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Items: 1 to 20 of 27

1.

Tutorial on Protein Ontology Resources.

Arighi CN, Drabkin H, Christie KR, Ross KE, Natale DA.

Methods Mol Biol. 2017;1558:57-78. doi: 10.1007/978-1-4939-6783-4_3.

PMID:
28150233
2.

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. Epub 2016 Nov 28.

3.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.

Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M.

Database (Oxford). 2016 Jun 5;2016. pii: baw088. doi: 10.1093/database/baw088. Print 2016.

4.

Application of comparative biology in GO functional annotation: the mouse model.

Drabkin HJ, Christie KR, Dolan ME, Hill DP, Ni L, Sitnikov D, Blake JA.

Mamm Genome. 2015 Oct;26(9-10):574-83. doi: 10.1007/s00335-015-9580-0. Epub 2015 Jul 4.

5.

Gene Ontology Consortium: going forward.

Gene Ontology Consortium..

Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26.

6.

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M.

Database (Oxford). 2014 Jul 22;2014. pii: bau075. doi: 10.1093/database/bau075. Print 2014.

7.

Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

8.

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A.

Database (Oxford). 2013 Aug 27;2013:bat062. doi: 10.1093/database/bat062. Print 2013.

9.

Saccharomyces Genome Database: the genomics resource of budding yeast.

Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED.

Nucleic Acids Res. 2012 Jan;40(Database issue):D700-5. doi: 10.1093/nar/gkr1029. Epub 2011 Nov 21.

10.

The Gene Ontology: enhancements for 2011.

Gene Ontology Consortium..

Nucleic Acids Res. 2012 Jan;40(Database issue):D559-64. doi: 10.1093/nar/gkr1028. Epub 2011 Nov 18.

11.

How the gene ontology evolves.

Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J.

BMC Bioinformatics. 2011 Aug 5;12:325. doi: 10.1186/1471-2105-12-325.

12.

The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium..

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. Epub 2009 Nov 17.

13.

Saccharomyces Genome Database provides mutant phenotype data.

Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2010 Jan;38(Database issue):D433-6. doi: 10.1093/nar/gkp917. Epub 2009 Nov 11.

14.

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Reference Genome Group of the Gene Ontology Consortium..

PLoS Comput Biol. 2009 Jul;5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3.

15.

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns.

Christie KR, Hong EL, Cherry JM.

Trends Microbiol. 2009 Jul;17(7):286-94. doi: 10.1016/j.tim.2009.04.005. Epub 2009 Jul 2. Review.

16.

The Rice Annotation Project Database (RAP-DB): 2008 update.

Rice Annotation Project., Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D1028-33. Epub 2007 Dec 17.

17.

Gene Ontology annotations at SGD: new data sources and annotation methods.

Hong EL, Balakrishnan R, Dong Q, Christie KR, Park J, Binkley G, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Krieger CJ, Livstone MS, Miyasato SR, Nash RS, Oughtred R, Skrzypek MS, Weng S, Wong ED, Zhu KK, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D577-81. Epub 2007 Nov 3.

18.

Expanded protein information at SGD: new pages and proteome browser.

Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2007 Jan;35(Database issue):D468-71. Epub 2006 Nov 16.

19.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome.

Hirschman JE, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hong EL, Livstone MS, Nash R, Park J, Oughtred R, Skrzypek M, Starr B, Theesfeld CL, Williams J, Andrada R, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Thanawala MK, Weng S, Dolinski K, Botstein D, Cherry JM.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D442-5.

20.

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD).

Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Nash R, Oughtred R, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Sethuraman A, Weng S, Botstein D, Cherry JM.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D374-7.

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