenny, Eimear E., Kishore, Ranjana, Lawson, Dan, Lee, Raymond, Müller, Hans-Michael, Nakamura, Cecilia, Ozersky, Phil, Petcherski, Andrei, Rogers, Anthony, Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Durbin, Richard, Spieth, John, Stein, Lincoln D., and Sternberg, Paul W.

Published
2006

13. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

Author

Chen, Nansheng, Harris, Todd W., Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Bradnam, Keith, Canaran, Payan, Chan, Juancarlos, Chen, Chao-Kung, Chen, Wen J., Cunningham, Fiona, Davis, Paul, Kenny, Eimear, Kishore, Ranjana, Lawson, Daniel, Lee, Raymond, Muller, Hans-Michael, Nakamura, Cecilia, Pai, Shraddha, Ozersky, Philip, Petcherski, Andrei, Rogers, Anthony, Sabo, Aniko, Schwarz, Erich M., Van Auken, Kimberly, Wang, Qinghua, Durbin, Richard, Spieth, John, Sternberg, Paul W., and Stein, Lincoln D.

Published
2005

14. WormBase: a multi-species resource for nematode biology and genomics

Author

Harris, Todd W., Chen, Nansheng, Cunningham, Fiona, Tello-Ruiz, Marcela, Antoshechkin, Igor, Bastiani, Carol, Bieri, Tamberlyn, Blasiar, Darin, Bradnam, Keith, Chan, Juancarlos, Chen, Chao-Kung, Chen, Wen J., Davis, Paul, Kenny, Eimear, Kishore, Ranjana, Lawson, Daniel, Lee, Raymond, Muller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Petcherski, Andrei, Rogers, Anthony, Sabo, Aniko, Schwarz, Erich M., Van Auken, Kimberly, Wang, Qinghua, Durbin, Richard, Spieth, John, Sternberg, Paul W., and Stein, Lincoln D.

Published
2004

15. WormBase: a modern Model Organism Information Resource

Author

Harris, Todd W, primary, Arnaboldi, Valerio, additional, Cain, Scott, additional, Chan, Juancarlos, additional, Chen, Wen J, additional, Cho, Jaehyoung, additional, Davis, Paul, additional, Gao, Sibyl, additional, Grove, Christian A, additional, Kishore, Ranjana, additional, Lee, Raymond Y N, additional, Muller, Hans-Michael, additional, Nakamura, Cecilia, additional, Nuin, Paulo, additional, Paulini, Michael, additional, Raciti, Daniela, additional, Rodgers, Faye H, additional, Russell, Matthew, additional, Schindelman, Gary, additional, Auken, Kimberly V, additional, Wang, Qinghua, additional, Williams, Gary, additional, Wright, Adam J, additional, Yook, Karen, additional, Howe, Kevin L, additional, Schedl, Tim, additional, Stein, Lincoln, additional, and Sternberg, Paul W, additional

Published
2019
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16. Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes

Author

Kollmar, Martin, Grove, Christian, Cain, Scott, Chen, Wen J., Davis, Paul, Harris, Todd W., Howe, Kevin L., Kishore, Ranjana, Lee, Raymond, Paulini, Michael, Raciti, Daniela, Tuli, Mary Ann, Van Auken, Kimberly, Williams, Gary, Kollmar, Martin, Grove, Christian, Cain, Scott, Chen, Wen J., Davis, Paul, Harris, Todd W., Howe, Kevin L., Kishore, Ranjana, Lee, Raymond, Paulini, Michael, Raciti, Daniela, Tuli, Mary Ann, Van Auken, Kimberly, and Williams, Gary

Abstract

WormBase (www.wormbase.org) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.

Published
2018

17. We have mail

Author

Wheeler, Scott, Moench, William C., Evans, Frank, Gailar, Owen, Greissman, Adam, and Chen, Wen J.

Abstract

Dear Sir, I see that Randall Bart has raised the question of C++ vs. ++C. My own understanding is that the language is so named because every time you think […]

Published
1992

18. WormBase 2024: status and transitioning to Alliance infrastructure

Author

Sternberg, Paul W, Van Auken, Kimberly, Wang, Qinghua, Wright, Adam, Yook, Karen, Zarowiecki, Magdalena, Arnaboldi, Valerio, Becerra, Andrés, Brown, Stephanie, Cain, Scott, Chan, Juancarlos, Chen, Wen J, Cho, Jaehyoung, Davis, Paul, Diamantakis, Stavros, Dyer, Sarah, Grigoriadis, Dionysis, Grove, Christian A, Harris, Todd, Howe, Kevin, Kishore, Ranjana, Lee, Raymond, Longden, Ian, Luypaert, Manuel, Müller, Hans-Michael, Nuin, Paulo, Quinton-Tulloch, Mark, Raciti, Daniela, Schedl, Tim, Schindelman, Gary, and Stein, Lincoln

Abstract

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegansand other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegansresearch, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. eleganscommunity, develop new features as needed, and curate key information from the literature and large-scale projects.

