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@article{DBLP:journals/corr/abs-2305-00006,
author = {Meenakshi S. Kagda and
Bonita Lam and
Casey Litton and
Corinn Small and
Cricket A. Sloan and
Emma Spragins and
Forrest Tanaka and
Ian Whaling and
Idan Gabdank and
Ingrid Youngworth and
J. Seth Strattan and
Jason A. Hilton and
Jennifer Jou and
Jessica Au and
Jin{-}Wook Lee and
Kalina Andreeva and
Keenan Graham and
Khine Lin and
Matt Simison and
Otto Jolanki and
Paul Sud and
Pedro Assis and
Philip Adenekan and
Eric Douglass and
Mingjie Li and
Stuart R. Miyasato and
Weiwei Zhong and
Yunhai Luo and
Zachary Myers and
J. Michael Cherry and
Benjamin C. Hitz},
title = {Data navigation on the {ENCODE} portal},
journal = {CoRR},
volume = {abs/2305.00006},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.00006},
doi = {10.48550/ARXIV.2305.00006},
eprinttype = {arXiv},
eprint = {2305.00006},
timestamp = {Tue, 09 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-00006.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CarbonDGUHMBCDH21,
author = {Seth Carbon and
Eric Douglass and
Benjamin M. Good and
Deepak R. Unni and
Nomi L. Harris and
Christopher J. Mungall and
Siddartha Basu and
Rex L. Chisholm and
Robert J. Dodson and
Eric Hartline and
Petra Fey and
Paul D. Thomas and
Laurent{-}Philippe Albou and
Dustin Ebert and
Michael J. Kesling and
Huaiyu Mi and
Anushya Muruganujan and
Xiaosong Huang and
Tremayne Mushayahama and
Sandra A. LaBonte and
Deborah A. Siegele and
Giulia Antonazzo and
Helen Attrill and
Nick H. Brown and
Phani V. Garapati and
Steven J. Marygold and
Vitor Trovisco and
Gilberto dos Santos and
Kathleen Falls and
Christopher J. Tabone and
Pinglei Zhou and
Joshua L. Goodman and
Victor B. Strelets and
Jim Thurmond and
Penelope Garmiri and
Rizwan Ishtiaq and
Milagros Rodr{\'{\i}}guez{-}L{\'{o}}pez and
Marcio Luis Acencio and
Martin Kuiper and
Astrid L{\ae}greid and
Colin Logie and
Ruth C. Lovering and
Barbara Kramarz and
Shirin C. C. Saverimuttu and
Sandra M. Pinheiro and
Heather Gunn and
Renzhi Su and
Katherine E. Thurlow and
Marcus C. Chibucos and
Michelle G. Giglio and
Suvarna Nadendla and
James B. Munro and
Rebecca C. Jackson and
Margaret J. Duesbury and
Noemi del{-}Toro and
Birgit H. M. Meldal and
Kalpana Paneerselvam and
Livia Perfetto and
Pablo Porras and
Sandra E. Orchard and
Anjali Shrivastava and
Hsin{-}Yu Chang and
Robert D. Finn and
Alex L. Mitchell and
Neil D. Rawlings and
Lorna J. Richardson and
Amaia Sangrador{-}Vegas and
Judith A. Blake and
Karen R. Christie and
Mary E. Dolan and
Harold J. Drabkin and
David P. Hill and
Li Ni and
Dmitry M. Sitnikov and
Midori A. Harris and
Stephen G. Oliver and
Kim Rutherford and
Valerie Wood and
Jaqueline Hayles and
J{\"{u}}rg B{\"{a}}hler and
Elizabeth R. Bolton and
Jeffrey DePons and
Melinda R. Dwinell and
G. Thomas Hayman and
Mary L. Kaldunski and
Anne E. Kwitek and
Stanley J. F. Laulederkind and
Cody Plasterer and
Marek Tutaj and
Mahima Vedi and
Shur{-}Jen Wang and
Peter D'Eustachio and
Lisa Matthews and
James P. Balhoff and
Suzi A. Aleksander and
Michael J. Alexander and
J. Michael Cherry and
Stacia R. Engel and
Felix Gondwe and
Kalpana Karra and
Stuart R. Miyasato and
Robert S. Nash and
Matt Simison and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
Marc Feuermann and
Pascale Gaudet and
Anne Morgat and
Erica Bakker and
Tanya Z. Berardini and
Leonore Reiser and
Shabari Subramaniam and
Eva Huala and
Cecilia N. Arighi and
Andrea H. Auchincloss and
Kristian B. Axelsen and
Ghislaine Argoud{-}Puy and
Alex Bateman and
Marie{-}Claude Blatter and
Emmanuel Boutet and
Emily Bowler and
Lionel Breuza and
Alan J. Bridge and
Ramona Britto and
Hema Bye{-}A{-}Jee and
Cristina Casals{-}Casas and
Elisabeth Coudert and
Paul Denny and
Anne Estreicher and
Maria Livia Famiglietti and
George E. Georghiou and
Arnaud Gos and
Nadine Gruaz{-}Gumowski and
Emma Hatton{-}Ellis and
Chantal Hulo and
Alexandr Ignatchenko and
Florence Jungo and
Kati Laiho and
Philippe Le Mercier and
Damien Lieberherr and
Antonia Lock and
Yvonne Lussi and
Alistair MacDougall and
Michele Magrane and
Maria Jesus Martin and
Patrick Masson and
Darren A. Natale and
Nevila Hyka{-}Nouspikel and
Ivo Pedruzzi and
Lucille Pourcel and
Sylvain Poux and
Sangya Pundir and
Catherine Rivoire and
Elena Speretta and
Shyamala Sundaram and
Nidhi Tyagi and
Kate Warner and
Rossana Zaru and
Cathy H. Wu and
Alexander D. Diehl and
Juancarlos Chan and
Christian A. Grove and
Raymond Y. N. Lee and
Hans{-}Michael M{\"{u}}ller and
Daniela Raciti and
Kimberly Van Auken and
Paul W. Sternberg and
Matthew Berriman and
Michael Paulini and
Kevin L. Howe and
Sibyl Gao and
Adam Wright and
Lincoln Stein and
Douglas G. Howe and
Sabrina Toro and
Monte Westerfield and
Pankaj Jaiswal and
Laurel Cooper and
Justin Elser},
title = {The Gene Ontology resource: enriching a GOld mine},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D325--D334},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1113},
doi = {10.1093/NAR/GKAA1113},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/CarbonDGUHMBCDH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/NashWKWECP20,
author = {Robert S. Nash and
Shuai Weng and
Kalpana Karra and
Edith D. Wong and
Stacia R. Engel and
J. Michael Cherry and
SGD Project},
title = {Incorporation of a unified protein abundance dataset into the Saccharomyces
genome database},
journal = {Database J. Biol. Databases Curation},
volume = {2020},
pages = {baaa008},
year = {2020},
url = {https://doi.org/10.1093/database/baaa008},
doi = {10.1093/DATABASE/BAAA008},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/NashWKWECP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AgapiteAAAAABBB20,
author = {Julie Agapite and
Laurent{-}Philippe Albou and
Suzi A. Aleksander and
Joanna Argasinska and
Valerio Arnaboldi and
Helen Attrill and
Susan M. Bello and
Judith A. Blake and
Olin Blodgett and
Yvonne M. Bradford and
Carol J. Bult and
Scott Cain and
Brian R. Calvi and
Seth Carbon and
Juancarlos Chan and
Wen J. Chen and
J. Michael Cherry and
Jae{-}Hyoung Cho and
Karen R. Christie and
Madeline A. Crosby and
Jeff de Pons and
Mary E. Dolan and
Gilberto dos Santos and
Barbara Dunn and
Nathan A. Dunn and
