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2020 – today
- 2023
[i1]Meenakshi S. Kagda, Bonita Lam, Casey Litton, Corinn Small, Cricket A. Sloan, Emma Spragins, Forrest Tanaka, Ian Whaling, Idan Gabdank, Ingrid Youngworth, J. Seth Strattan, Jason A. Hilton, Jennifer Jou, Jessica Au, Jin-Wook Lee, Kalina Andreeva, Keenan Graham, Khine Lin, Matt Simison, Otto Jolanki, Paul Sud, Pedro Assis, Philip Adenekan, Eric Douglass, Mingjie Li, Stuart R. Miyasato, Weiwei Zhong, Yunhai Luo, Zachary Myers, J. Michael Cherry, Benjamin C. Hitz:
Data navigation on the ENCODE portal. CoRR abs/2305.00006 (2023)- 2021
- [j59]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni
, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - 2020
- [j58]Robert S. Nash, Shuai Weng, Kalpana Karra, Edith D. Wong, Stacia R. Engel, J. Michael Cherry, SGD Project:
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. Database J. Biol. Databases Curation 2020: baaa008 (2020) - [j57]Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook:
Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 48(Database-Issue): D650-D658 (2020) - [j56]Patrick C. Ng, Edith D. Wong, Kevin A. MacPherson, Suzi A. Aleksander, Joanna Argasinska, Barbara Dunn, Robert S. Nash, Marek S. Skrzypek, Felix Gondwe, Sagar Jha, Kalpana Karra, Shuai Weng, Stuart R. Miyasato, Matt Simison, Stacia R. Engel, J. Michael Cherry:
Transcriptome visualization and data availability at the Saccharomyces Genome Database. Nucleic Acids Res. 48(Database-Issue): D743-D748 (2020) - [j55]Yunhai Luo, Benjamin C. Hitz, Idan Gabdank, Jason A. Hilton, Meenakshi S. Kagda, Bonita Lam, Zachary Myers, Paul Sud, Jennifer Jou, Khine Lin, Ulugbek K. Baymuradov, Keenan Graham, Casey Litton, Stuart R. Miyasato, J. Seth Strattan, Otto Jolanki, Jin-Wook Lee, Forrest Tanaka, Philip Adenekan, Emma O'Neill, J. Michael Cherry:
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 48(Database-Issue): D882-D889 (2020)
2010 – 2019
- 2019
- [j54]Edith D. Wong, Marek S. Skrzypek, Shuai Weng, Gail Binkley, Birgit H. M. Meldal, Livia Perfetto, Sandra E. Orchard, Stacia R. Engel, J. Michael Cherry, SGD Project:
Integration of macromolecular complex data into the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2019: baz008 (2019) - 2018
- [j53]Stacia R. Engel, Marek S. Skrzypek, Sage T. Hellerstedt, Edith D. Wong, Robert S. Nash, Shuai Weng, Gail Binkley, Travis K. Sheppard, Kalpana Karra, J. Michael Cherry:
Updated regulation curation model at the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2018: bay007 (2018) - [j52]Idan Gabdank, Esther T. Chan, Jean M. Davidson, Jason A. Hilton, Carrie A. Davis, Ulugbek K. Baymuradov, Aditi K. Narayanan, Kathrina C. Onate, Keenan Graham, Stuart R. Miyasato, Timothy R. Dreszer, J. Seth Strattan, Otto Jolanki, Forrest Tanaka, Benjamin C. Hitz, Cricket A. Sloan, J. Michael Cherry:
Prevention of data duplication for high throughput sequencing repositories. Database J. Biol. Databases Curation 2018: bay008 (2018) - [j51]Marek S. Skrzypek, Robert S. Nash, Edith D. Wong, Kevin A. MacPherson, Sage T. Hellerstedt, Stacia R. Engel, Kalpana Karra, Shuai Weng, Travis K. Sheppard, Gail Binkley, Matt Simison, Stuart R. Miyasato, J. Michael Cherry:
Saccharomyces genome database informs human biology. Nucleic Acids Res. 46(Database-Issue): D736-D742 (2018) - [j50]Carrie A. Davis, Benjamin C. Hitz, Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Idan Gabdank, Jason A. Hilton, Kriti Jain, Ulugbek K. Baymuradov, Aditi K. Narayanan, Kathrina C. Onate, Keenan Graham, Stuart R. Miyasato, Timothy R. Dreszer, J. Seth Strattan, Otto Jolanki, Forrest Tanaka, J. Michael Cherry:
The Encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res. 46(Database-Issue): D794-D801 (2018) - 2017
- [j49]Kevin A. MacPherson, Barry Starr, Edith D. Wong, Kyla S. Dalusag, Sage T. Hellerstedt, Olivia W. Lang, Robert S. Nash, Marek S. Skrzypek, Stacia R. Engel, J. Michael Cherry:
Outreach and online training services at the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2017: bax002 (2017) - [j48]Sage T. Hellerstedt, Robert S. Nash, Shuai Weng, Kelley M. Paskov, Edith D. Wong, Kalpana Karra, Stacia R. Engel, J. Michael Cherry:
Curated protein information in the Saccharomyces genome database. Database J. Biol. Databases Curation 2017: bax011 (2017) - 2016
- [j47]Stacia R. Engel, Shuai Weng, Gail Binkley, Kelley M. Paskov, Giltae Song, J. Michael Cherry:
From one to many: expanding the Saccharomyces cerevisiae reference genome panel. Database J. Biol. Databases Curation 2016 (2016) - [j46]Eurie L. Hong, Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer, Greg R. Roe, Nikhil R. Podduturi, Forrest Tanaka, Jason A. Hilton, J. Michael Cherry:
Principles of metadata organization at the ENCODE data coordination center. Database J. Biol. Databases Curation 2016 (2016) - [j45]Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Stacia R. Engel, Sage T. Hellerstedt, Kalpana Karra, Benjamin C. Hitz, Robert S. Nash, Kelley M. Paskov, Travis K. Sheppard, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry:
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. Database J. Biol. Databases Curation 2016 (2016) - [j44]Travis K. Sheppard, Benjamin C. Hitz, Stacia R. Engel, Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Sage T. Hellerstedt, Kalpana Karra, Robert S. Nash, Kelley M. Paskov, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry:
The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res. 44(Database-Issue): 698-702 (2016) - [j43]Cricket A. Sloan, Esther T. Chan, Jean M. Davidson, Venkat S. Malladi, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho, Brian T. Lee, Laurence D. Rowe, Timothy R. Dreszer, Greg Roe, Nikhil R. Podduturi, Forrest Tanaka, Eurie L. Hong, J. Michael Cherry:
ENCODE data at the ENCODE portal. Nucleic Acids Res. 44(Database-Issue): 726-732 (2016) - [c4]Maxime Déraspe, Kalpana Karra, Gail Binkley, Julie M. Sullivan, Gos Micklem, Jacques Corbeil, J. Michael Cherry, Michel Dumontier:
Semantic Research Platform for Model Organisms. BMDID@ISWC 2016 - [c3]Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Joshua Heimbach, Kalpana Karra, Rachel Lyne, Julie M. Sullivan, Yo Yehudi, Gos Micklem, Michel Dumontier:
Making Linked Data SPARQL with the InterMine Biological Data Warehouse. SWAT4LS 2016 - 2015
- [j42]Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart R. Miyasato, Greg R. Roe, Matt Simison, Cricket A. Sloan, J. Seth Strattan, Forrest Tanaka, W. James Kent, J. Michael Cherry, Eurie L. Hong:
Ontology application and use at the ENCODE DCC. Database J. Biol. Databases Curation 2015 (2015) - 2014
- [j41]Maria C. Costanzo, Stacia R. Engel, Edith D. Wong, Paul Lloyd, Kalpana Karra, Esther T. Chan, Shuai Weng, Kelley M. Paskov, Greg R. Roe, Gail Binkley, Benjamin C. Hitz, J. Michael Cherry:
Saccharomyces genome database provides new regulation data. Nucleic Acids Res. 42(Database-Issue): 717-725 (2014) - 2013
- [j40]Rama Balakrishnan, Midori A. Harris, Rachael P. Huntley, Kimberly Van Auken, J. Michael Cherry:
A guide to best practices for Gene Ontology (GO) manual annotation. Database J. Biol. Databases Curation 2013 (2013) - [j39]Stacia R. Engel, J. Michael Cherry:
The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2013 (2013) - [j38]Pascale Gaudet, Monica C. Munoz-Torres, Marc Robinson-Rechavi, Teresa K. Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki:
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database J. Biol. Databases Curation 2013 (2013) - [j37]Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry:
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. Database J. Biol. Databases Curation 2013 (2013) - 2012
- [j36]Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie M. Sullivan, Gos Micklem, J. Michael Cherry:
YeastMine - an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database J. Biol. Databases Curation 2012 (2012) - [j35]Sarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet:
Biocurators and Biocuration: surveying the 21st century challenges. Database J. Biol. Databases Curation 2012 (2012) - [j34]Esther T. Chan, J. Michael Cherry:
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. Database J. Biol. Databases Curation 2012 (2012) - [j33]Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation 2012 (2012) - [j32]Julie Park, Maria C. Costanzo, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong:
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. Database J. Biol. Databases Curation 2012 (2012) - [j31]J. Michael Cherry, Eurie L. Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Esther T. Chan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Kalpana Karra, Cynthia J. Krieger, Stuart R. Miyasato, Robert S. Nash, Julie Park, Marek S. Skrzypek, Matt Simison, Shuai Weng, Edith D. Wong:
Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 40(Database-Issue): 700-705 (2012) - 2011
- [j30]Maria C. Costanzo, Julie Park, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong:
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study. Database J. Biol. Databases Curation 2011 (2011) - [j29]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database J. Biol. Databases Curation 2011 (2011) - [j28]Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S. Skrzypek, J. Michael Cherry, Paul W. Sternberg, Hans-Michael Müller:
Toward an interactive article: integrating journals and biological databases. BMC Bioinform. 12: 175 (2011) - [j27]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database-Issue): 7-10 (2011) - 2010
- [j26]Stacia R. Engel, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Eurie L. Hong, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Julie Park, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kara Dolinski, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 38(Database-Issue): 433-436 (2010)
2000 – 2009
- 2009
- [j25]Maria C. Costanzo, Marek S. Skrzypek, Robert S. Nash, Edith D. Wong, Gail Binkley, Stacia R. Engel, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry:
New mutant phenotype data curation system in the Saccharomyces Genome Database. Database J. Biol. Databases Curation 2009 (2009) - 2008
- [j24]Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, J. Michael Cherry:
Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 36(Database-Issue): 577-581 (2008) - 2007
- [j23]Colleen E. Crangle, J. Michael Cherry, Eurie L. Hong, Alex Zbyslaw:
Mining experimental evidence of molecular function claims from the literature. Bioinform. 23(23): 3232-3240 (2007) - [j22]Robert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry:
Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res. 35(Database-Issue): 468-471 (2007) - 2006
- [j21]Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert S. Nash, Julie Park, Rose Oughtred, Marek S. Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer M. Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, J. Michael Cherry:
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 34(Database-Issue): 442-445 (2006) - [j20]Nicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert S. Nash, Anand Sethuraman, Shuai Weng, J. Michael Cherry:
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Res. 34(Database-Issue): 500-503 (2006) - 2005
- [j19]Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry:
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 33(Database-Issue): 374-377 (2005) - [j18]Thomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, Seung Yon Rhee:
PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res. 33(Web-Server-Issue): 262-266 (2005) - 2004
- [j17]Selina S. Dwight, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, Shuai Weng, David Botstein, J. Michael Cherry:
Saccharomyces genome database: Underlying principles and organisation. Briefings Bioinform. 5(1): 9-22 (2004) - [j16]Christa Niederhauser-Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, R. Koch, U. Schlecht, Leandro Hermida, Benjamin Masdoua, Ryohei Ishii, V. Cassen, M. Yamamoto, Christopher Lane, J. Michael Cherry, N. Lamb, Michael Primig:
Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation. Bioinform. 20(5): 808-811 (2004) - [j15]Elizabeth I. Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J. Michael Cherry, Gavin Sherlock:
GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinform. 20(18): 3710-3715 (2004) - [j14]Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32(Database-Issue): 311-314 (2004) - [j13]Christa Niederhauser-Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, Leandro Hermida, R. Koch, U. Schlecht, A. Amon, Sophie Brachat, Michael Breitenbach, Peter Briza, Sandrine Caburet, J. Michael Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. Anton Grootegoed, R. Scott Hawley, Ryohei Ishii, B. Jégou, R. J. Kaufman, Franz Klein, N. Lamb, B. Maro, Kim Nasmyth, A. Nicolas, T. Orr-Weaver, Peter Philippsen, Charles Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, Tim Schedl, M. Siep, A. Villeneuve, Debra J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, Michael Primig:
GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res. 32(Database-Issue): 560-567 (2004) - [j12]Michael Bada, Robert Stevens, Carole A. Goble, Yolanda Gil, Michael Ashburner, Judith A. Blake, J. Michael Cherry, Midori A. Harris, Suzanna Lewis:
A short study on the success of the Gene Ontology. J. Web Semant. 1(2): 235-240 (2004) - [c2]Colleen E. Crangle, Alex Zbyslaw, J. Michael Cherry, Eurie L. Hong:
Concept Extraction and Synonymy Management for Biomedical Information Retrieval. TREC 2004 - 2003
- [j11]Shuai Weng, Qing Dong, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 31(1): 216-218 (2003) - [j10]Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, Ash A. Alizadeh:
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Res. 31(1): 219-223 (2003) - [c1]Qing Dong, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Shuai Weng, David Botstein, J. Michael Cherry:
Gene Function, Metabolic Pathways and Comparative Genomics in Yeast. CSB 2003: 437-438 - 2002
- [j9]Selina S. Dwight, Midori A. Harris, Kara Dolinski, Catherine A. Ball, Gail Binkley, Karen R. Christie, Dianna G. Fisk, Laurie Issel-Tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30(1): 69-72 (2002) - 2001
- [j8]Rob M. Ewing, J. Michael Cherry:
Visualization of expression clusters using Sammon's non-linear mapping. Bioinform. 17(7): 658-659 (2001) - [j7]Catherine A. Ball, Heng Jin, Gavin Sherlock, Shuai Weng, John C. Matese, Rey Andrada, Gail Binkley, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 29(1): 80-81 (2001) - [j6]Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, J. Michael Cherry:
The Stanford Microarray Database. Nucleic Acids Res. 29(1): 152-155 (2001) - 2000
- [j5]Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Andrew Kasarskis, Charles R. Scafe, Gavin Sherlock, Gail Binkley, Heng Jin, Miroslava Kaloper, Sidney D. Orr, Mark Schroeder, Shuai Weng, Yan Zhu, David Botstein, J. Michael Cherry:
Integrating functional genomic information into the Saccharomyces Genome Database. Nucleic Acids Res. 28(1): 77-80 (2000)
1990 – 1999
- 1999
- [j4]Stephen A. Chervitz, Erich T. Hester, Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Gail Juvik, Alice Malekian, Shannon Roberts, TaiYun Roe, Charles R. Scafe, Mark Schroeder, Gavin Sherlock, Shuai Weng, Yan Zhu, J. Michael Cherry, David Botstein:
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 27(1): 74-78 (1999) - [j3]Seung Yon Rhee, Shuai Weng, Deverie K. Bongard-Pierce, Margarita Garcia-Hernandez, Alice Malekian, David J. Flanders, J. Michael Cherry:
Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. Nucleic Acids Res. 27(1): 79-84 (1999) - 1998
- [j2]J. Michael Cherry, Caroline Adler, Catherine A. Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, Yankai Jia, Gail Juvik, TaiYun Roe, Mark Schroeder, Shuai Weng, David Botstein:
SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26(1): 73-79 (1998) - [j1]David J. Flanders, Shuai Weng, Fabien X. Petel, J. Michael Cherry:
AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. Nucleic Acids Res. 26(1): 80-84 (1998)
Coauthor Index
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