Published
2024
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19. WormBase: a modern Model Organism Information Resource.

Author

Harris, Todd W, Arnaboldi, Valerio, Cain, Scott, Chan, Juancarlos, Chen, Wen J, Cho, Jaehyoung, Davis, Paul, Gao, Sibyl, Grove, Christian A, Kishore, Ranjana, Lee, Raymond Y N, Muller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, Raciti, Daniela, Rodgers, Faye H, Russell, Matthew, Schindelman, Gary, and Auken, Kimberly V

Published
2020
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20. WormBase 2017: molting into a new stage

Author

Lee, Raymond Y N, primary, Howe, Kevin L, additional, Harris, Todd W, additional, Arnaboldi, Valerio, additional, Cain, Scott, additional, Chan, Juancarlos, additional, Chen, Wen J, additional, Davis, Paul, additional, Gao, Sibyl, additional, Grove, Christian, additional, Kishore, Ranjana, additional, Muller, Hans-Michael, additional, Nakamura, Cecilia, additional, Nuin, Paulo, additional, Paulini, Michael, additional, Raciti, Daniela, additional, Rodgers, Faye, additional, Russell, Matt, additional, Schindelman, Gary, additional, Tuli, Mary Ann, additional, Van Auken, Kimberly, additional, Wang, Qinghua, additional, Williams, Gary, additional, Wright, Adam, additional, Yook, Karen, additional, Berriman, Matthew, additional, Kersey, Paul, additional, Schedl, Tim, additional, Stein, Lincoln, additional, and Sternberg, Paul W, additional

Published
2017
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22. WormBase 2016: expanding to enable helminth genomic research

Author

Howe, Kevin L., primary, Bolt, Bruce J., additional, Cain, Scott, additional, Chan, Juancarlos, additional, Chen, Wen J., additional, Davis, Paul, additional, Done, James, additional, Down, Thomas, additional, Gao, Sibyl, additional, Grove, Christian, additional, Harris, Todd W., additional, Kishore, Ranjana, additional, Lee, Raymond, additional, Lomax, Jane, additional, Li, Yuling, additional, Muller, Hans-Michael, additional, Nakamura, Cecilia, additional, Nuin, Paulo, additional, Paulini, Michael, additional, Raciti, Daniela, additional, Schindelman, Gary, additional, Stanley, Eleanor, additional, Tuli, Mary Ann, additional, Van Auken, Kimberly, additional, Wang, Daniel, additional, Wang, Xiaodong, additional, Williams, Gary, additional, Wright, Adam, additional, Yook, Karen, additional, Berriman, Matthew, additional, Kersey, Paul, additional, Schedl, Tim, additional, Stein, Lincoln, additional, and Sternberg, Paul W., additional

Published
2015
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23. Extragenic Suppresors of Heat Shock Activated GOα. Topic I: Cyclin in Heat Shock Response. Topic II: Signalling by Go and Gq in C. elegans

Author

Chen, Wen J.

Subjects
FOS: Biological sciences, Behavior Biology, Genetics, G protein, Biology, Signal Transduction
Abstract

In the nematode C. elegans, heterotrimeric G proteins have been shown to regulate the behavior of locomotion, feeding and egg-laying. Go belongs to Gi family and only exists in organisms with a nervous system. The signaling downstream of Go has been a mystery since its discovery, and it is what we are determined to find out. Loss of Goα causes animals to be hyperactive and lay eggs constitutively. Overexpressing Goα causes opposite phenotypes. Another α protein a subunit, Gq, causes phenotypes opposite to Go. To identify G protein effectors in C. elegans, we performed a forward genetic screen for suppressors of activated Goα under the control of the heat-shock promoter hsp16-2. Because of the nature of the screen design, we identified two categories of genes. One category acts on heat shock response and the other category acts on G protein pathways. We characterized and positional cloned genes from both categories. The second chapter of the thesis described sag-4, a cyclin L homologue that specifically affects heat shock promoters and decreases heat-shock induced protein expression. We propose that cyclin Lis likely to be involved in heat shock induced transcription. Other genes in this category, sag-3, sag-5 and sag-8, may also function in similar mechanisms. The third chapter of the thesis focused on G protein signaling. eat-16 was identified in the screen for suppressors of activated Goα. We positional cloned it and found it encodes a RGS7 homologue. RGS proteins have been studied as GTPase Activating Protein for the α subunits of heterotrimeric G proteins. Although eat-16 was identified in a suppressor screen for activated Go (goa-1), both genetic and biochemical evidence showed that eat-16 is a GAP for Gq (egl-30). We propose that Go and Gq antagonize each other, thereby regulating behaviors. Go might negatively regulate Gq signaling, possibly through eat-16 or other unrevealed genes. Chapter four describes our reconstituted system in mammalian cell culture. EAT-16 decreases Gq/G11 mediated PLC activity. GOA-1 and GPB-2 (C. elegans Gβ5 homologue) also decrease PLC activity induced by Gq/G11. These results are consistent with the hypothesis that Go negatively regulate Gq signaling, and the interaction between Gβ5 and RGS7 can be one of the steps between Go and Gq.