Anne E. Eagle and
Dustin Ebert and
Stacia R. Engel and
David Fashena and
Ken Frazer and
Sibyl Gao and
Felix Gondwe and
Joshua L. Goodman and
L. Sian Gramates and
Christian A. Grove and
Todd W. Harris and
Marie{-}Claire Harrison and
Douglas G. Howe and
Kevin L. Howe and
Sagar Jha and
James A. Kadin and
Thomas C. Kaufman and
Patrick Kalita and
Kalpana Karra and
Ranjana Kishore and
Stanley J. F. Laulederkind and
Raymond Y. N. Lee and
Kevin A. MacPherson and
Steven J. Marygold and
Beverley Matthews and
Gillian H. Millburn and
Stuart R. Miyasato and
Sierra A. T. Moxon and
Hans{-}Michael M{\"{u}}ller and
Christopher J. Mungall and
Anushya Muruganujan and
Tremayne Mushayahama and
Robert S. Nash and
Patrick Ng and
Michael Paulini and
Norbert Perrimon and
Christian Pich and
Daniela Raciti and
Joel E. Richardson and
Matthew Russell and
Susan Russo Gelbart and
Leyla Ruzicka and
Kevin Schaper and
Mary Shimoyama and
Matt Simison and
Cynthia L. Smith and
David R. Shaw and
Ajay Shrivatsav and
Marek S. Skrzypek and
Jennifer R. Smith and
Paul W. Sternberg and
Christopher J. Tabone and
Paul D. Thomas and
Jyothi Thota and
Sabrina Toro and
Monika Tomczuk and
Marek Tutaj and
Monika Tutaj and
Jose{-}Maria Urbano and
Kimberly Van Auken and
Ceri E. Van Slyke and
Shur{-}Jen Wang and
Shuai Weng and
Monte Westerfield and
Gary Williams and
Edith D. Wong and
Adam Wright and
Karen Yook},
title = {Alliance of Genome Resources Portal: unified model organism research
platform},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D650--D658},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz813},
doi = {10.1093/NAR/GKZ813},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/AgapiteAAAAABBB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NgWMAADNSGJKWMS20,
author = {Patrick C. Ng and
Edith D. Wong and
Kevin A. MacPherson and
Suzi A. Aleksander and
Joanna Argasinska and
Barbara Dunn and
Robert S. Nash and
Marek S. Skrzypek and
Felix Gondwe and
Sagar Jha and
Kalpana Karra and
Shuai Weng and
Stuart R. Miyasato and
Matt Simison and
Stacia R. Engel and
J. Michael Cherry},
title = {Transcriptome visualization and data availability at the Saccharomyces
Genome Database},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D743--D748},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz892},
doi = {10.1093/NAR/GKZ892},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/NgWMAADNSGJKWMS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LuoHGHKLMSJLBGL20,
author = {Yunhai Luo and
Benjamin C. Hitz and
Idan Gabdank and
Jason A. Hilton and
Meenakshi S. Kagda and
Bonita Lam and
Zachary Myers and
Paul Sud and
Jennifer Jou and
Khine Lin and
Ulugbek K. Baymuradov and
Keenan Graham and
Casey Litton and
Stuart R. Miyasato and
J. Seth Strattan and
Otto Jolanki and
Jin{-}Wook Lee and
Forrest Tanaka and
Philip Adenekan and
Emma O'Neill and
J. Michael Cherry},
title = {New developments on the Encyclopedia of {DNA} Elements {(ENCODE)}
data portal},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D882--D889},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz1062},
doi = {10.1093/NAR/GKZ1062},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/LuoHGHKLMSJLBGL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/WongSWBMPOECP19,
author = {Edith D. Wong and
Marek S. Skrzypek and
Shuai Weng and
Gail Binkley and
Birgit H. M. Meldal and
Livia Perfetto and
Sandra E. Orchard and
Stacia R. Engel and
J. Michael Cherry and
SGD Project},
title = {Integration of macromolecular complex data into the Saccharomyces
Genome Database},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz008},
year = {2019},
url = {https://doi.org/10.1093/database/baz008},
doi = {10.1093/DATABASE/BAZ008},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/WongSWBMPOECP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/EngelSHWNWBSKC18,
author = {Stacia R. Engel and
Marek S. Skrzypek and
Sage T. Hellerstedt and
Edith D. Wong and
Robert S. Nash and
Shuai Weng and
Gail Binkley and
Travis K. Sheppard and
Kalpana Karra and
J. Michael Cherry},
title = {Updated regulation curation model at the Saccharomyces Genome Database},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay007},
year = {2018},
url = {https://doi.org/10.1093/database/bay007},
doi = {10.1093/DATABASE/BAY007},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/EngelSHWNWBSKC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GabdankCDHDBNOG18,
author = {Idan Gabdank and
Esther T. Chan and
Jean M. Davidson and
Jason A. Hilton and
Carrie A. Davis and
Ulugbek K. Baymuradov and
Aditi K. Narayanan and
Kathrina C. Onate and
Keenan Graham and
Stuart R. Miyasato and
Timothy R. Dreszer and
J. Seth Strattan and
Otto Jolanki and
Forrest Tanaka and
Benjamin C. Hitz and
Cricket A. Sloan and
J. Michael Cherry},
title = {Prevention of data duplication for high throughput sequencing repositories},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay008},
year = {2018},
url = {https://doi.org/10.1093/database/bay008},
doi = {10.1093/DATABASE/BAY008},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/GabdankCDHDBNOG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SkrzypekNWMHEKW18,
author = {Marek S. Skrzypek and
Robert S. Nash and
Edith D. Wong and
Kevin A. MacPherson and
Sage T. Hellerstedt and
Stacia R. Engel and
Kalpana Karra and
Shuai Weng and
Travis K. Sheppard and
Gail Binkley and
Matt Simison and
Stuart R. Miyasato and
J. Michael Cherry},
title = {Saccharomyces genome database informs human biology},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D736--D742},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1112},
doi = {10.1093/NAR/GKX1112},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SkrzypekNWMHEKW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DavisHSCDGHJBNO18,
author = {Carrie A. Davis and
Benjamin C. Hitz and
Cricket A. Sloan and
Esther T. Chan and
Jean M. Davidson and
Idan Gabdank and
Jason A. Hilton and
Kriti Jain and
Ulugbek K. Baymuradov and
Aditi K. Narayanan and
Kathrina C. Onate and
Keenan Graham and
Stuart R. Miyasato and
Timothy R. Dreszer and
J. Seth Strattan and
Otto Jolanki and
Forrest Tanaka and
J. Michael Cherry},