Published
2000
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24. Antagonism between Goα and Gqα in Caenorhabditis elegans: the RGS protein EAT-16 is necessary for Goα signaling and regulates Gqα activity

Author

Hajdu-Cronin, Yvonne M., Chen, Wen J., Patikoglou, Georgia, Koelle, Michael R., and Sternberg, Paul W.

Subjects
Base Sequence, Sequence Homology, Amino Acid, Molecular Sequence Data, Helminth Proteins, GTP-Binding Protein Regulators, Gene Expression Regulation, GTP-Binding Proteins, COS Cells, Mutation, Animals, Amino Acid Sequence, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Genes, Suppressor, Research Paper, DNA Primers, Signal Transduction
Abstract

To elucidate the cellular role of the heterotrimeric G protein G(o), we have taken a molecular genetic approach in Caenorhabditis elegans. We screened for suppressors of activated GOA-1 (G(o)alpha) that do not simply decrease its expression and found mutations in only two genes, sag-1 and eat-16. Animals defective in either gene display a hyperactive phenotype similar to that of goa-1 loss-of-function mutants. Double-mutant analysis indicates that both sag-1 and eat-16 act downstream of, or parallel to, G(o)alpha and negatively regulate EGL-30 (G(q)alpha) signaling. eat-16 encodes a regulator of G protein signaling (RGS) most similar to the mammalian RGS7 and RGS9 proteins and can inhibit endogenous mammalian G(q)/G(11) in COS-7 cells. Animals defective in both sag-1 and eat-16 are inviable, but reducing function in egl-30 restores viability, indicating that the lethality of the eat-16; sag-1 double mutant is due to excessive G(q)alpha activity. Analysis of these mutations indicates that the G(o) and G(q) pathways function antagonistically in C. elegans, and that G(o)alpha negatively regulates the G(q) pathway, possibly via EAT-16 or SAG-1. We propose that a major cellular role of G(o) is to antagonize signaling by G(q).

Published
1999

25. WormBase 2014: new views of curated biology

Author

Harris, Todd W., primary, Baran, Joachim, additional, Bieri, Tamberlyn, additional, Cabunoc, Abigail, additional, Chan, Juancarlos, additional, Chen, Wen J., additional, Davis, Paul, additional, Done, James, additional, Grove, Christian, additional, Howe, Kevin, additional, Kishore, Ranjana, additional, Lee, Raymond, additional, Li, Yuling, additional, Muller, Hans-Michael, additional, Nakamura, Cecilia, additional, Ozersky, Philip, additional, Paulini, Michael, additional, Raciti, Daniela, additional, Schindelman, Gary, additional, Tuli, Mary Ann, additional, Auken, Kimberly Van, additional, Wang, Daniel, additional, Wang, Xiaodong, additional, Williams, Gary, additional, Wong, J. D., additional, Yook, Karen, additional, Schedl, Tim, additional, Hodgkin, Jonathan, additional, Berriman, Matthew, additional, Kersey, Paul, additional, Spieth, John, additional, Stein, Lincoln, additional, and Sternberg, Paul W., additional

Published
2013
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26. WormBase 2016: expanding to enable helminth genomic research.