title = {The Encyclopedia of {DNA} elements {(ENCODE):} data portal update},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D794--D801},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1081},
doi = {10.1093/NAR/GKX1081},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/DavisHSCDGHJBNO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MacPhersonSWDH17,
author = {Kevin A. MacPherson and
Barry Starr and
Edith D. Wong and
Kyla S. Dalusag and
Sage T. Hellerstedt and
Olivia W. Lang and
Robert S. Nash and
Marek S. Skrzypek and
Stacia R. Engel and
J. Michael Cherry},
title = {Outreach and online training services at the Saccharomyces Genome
Database},
journal = {Database J. Biol. Databases Curation},
volume = {2017},
pages = {bax002},
year = {2017},
url = {https://doi.org/10.1093/database/bax002},
doi = {10.1093/DATABASE/BAX002},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MacPhersonSWDH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HellerstedtNWPW17,
author = {Sage T. Hellerstedt and
Robert S. Nash and
Shuai Weng and
Kelley M. Paskov and
Edith D. Wong and
Kalpana Karra and
Stacia R. Engel and
J. Michael Cherry},
title = {Curated protein information in the Saccharomyces genome database},
journal = {Database J. Biol. Databases Curation},
volume = {2017},
pages = {bax011},
year = {2017},
url = {https://doi.org/10.1093/database/bax011},
doi = {10.1093/DATABASE/BAX011},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HellerstedtNWPW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/EngelWBPSC16,
author = {Stacia R. Engel and
Shuai Weng and
Gail Binkley and
Kelley M. Paskov and
Giltae Song and
J. Michael Cherry},
title = {From one to many: expanding the \emph{Saccharomyces cerevisiae} reference
genome panel},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw020},
doi = {10.1093/DATABASE/BAW020},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/EngelWBPSC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HongSCDMSHGNHLR16,
author = {Eurie L. Hong and
Cricket A. Sloan and
Esther T. Chan and
Jean M. Davidson and
Venkat S. Malladi and
J. Seth Strattan and
Benjamin C. Hitz and
Idan Gabdank and
Aditi K. Narayanan and
Marcus Ho and
Brian T. Lee and
Laurence D. Rowe and
Timothy R. Dreszer and
Greg R. Roe and
Nikhil R. Podduturi and
Forrest Tanaka and
Jason A. Hilton and
J. Michael Cherry},
title = {Principles of metadata organization at the {ENCODE} data coordination
center},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw001},
doi = {10.1093/DATABASE/BAW001},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HongSCDMSHGNHLR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/SongBBCDDEHKHNP16,
author = {Giltae Song and
Rama Balakrishnan and
Gail Binkley and
Maria C. Costanzo and
Kyla S. Dalusag and
Janos Demeter and
Stacia R. Engel and
Sage T. Hellerstedt and
Kalpana Karra and
Benjamin C. Hitz and
Robert S. Nash and
Kelley M. Paskov and
Travis K. Sheppard and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
J. Michael Cherry},
title = {Integration of new alternative reference strain genome sequences into
the \emph{Saccharomyces} genome database},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw074},
doi = {10.1093/DATABASE/BAW074},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/SongBBCDDEHKHNP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SheppardHESBBCD16,
author = {Travis K. Sheppard and
Benjamin C. Hitz and
Stacia R. Engel and
Giltae Song and
Rama Balakrishnan and
Gail Binkley and
Maria C. Costanzo and
Kyla S. Dalusag and
Janos Demeter and
Sage T. Hellerstedt and
Kalpana Karra and
Robert S. Nash and
Kelley M. Paskov and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
J. Michael Cherry},
title = {The \emph{Saccharomyces} Genome Database Variant Viewer},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {698--702},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1250},
doi = {10.1093/NAR/GKV1250},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SheppardHESBBCD16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SloanCDMSHGNHLR16,
author = {Cricket A. Sloan and
Esther T. Chan and
Jean M. Davidson and
Venkat S. Malladi and
J. Seth Strattan and
Benjamin C. Hitz and
Idan Gabdank and
Aditi K. Narayanan and
Marcus Ho and
Brian T. Lee and
Laurence D. Rowe and
Timothy R. Dreszer and
Greg Roe and
Nikhil R. Podduturi and
Forrest Tanaka and
Eurie L. Hong and
J. Michael Cherry},
title = {{ENCODE} data at the {ENCODE} portal},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {726--732},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1160},
doi = {10.1093/NAR/GKV1160},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SloanCDMSHGNHLR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/semweb/DeraspeKBSMCCD16,
author = {Maxime D{\'{e}}raspe and
Kalpana Karra and
Gail Binkley and
Julie M. Sullivan and
Gos Micklem and
Jacques Corbeil and
J. Michael Cherry and
Michel Dumontier},
editor = {Cui Tao and
Guoqian Jiang and
Dezhao Song and
Jeff Heflin and
Frank Schilder},
title = {Semantic Research Platform for Model Organisms},
booktitle = {Proceedings of the First International Workshop on Biomedical Data
Integration and Discovery {(BMDID} 2016) co-located with The 15th
International Semantic Web Conference {(ISWC} 2016), Kobe, Japan,
October 17, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1709},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1709/BMDID\_2016\_paper\_1.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:07 +0100},
biburl = {https://dblp.org/rec/conf/semweb/DeraspeKBSMCCD16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Maxime D{\'{e}}raspe and
Gail Binkley and
Daniela Butano and
Matthew Chadwick and
J. Michael Cherry and
Justin Clark{-}Casey and
Sergio Contrino and
Jacques Corbeil and
Joshua Heimbach and
Kalpana Karra and
Rachel Lyne and
Julie M. Sullivan and
Yo Yehudi and
Gos Micklem and
Michel Dumontier},
editor = {Adrian Paschke and
Albert Burger and
Andrea Splendiani and
M. Scott Marshall and
Paolo Romano},
title = {Making Linked Data {SPARQL} with the InterMine Biological Data Warehouse},
booktitle = {Proceedings of the 9th International Conference Semantic Web Applications
and Tools for Life Sciences, Amsterdam, The Netherlands, December
5-8, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1795},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1795/paper8.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/swat4ls/DeraspeBBCCCCCH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Venkat S. Malladi and
Drew T. Erickson and
Nikhil R. Podduturi and
Laurence D. Rowe and
Esther T. Chan and
Jean M. Davidson and
Benjamin C. Hitz and
Marcus Ho and
Brian T. Lee and
Stuart R. Miyasato and
Greg R. Roe and
Matt Simison and
Cricket A. Sloan and
J. Seth Strattan and
Forrest Tanaka and
W. James Kent and
J. Michael Cherry and
Eurie L. Hong},
title = {Ontology application and use at the {ENCODE} {DCC}},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015},
url = {https://doi.org/10.1093/database/bav010},
doi = {10.1093/DATABASE/BAV010},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MalladiEPRCDHHL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CostanzoEWLKCWPRBHC14,
author = {Maria C. Costanzo and
Stacia R. Engel and
Edith D. Wong and
Paul Lloyd and
Kalpana Karra and
Esther T. Chan and
Shuai Weng and
Kelley M. Paskov and
Greg R. Roe and
Gail Binkley and
Benjamin C. Hitz and
J. Michael Cherry},
title = {\emph{Saccharomyces} genome database provides new regulation data},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {717--725},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1158},
doi = {10.1093/NAR/GKT1158},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CostanzoEWLKCWPRBHC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/BalakrishnanHHAC13,
author = {Rama Balakrishnan and
Midori A. Harris and
Rachael P. Huntley and
Kimberly Van Auken and
J. Michael Cherry},
title = {A guide to best practices for Gene Ontology {(GO)} manual annotation},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat054},
doi = {10.1093/DATABASE/BAT054},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/BalakrishnanHHAC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/EngelC13,
author = {Stacia R. Engel and
J. Michael Cherry},
title = {The new modern era of yeast genomics: community sequencing and the
resulting annotation of multiple \emph{Saccharomyces cerevisiae} strains
at the \emph{Saccharomyces} Genome Database},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat012},
doi = {10.1093/DATABASE/BAT012},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/EngelC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GaudetMRABCKOY13,
author = {Pascale Gaudet and
Monica C. Munoz{-}Torres and
Marc Robinson{-}Rechavi and
Teresa K. Attwood and
Alex Bateman and
J. Michael Cherry and
Renate Kania and
Claire O'Donovan and
Chisato Yamasaki},
title = {DATABASE, \emph{The Journal of Biological Databases and Curation},
is now the official journal of the International Society for Biocuration},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat077},
doi = {10.1093/DATABASE/BAT077},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GaudetMRABCKOY13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Edith D. Wong and
Kalpana Karra and
Benjamin C. Hitz and
Eurie L. Hong and
J. Michael Cherry},
title = {The YeastGenome app: the \emph{Saccharomyces} Genome Database at your
fingertips},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat004},
doi = {10.1093/DATABASE/BAT004},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/WongKHHC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/BalakrishnanPKHBHSMC12,
author = {Rama Balakrishnan and
Julie Park and
Kalpana Karra and
Benjamin C. Hitz and
Gail Binkley and
Eurie L. Hong and
Julie M. Sullivan and
Gos Micklem and
J. Michael Cherry},
title = {YeastMine - an integrated data warehouse for \emph{Saccharomyces cerevisiae}
data as a multipurpose tool-kit},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bar062},
doi = {10.1093/DATABASE/BAR062},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/BalakrishnanPKHBHSMC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/BurgeABBCOXG12,
author = {Sarah W. Burge and
Teresa K. Attwood and
Alex Bateman and
Tanya Z. Berardini and
J. Michael Cherry and
Claire O'Donovan and
Ioannis Xenarios and
Pascale Gaudet},
title = {Biocurators and Biocuration: surveying the 21st century challenges},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bar059},
doi = {10.1093/DATABASE/BAR059},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/BurgeABBCOXG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ChanC12,
author = {Esther T. Chan and
J. Michael Cherry},
title = {Considerations for creating and annotating the budding yeast Genome
Map at {SGD:} a progress report},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bar057},
doi = {10.1093/DATABASE/BAR057},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ChanC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GaudetABBBCDFGHKKMKMNOOPRSSSAVWYM12,
author = {Pascale Gaudet and
Cecilia N. Arighi and
Frederic B. Bastian and
Alex Bateman and
Judith A. Blake and
J. Michael Cherry and
Peter D'Eustachio and
Robert D. Finn and
Michelle G. Giglio and
Lynette Hirschman and
Renate Kania and
William Klimke and
Maria Jesus Martin and
Ilene Karsch{-}Mizrachi and
Monica C. Munoz{-}Torres and
Darren A. Natale and
Claire O'Donovan and
B. F. Francis Ouellette and
Kim D. Pruitt and
Marc Robinson{-}Rechavi and
Susanna{-}Assunta Sansone and
Paul N. Schofield and
Granger G. Sutton and
Kimberly Van Auken and
Sona Vasudevan and
Cathy H. Wu and
Jasmine Young and
Raja Mazumder},
title = {Recent advances in biocuration: Meeting Report from the fifth International
Biocuration Conference},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas036},
doi = {10.1093/DATABASE/BAS036},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GaudetABBBCDFGHKKMKMNOOPRSSSAVWYM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ParkCBCH12,
author = {Julie Park and
Maria C. Costanzo and
Rama Balakrishnan and
J. Michael Cherry and
Eurie L. Hong},
title = {CvManGO, a method for leveraging computational predictions to improve
literature-based Gene Ontology annotations},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas001},