Author

Howe, Kevin L., Bolt, Bruce J., Cain, Scott, Chan, Juancarlos, Chen, Wen J., Davis, Paul, Done, James, Down, Thomas, Gao, Sibyl, Grove, Christian, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, Lomax, Jane, Yuling Li, Muller, Hans-Michael, Nakamura, Cecilia, Nuin, Paulo, Paulini, Michael, and Raciti, Daniela

Published
2016
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27. WormBase: new content and better access

Author

Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Petcherski, Andrei, Rangarajan, Arun, Rogers, Anthony, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Durbin, Richard, Stein, Lincoln D., Sternberg, Paul W., Spieth, John, Bieri, Tamberlyn, Blasiar, Darin, Ozersky, Philip, Antoshechkin, Igor, Bastiani, Carol, Canaran, Payan, Chan, Juancarlos, Chen, Nansheng, Chen, Wen J., Davis, Paul, Fiedler, Tristan J., Girard, Lisa, Han, Michael, Harris, Todd W., Kishore, Ranjana, Lee, Raymond, McKay, Sheldon, Müller, Hans-Michael, Nakamura, Cecilia, Petcherski, Andrei, Rangarajan, Arun, Rogers, Anthony, Schindelman, Gary, Schwarz, Erich M., Spooner, Will, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Durbin, Richard, Stein, Lincoln D., Sternberg, Paul W., and Spieth, John

Abstract

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 C.elegans, including data on classical genetics, cell biology and functional genomics; expanded the annotation of closely related nematodes with a new genome browser for Caenorhabditis remanei; and deployed new hardware for stronger performance. Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content. New datasets such as the C.remanei draft assembly and annotations, the Vancouver Fosmid library and TEC-RED 5' end sites are now available as well. Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.

Published
2006

28. WormBase: a comprehensive resource for nematode research

Author

Harris, Todd W., primary, Antoshechkin, Igor, additional, Bieri, Tamberlyn, additional, Blasiar, Darin, additional, Chan, Juancarlos, additional, Chen, Wen J., additional, De La Cruz, Norie, additional, Davis, Paul, additional, Duesbury, Margaret, additional, Fang, Ruihua, additional, Fernandes, Jolene, additional, Han, Michael, additional, Kishore, Ranjana, additional, Lee, Raymond, additional, Müller, Hans-Michael, additional, Nakamura, Cecilia, additional, Ozersky, Philip, additional, Petcherski, Andrei, additional, Rangarajan, Arun, additional, Rogers, Anthony, additional, Schindelman, Gary, additional, Schwarz, Erich M., additional, Tuli, Mary Ann, additional, Van Auken, Kimberly, additional, Wang, Daniel, additional, Wang, Xiaodong, additional, Williams, Gary, additional, Yook, Karen, additional, Durbin, Richard, additional, Stein, Lincoln D., additional, Spieth, John, additional, and Sternberg, Paul W., additional

Published
2009
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29. WormBase: new content and better access

Author

Bieri, Tamberlyn, primary, Blasiar, Darin, additional, Ozersky, Philip, additional, Antoshechkin, Igor, additional, Bastiani, Carol, additional, Canaran, Payan, additional, Chan, Juancarlos, additional, Chen, Nansheng, additional, Chen, Wen J., additional, Davis, Paul, additional, Fiedler, Tristan J., additional, Girard, Lisa, additional, Han, Michael, additional, Harris, Todd W., additional, Kishore, Ranjana, additional, Lee, Raymond, additional, McKay, Sheldon, additional, Müller, Hans-Michael, additional, Nakamura, Cecilia, additional, Petcherski, Andrei, additional, Rangarajan, Arun, additional, Rogers, Anthony, additional, Schindelman, Gary, additional, Schwarz, Erich M., additional, Spooner, Will, additional, Tuli, Mary Ann, additional, Auken, Kimberly Van, additional, Wang, Daniel, additional, Wang, Xiaodong, additional, Williams, Gary, additional, Durbin, Richard, additional, Stein, Lincoln D., additional, Sternberg, Paul W., additional, and Spieth, John, additional

Published
2006
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30. Argininemia

Author

Snyderman, Selma E., primary, Sansaricq, Claude, additional, Chen, Wen J., additional, Norton, Patricia M., additional, and Phansalkar, Sadashiv V., additional

Published
1977
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31. Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes.

Author

Grove C, Cain S, Chen WJ, Davis P, Harris T, Howe KL, Kishore R, Lee R, Paulini M, Raciti D, Tuli MA, Van Auken K, and Williams G

Subjects
Animals, Computational Biology methods, Data Mining methods, Epistasis, Genetic, Gene Ontology, Genes, Helminth, Humans, Phenotype, Proteome, Search Engine, Software, Transcriptome, User-Computer Interface, Web Browser, Caenorhabditis elegans genetics, Databases, Genetic, Genome, Helminth, Genomics methods
Abstract

WormBase ( www.wormbase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries. Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.

Published
2018
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