doi = {10.1093/DATABASE/BAS001},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ParkCBCH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CherryHABBCCCDEFHHKKMNPSSWW12,
author = {J. Michael Cherry and
Eurie L. Hong and
Craig Amundsen and
Rama Balakrishnan and
Gail Binkley and
Esther T. Chan and
Karen R. Christie and
Maria C. Costanzo and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Jodi E. Hirschman and
Benjamin C. Hitz and
Kalpana Karra and
Cynthia J. Krieger and
Stuart R. Miyasato and
Robert S. Nash and
Julie Park and
Marek S. Skrzypek and
Matt Simison and
Shuai Weng and
Edith D. Wong},
title = {Saccharomyces Genome Database: the genomics resource of budding yeast},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {700--705},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1029},
doi = {10.1093/NAR/GKR1029},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CherryHABBCCCDEFHHKKMNPSSWW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/CostanzoPBCH11,
author = {Maria C. Costanzo and
Julie Park and
Rama Balakrishnan and
J. Michael Cherry and
Eurie L. Hong},
title = {Using computational predictions to improve literature-based Gene Ontology
annotations: a feasibility study},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011},
url = {https://doi.org/10.1093/database/bar004},
doi = {10.1093/DATABASE/BAR004},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/CostanzoPBCH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11,
author = {Pascale Gaudet and
Amos Bairoch and
Dawn Field and
Susanna{-}Assunta Sansone and
Chris F. Taylor and
Teresa K. Attwood and
Alex Bateman and
Judith A. Blake and
Carol J. Bult and
J. Michael Cherry and
Rex L. Chisholm and
Guy Cochrane and
Charles E. Cook and
Janan T. Eppig and
Michael Y. Galperin and
Robert Gentleman and
Carole A. Goble and
Takashi Gojobori and
John M. Hancock and
Douglas G. Howe and
Tadashi Imanishi and
Janet Kelso and
David Landsman and
Suzanna E. Lewis and
Ilene Karsch{-}Mizrachi and
Sandra E. Orchard and
B. F. Francis Ouellette and
Shoba Ranganathan and
Lorna J. Richardson and
Philippe Rocca{-}Serra and
Paul N. Schofield and
Damian Smedley and
Christopher Southan and
Tin Wee Tan and
Tatiana A. Tatusova and
Patricia L. Whetzel and
Owen White and
Chisato Yamasaki},
title = {Towards BioDBcore: a community-defined information specification for
biological databases},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011},
url = {https://doi.org/10.1093/database/baq027},
doi = {10.1093/DATABASE/BAQ027},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Arun Rangarajan and
Tim Schedl and
Karen Yook and
Juancarlos Chan and
Stephen Haenel and
Lolly Otis and
Sharon Faelten and
Tracey DePellegrin{-}Connelly and
Ruth Isaacson and
Marek S. Skrzypek and
J. Michael Cherry and
Paul W. Sternberg and
Hans{-}Michael M{\"{u}}ller},
title = {Toward an interactive article: integrating journals and biological
databases},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {175},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-175},
doi = {10.1186/1471-2105-12-175},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RangarajanSYCHOFDISCSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11,
author = {Pascale Gaudet and
Amos Bairoch and
Dawn Field and
Susanna{-}Assunta Sansone and
Chris F. Taylor and
Teresa K. Attwood and
Alex Bateman and
Judith A. Blake and
Carol J. Bult and
J. Michael Cherry and
Rex L. Chisholm and
Guy Cochrane and
Charles E. Cook and
Janan T. Eppig and
Michael Y. Galperin and
Robert Gentleman and
Carole A. Goble and
Takashi Gojobori and
John M. Hancock and
Douglas G. Howe and
Tadashi Imanishi and
Janet Kelso and
David Landsman and
Suzanna E. Lewis and
Ilene Karsch{-}Mizrachi and
Sandra E. Orchard and
B. F. Francis Ouellette and
Shoba Ranganathan and
Lorna J. Richardson and
Philippe Rocca{-}Serra and
Paul N. Schofield and
Damian Smedley and
Christopher Southan and
Tin Wee Tan and
Tatiana A. Tatusova and
Patricia L. Whetzel and
Owen White and
Chisato Yamasaki},
title = {Towards BioDBcore: a community-defined information specification for
biological databases},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {7--10},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1173},
doi = {10.1093/NAR/GKQ1173},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GaudetBFSTABBBCCCCEGGGGHHIKLLKOORRRSSSTTWWY11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/EngelBBCCDFHHHKLMNOPSWWDBC10,
author = {Stacia R. Engel and
Rama Balakrishnan and
Gail Binkley and
Karen R. Christie and
Maria C. Costanzo and
Selina S. Dwight and
Dianna G. Fisk and
Jodi E. Hirschman and
Benjamin C. Hitz and
Eurie L. Hong and
Cynthia J. Krieger and
Michael S. Livstone and
Stuart R. Miyasato and
Robert S. Nash and
Rose Oughtred and
Julie Park and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
Kara Dolinski and
David Botstein and
J. Michael Cherry},
title = {\emph{Saccharomyces} Genome Database provides mutant phenotype data},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {433--436},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp917},
doi = {10.1093/NAR/GKP917},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/EngelBBCCDFHHHKLMNOPSWWDBC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/CostanzoSNWBEHHC09,
author = {Maria C. Costanzo and
Marek S. Skrzypek and
Robert S. Nash and
Edith D. Wong and
Gail Binkley and
Stacia R. Engel and
Benjamin C. Hitz and
Eurie L. Hong and
J. Michael Cherry},
title = {New mutant phenotype data curation system in the \emph{Saccharomyces}
Genome Database},
journal = {Database J. Biol. Databases Curation},
volume = {2009},
year = {2009},
url = {https://doi.org/10.1093/database/bap001},
doi = {10.1093/DATABASE/BAP001},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/CostanzoSNWBEHHC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HongBDCPBCDEFHHKLMNOSWWZDBC08,
author = {Eurie L. Hong and
Rama Balakrishnan and
Qing Dong and
Karen R. Christie and
Julie Park and
Gail Binkley and
Maria C. Costanzo and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Jodi E. Hirschman and
Benjamin C. Hitz and
Cynthia J. Krieger and
Michael S. Livstone and
Stuart R. Miyasato and
Robert S. Nash and
Rose Oughtred and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
Kathy K. Zhu and
Kara Dolinski and
David Botstein and
J. Michael Cherry},
title = {Gene Ontology annotations at {SGD:} new data sources and annotation
methods},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {577--581},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm909},
doi = {10.1093/NAR/GKM909},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HongBDCPBCDEFHHKLMNOSWWZDBC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CrangleCHZ07,
author = {Colleen E. Crangle and
J. Michael Cherry and
Eurie L. Hong and
Alex Zbyslaw},
title = {Mining experimental evidence of molecular function claims from the
literature},
journal = {Bioinform.},
volume = {23},
number = {23},
pages = {3232--3240},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm495},
doi = {10.1093/BIOINFORMATICS/BTM495},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CrangleCHZ07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NashWHBCCDEFHHLOPSTBDLMSSDBC07,
author = {Robert S. Nash and
Shuai Weng and
Benjamin C. Hitz and
Rama Balakrishnan and
Karen R. Christie and
Maria C. Costanzo and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Jodi E. Hirschman and
Eurie L. Hong and
Michael S. Livstone and
Rose Oughtred and
Julie Park and
Marek S. Skrzypek and
Chandra L. Theesfeld and
Gail Binkley and
Qing Dong and
Christopher Lane and
Stuart R. Miyasato and
Anand Sethuraman and
Mark Schroeder and
Kara Dolinski and
David Botstein and
J. Michael Cherry},
title = {Expanded protein information at {SGD:} new pages and proteome browser},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {468--471},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl931},
doi = {10.1093/NAR/GKL931},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/NashWHBCCDEFHHLOPSTBDLMSSDBC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Jodi E. Hirschman and
Rama Balakrishnan and
Karen R. Christie and
Maria C. Costanzo and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Eurie L. Hong and
Michael S. Livstone and
Robert S. Nash and
Julie Park and
Rose Oughtred and
Marek S. Skrzypek and
Barry Starr and
Chandra L. Theesfeld and
Jennifer M. Williams and
Rey Andrada and
Gail Binkley and
Qing Dong and
Christopher Lane and
Stuart R. Miyasato and
Anand Sethuraman and
Mark Schroeder and
Mayank K. Thanawala and
Shuai Weng and
Kara Dolinski and
David Botstein and
J. Michael Cherry},
title = {Genome Snapshot: a new resource at the \emph{Saccharomyces} Genome
Database {(SGD)} presenting an overview of the \emph{Saccharomyces
cerevisiae} genome},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {442--445},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj117},
doi = {10.1093/NAR/GKJ117},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HirschmanBCCDEFHLNPOSSTWABDLMSSTWDBC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/StoverKBDFNSWC06,
author = {Nicholas A. Stover and
Cynthia J. Krieger and
Gail Binkley and
Qing Dong and
Dianna G. Fisk and
Robert S. Nash and
Anand Sethuraman and
Shuai Weng and
J. Michael Cherry},
title = {\emph{Tetrahymena} Genome Database {(TGD):} a new genomic resource
for \emph{Tetrahymena thermophila} research},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {500--503},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj054},
doi = {10.1093/NAR/GKJ054},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/StoverKBDFNSWC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BalakrishnanCCDDEFHHNOSTBDLSWBC05,
author = {Rama Balakrishnan and
Karen R. Christie and
Maria C. Costanzo and
Kara Dolinski and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Jodi E. Hirschman and
Eurie L. Hong and
Robert S. Nash and
Rose Oughtred and
Marek S. Skrzypek and
Chandra L. Theesfeld and
Gail Binkley and
Qing Dong and
Christopher Lane and
Anand Sethuraman and
Shuai Weng and
David Botstein and
J. Michael Cherry},
title = {Fungal {BLAST} and Model Organism {BLASTP} Best Hits: new comparison
resources at the \emph{Saccharomyces} Genome Database {(SGD)}},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {374--377},
year = {2005},
url = {https://doi.org/10.1093/nar/gki023},
doi = {10.1093/NAR/GKI023},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BalakrishnanCCDDEFHHNOSTBDLSWBC05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/YanYBMWWCR05,
author = {Thomas Yan and
Danny Yoo and
Tanya Z. Berardini and
Lukas A. Mueller and
Dan C. Weems and
Shuai Weng and
J. Michael Cherry and
Seung Yon Rhee},
title = {PatMatch: a program for finding patterns in peptide and nucleotide
sequences},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Web-Server-Issue},
pages = {262--266},
year = {2005},
url = {https://doi.org/10.1093/nar/gki368},
doi = {10.1093/NAR/GKI368},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/YanYBMWWCR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DwightBCCDEFFHHINSSTABDLSWBC04,
author = {Selina S. Dwight and
Rama Balakrishnan and
Karen R. Christie and
Maria C. Costanzo and
Kara Dolinski and
Stacia R. Engel and
Becket Feierbach and
Dianna G. Fisk and
Jodi E. Hirschman and
Eurie L. Hong and
Laurie Issel{-}Tarver and
Robert S. Nash and
Anand Sethuraman and
Barry Starr and
Chandra L. Theesfeld and
Rey Andrada and
Gail Binkley and
Qing Dong and
Christopher Lane and
Mark Schroeder and
Shuai Weng and
David Botstein and
J. Michael Cherry},
title = {Saccharomyces genome database: Underlying principles and organisation},
journal = {Briefings Bioinform.},
volume = {5},
number = {1},
pages = {9--22},
year = {2004},
url = {https://doi.org/10.1093/bib/5.1.9},
doi = {10.1093/BIB/5.1.9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DwightBCCDEFFHHINSSTABDLSWBC04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WiederkehrBMKSHMICYLCLP04,
author = {Christa Niederhauser{-}Wiederkehr and
R. Basavaraj and
Cyril Sarrauste de Menthi{\`{e}}re and
R. Koch and
U. Schlecht and
Leandro Hermida and
Benjamin Masdoua and
Ryohei Ishii and
V. Cassen and
M. Yamamoto and
Christopher Lane and
J. Michael Cherry and
N. Lamb and
Michael Primig},
title = {Database model and specification of GermOnline Release 2.0, a cross-species
community annotation knowledgebase on germ cell differentiation},
journal = {Bioinform.},
volume = {20},
number = {5},
pages = {808--811},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth030},
doi = {10.1093/BIOINFORMATICS/BTH030},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WiederkehrBMKSHMICYLCLP04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BoyleWGJBCS04,
author = {Elizabeth I. Boyle and
Shuai Weng and
Jeremy Gollub and
Heng Jin and
David Botstein and
J. Michael Cherry and
Gavin Sherlock},
title = {{GO:} : TermFinder--open source software for accessing Gene Ontology
information and finding significantly enriched Gene Ontology terms
associated with a list of genes},
journal = {Bioinform.},
volume = {20},
number = {18},
pages = {3710--3715},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/bth456},
doi = {10.1093/BIOINFORMATICS/BTH456},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BoyleWGJBCS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChristieWBCDDEFFHHINSSTABDLSBC04,
author = {Karen R. Christie and
Shuai Weng and
Rama Balakrishnan and
Maria C. Costanzo and
Kara Dolinski and
Selina S. Dwight and
Stacia R. Engel and
Becket Feierbach and
Dianna G. Fisk and
Jodi E. Hirschman and
Eurie L. Hong and
Laurie Issel{-}Tarver and
Robert S. Nash and
Anand Sethuraman and
Barry Starr and
Chandra L. Theesfeld and
Rey Andrada and
Gail Binkley and
Qing Dong and
Christopher Lane and
Mark Schroeder and
David Botstein and
J. Michael Cherry},
title = {Saccharomyces Genome Database {(SGD)} provides tools to identify and
analyze sequences from Saccharomyces cerevisiae and related sequences
from other organisms},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {311--314},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh033},
doi = {10.1093/NAR/GKH033},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ChristieWBCDDEFFHHINSSTABDLSBC04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WiederkehrBM04,
author = {Christa Niederhauser{-}Wiederkehr and
R. Basavaraj and
Cyril Sarrauste de Menthi{\`{e}}re and
Leandro Hermida and
R. Koch and
U. Schlecht and
A. Amon and
Sophie Brachat and
Michael Breitenbach and
Peter Briza and
Sandrine Caburet and
J. Michael Cherry and
R. Davis and
A. Deutschbauer and
H. G. Dickinson and
T. Dumitrescu and
M. Fellous and
A. Goldman and
J. Anton Grootegoed and
R. Scott Hawley and
Ryohei Ishii and
B. J{\'{e}}gou and
R. J. Kaufman and
Franz Klein and
N. Lamb and
B. Maro and
Kim Nasmyth and
A. Nicolas and
T. Orr{-}Weaver and
Peter Philippsen and
Charles Pineau and
K. P. Rabitsch and
V. Reinke and
H. Roest and
W. Saunders and
M. Schr{\"{o}}der and
Tim Schedl and
M. Siep and
A. Villeneuve and
Debra J. Wolgemuth and
M. Yamamoto and
D. Zickler and
R. E. Esposito and
Michael Primig},
title = {GermOnline, a cross-species community knowledgebase on germ cell differentiation},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {560--567},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh055},
doi = {10.1093/NAR/GKH055},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/WiederkehrBM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ws/BadaSGGABCHL04,
author = {Michael Bada and
Robert Stevens and
Carole A. Goble and
Yolanda Gil and
Michael Ashburner and
Judith A. Blake and
J. Michael Cherry and
Midori A. Harris and
Suzanna Lewis},
title = {A short study on the success of the Gene Ontology},
journal = {J. Web Semant.},
volume = {1},
number = {2},
pages = {235--240},
year = {2004},
url = {https://doi.org/10.1016/j.websem.2003.12.003},
doi = {10.1016/J.WEBSEM.2003.12.003},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ws/BadaSGGABCHL04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/trec/CrangleZCH04,
author = {Colleen E. Crangle and
Alex Zbyslaw and
J. Michael Cherry and
Eurie L. Hong},
editor = {Ellen M. Voorhees and
Lori P. Buckland},
title = {Concept Extraction and Synonymy Management for Biomedical Information
Retrieval},
booktitle = {Proceedings of the Thirteenth Text REtrieval Conference, {TREC} 2004,
Gaithersburg, Maryland, USA, November 16-19, 2004},
series = {{NIST} Special Publication},
volume = {500-261},
publisher = {National Institute of Standards and Technology {(NIST)}},
year = {2004},
url = {http://trec.nist.gov/pubs/trec13/papers/converspeech.geo.pdf},
timestamp = {Wed, 07 Jul 2021 16:44:22 +0200},
biburl = {https://dblp.org/rec/conf/trec/CrangleZCH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WengDBCCDDEFHISTABLSBC03,
author = {Shuai Weng and
Qing Dong and
Rama Balakrishnan and
Karen R. Christie and
Maria C. Costanzo and
Kara Dolinski and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Eurie L. Hong and
Laurie Issel{-}Tarver and
Anand Sethuraman and
Chandra L. Theesfeld and
Rey Andrada and
Gail Binkley and
Christopher Lane and
Mark Schroeder and
David Botstein and
J. Michael Cherry},
title = {Saccharomyces Genome Database {(SGD)} provides biochemical and structural
information for budding yeast proteins},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {216--218},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg054},
doi = {10.1093/NAR/GKG054},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/WengDBCCDDEFHISTABLSBC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DiehnSBJMHRCBBA03,
author = {Maximilian Diehn and
Gavin Sherlock and
Gail Binkley and
Heng Jin and
John C. Matese and
Tina Hernandez{-}Boussard and
Christian A. Rees and
J. Michael Cherry and
David Botstein and
Patrick O. Brown and
Ash A. Alizadeh},
title = {{SOURCE:} a unified genomic resource of functional annotations, ontologies,
and gene expression data},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {219--223},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg014},
doi = {10.1093/NAR/GKG014},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/DiehnSBJMHRCBBA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/DongBBCCDDEFHHNISTWBC03,
author = {Qing Dong and
Rama Balakrishnan and
Gail Binkley and
Karen R. Christie and
Maria C. Costanzo and
Kara Dolinski and
Selina S. Dwight and
Stacia R. Engel and
Dianna G. Fisk and
Jodi E. Hirschman and
Eurie L. Hong and
Robert S. Nash and
Laurie Issel{-}Tarver and
Anand Sethuraman and
Chandra L. Theesfeld and
Shuai Weng and
David Botstein and
J. Michael Cherry},
title = {Gene Function, Metabolic Pathways and Comparative Genomics in Yeast},
booktitle = {2nd {IEEE} Computer Society Bioinformatics Conference, {CSB} 2003,
Stanford, CA, USA, August 11-14, 2003},
pages = {437--438},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CSB.2003.1227362},
doi = {10.1109/CSB.2003.1227362},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/DongBBCCDDEFHHNISTWBC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DwightHDBBCFISSSWBC03,
author = {Selina S. Dwight and
Midori A. Harris and
Kara Dolinski and
Catherine A. Ball and
Gail Binkley and
Karen R. Christie and
Dianna G. Fisk and
Laurie Issel{-}Tarver and
Mark Schroeder and
Gavin Sherlock and
Anand Sethuraman and
Shuai Weng and
David Botstein and
J. Michael Cherry},
title = {Saccharomyces Genome Database {(SGD)} provides secondary gene annotation
using the Gene Ontology {(GO)}},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {69--72},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.69},
doi = {10.1093/NAR/30.1.69},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/DwightHDBBCFISSSWBC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EwingC01,
author = {Rob M. Ewing and
J. Michael Cherry},
title = {Visualization of expression clusters using Sammon's non-linear mapping},
journal = {Bioinform.},
volume = {17},
number = {7},
pages = {658--659},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.7.658},
doi = {10.1093/BIOINFORMATICS/17.7.658},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EwingC01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BallJSWMABDDHISBC01,
author = {Catherine A. Ball and
Heng Jin and
Gavin Sherlock and
Shuai Weng and
John C. Matese and
Rey Andrada and
Gail Binkley and
Kara Dolinski and
Selina S. Dwight and
Midori A. Harris and
Laurie Issel{-}Tarver and
Mark Schroeder and
David Botstein and
J. Michael Cherry},
title = {Saccharomyces Genome Database provides tools to survey gene expression
and functional analysis data},
journal = {Nucleic Acids Res.},
volume = {29},
number = {1},
pages = {80--81},
year = {2001},
url = {https://doi.org/10.1093/nar/29.1.80},
doi = {10.1093/NAR/29.1.80},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BallJSWMABDDHISBC01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SherlockHKBMDKWJBESBBC01,
author = {Gavin Sherlock and
Tina Hernandez{-}Boussard and
Andrew Kasarskis and
Gail Binkley and
John C. Matese and
Selina S. Dwight and
Miroslava Kaloper and
Shuai Weng and
Heng Jin and
Catherine A. Ball and
Michael B. Eisen and
Paul T. Spellman and
Patrick O. Brown and
David Botstein and
J. Michael Cherry},
title = {The Stanford Microarray Database},
journal = {Nucleic Acids Res.},
volume = {29},
number = {1},
pages = {152--155},
year = {2001},
url = {https://doi.org/10.1093/nar/29.1.152},
doi = {10.1093/NAR/29.1.152},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SherlockHKBMDKWJBESBBC01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BallDDHIKSSBJKOSWZBC00,
author = {Catherine A. Ball and
Kara Dolinski and
Selina S. Dwight and
Midori A. Harris and
Laurie Issel{-}Tarver and
Andrew Kasarskis and
Charles R. Scafe and
Gavin Sherlock and
Gail Binkley and
Heng Jin and
Miroslava Kaloper and
Sidney D. Orr and
Mark Schroeder and
Shuai Weng and
Yan Zhu and
David Botstein and
J. Michael Cherry},
title = {Integrating functional genomic information into the Saccharomyces
Genome Database},
journal = {Nucleic Acids Res.},
volume = {28},
number = {1},
pages = {77--80},
year = {2000},
url = {https://doi.org/10.1093/nar/28.1.77},
doi = {10.1093/NAR/28.1.77},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BallDDHIKSSBJKOSWZBC00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChervitzHBDDHJMRRSSSWZCB99,
author = {Stephen A. Chervitz and
Erich T. Hester and
Catherine A. Ball and
Kara Dolinski and
Selina S. Dwight and
Midori A. Harris and
Gail Juvik and
Alice Malekian and
Shannon Roberts and
TaiYun Roe and
Charles R. Scafe and
Mark Schroeder and
Gavin Sherlock and
Shuai Weng and
Yan Zhu and
J. Michael Cherry and
David Botstein},
title = {Using the Saccharomyces Genome Database {(SGD)} for analysis of protein
similarities and structure},
journal = {Nucleic Acids Res.},
volume = {27},
number = {1},
pages = {74--78},
year = {1999},
url = {https://doi.org/10.1093/nar/27.1.74},
doi = {10.1093/NAR/27.1.74},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ChervitzHBDDHJMRRSSSWZCB99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RheeWBGMFC99,
author = {Seung Yon Rhee and
Shuai Weng and
Deverie K. Bongard{-}Pierce and
Margarita Garcia{-}Hernandez and
Alice Malekian and
David J. Flanders and
J. Michael Cherry},
title = {Unified display of Arabidopsis thaliana physical maps from AtDB, the
A.thaliana database},
journal = {Nucleic Acids Res.},
volume = {27},
number = {1},
pages = {79--84},
year = {1999},
url = {https://doi.org/10.1093/nar/27.1.79},
doi = {10.1093/NAR/27.1.79},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RheeWBGMFC99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CherryABCDHJJRSWB98,
author = {J. Michael Cherry and
Caroline Adler and
Catherine A. Ball and
Stephen A. Chervitz and
Selina S. Dwight and
Erich T. Hester and
Yankai Jia and
Gail Juvik and
TaiYun Roe and
Mark Schroeder and
Shuai Weng and
David Botstein},
title = {{SGD:} Saccharomyces Genome Database},
journal = {Nucleic Acids Res.},
volume = {26},
number = {1},
pages = {73--79},
year = {1998},
url = {https://doi.org/10.1093/nar/26.1.73},
doi = {10.1093/NAR/26.1.73},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CherryABCDHJJRSWB98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FlandersWPC98,
author = {David J. Flanders and
Shuai Weng and
Fabien X. Petel and
J. Michael Cherry},
title = {AtDB, the Arabidopsis thaliana database, and graphical-web-display
of progress by the Arabidopsis Genome Initiative},
journal = {Nucleic Acids Res.},
volume = {26},
number = {1},
pages = {80--84},
year = {1998},
url = {https://doi.org/10.1093/nar/26.1.80},
doi = {10.1093/NAR/26.1.80},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FlandersWPC98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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