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Items: 1 to 50 of 60

1.

A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG.

Cell Syst. 2019 Feb 27;8(2):152-162.e6. doi: 10.1016/j.cels.2018.12.010. Epub 2019 Jan 23.

PMID:
30685436
2.

Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer.

Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ.

Plant Physiol. 2019 Apr;179(4):1893-1907. doi: 10.1104/pp.18.01216. Epub 2019 Jan 24.

3.

The BioGRID interaction database: 2019 update.

Oughtred R, Stark C, Breitkreutz BJ, Rust J, Boucher L, Chang C, Kolas N, O'Donnell L, Leung G, McAdam R, Zhang F, Dolma S, Willems A, Coulombe-Huntington J, Chatr-Aryamontri A, Dolinski K, Tyers M.

Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541. doi: 10.1093/nar/gky1079.

4.

Characterization of the pleiotropic roles of Sonic Hedgehog during retinal regeneration in adult zebrafish.

Thomas JL, Morgan GW, Dolinski KM, Thummel R.

Exp Eye Res. 2018 Jan;166:106-115. doi: 10.1016/j.exer.2017.10.003. Epub 2017 Oct 10.

5.

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.

Islamaj Dogan R, Kim S, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Wilbur WJ, Comeau DC, Dolinski K, Tyers M.

Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw147. Print 2017.

6.

The BioGRID interaction database: 2017 update.

Chatr-Aryamontri A, Oughtred R, Boucher L, Rust J, Chang C, Kolas NK, O'Donnell L, Oster S, Theesfeld C, Sellam A, Stark C, Breitkreutz BJ, Dolinski K, Tyers M.

Nucleic Acids Res. 2017 Jan 4;45(D1):D369-D379. doi: 10.1093/nar/gkw1102. Epub 2016 Dec 14.

7.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

Kim S, Islamaj Doğan R, Chatr-Aryamontri A, Chang CS, Oughtred R, Rust J, Batista-Navarro R, Carter J, Ananiadou S, Matos S, Santos A, Campos D, Oliveira JL, Singh O, Jonnagaddala J, Dai HJ, Su EC, Chang YC, Su YC, Chu CH, Chen CC, Hsu WL, Peng Y, Arighi C, Wu CH, Vijay-Shanker K, Aydın F, Hüsünbeyi ZM, Özgür A, Shin SY, Kwon D, Dolinski K, Tyers M, Wilbur WJ, Comeau DC.

Database (Oxford). 2016 Sep 1;2016. pii: baw121. doi: 10.1093/database/baw121. Print 2016.

8.

An extended set of yeast-based functional assays accurately identifies human disease mutations.

Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP.

Genome Res. 2016 May;26(5):670-80. doi: 10.1101/gr.192526.115. Epub 2016 Mar 14.

9.

BioGRID: A Resource for Studying Biological Interactions in Yeast.

Oughtred R, Chatr-aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M.

Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.top080754. doi: 10.1101/pdb.top080754.

10.

Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions.

Oughtred R, Chatr-aryamontri A, Breitkreutz BJ, Chang CS, Rust JM, Theesfeld CL, Heinicke S, Breitkreutz A, Chen D, Hirschman J, Kolas N, Livstone MS, Nixon J, O'Donnell L, Ramage L, Winter A, Reguly T, Sellam A, Stark C, Boucher L, Dolinski K, Tyers M.

Cold Spring Harb Protoc. 2016 Jan 4;2016(1):pdb.prot088880. doi: 10.1101/pdb.prot088880.

11.

Implications of Big Data for cell biology.

Dolinski K, Troyanskaya OG.

Mol Biol Cell. 2015 Jul 15;26(14):2575-8. doi: 10.1091/mbc.E13-12-0756.

12.

Understanding multicellular function and disease with human tissue-specific networks.

Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG.

Nat Genet. 2015 Jun;47(6):569-76. doi: 10.1038/ng.3259. Epub 2015 Apr 27.

13.

The BioGRID interaction database: 2015 update.

Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M.

Nucleic Acids Res. 2015 Jan;43(Database issue):D470-8. doi: 10.1093/nar/gku1204. Epub 2014 Nov 26.

14.

The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.

Sadowski I, Breitkreutz BJ, Stark C, Su TC, Dahabieh M, Raithatha S, Bernhard W, Oughtred R, Dolinski K, Barreto K, Tyers M.

Database (Oxford). 2013 May 13;2013:bat026. doi: 10.1093/database/bat026. Print 2013.

15.

Systematic curation of protein and genetic interaction data for computable biology.

Dolinski K, Chatr-Aryamontri A, Tyers M.

BMC Biol. 2013 Apr 15;11:43. doi: 10.1186/1741-7007-11-43. Review. No abstract available.

16.

Automating the construction of gene ontologies.

Dolinski K, Botstein D.

Nat Biotechnol. 2013 Jan;31(1):34-5. doi: 10.1038/nbt.2476. No abstract available.

PMID:
23302932
17.

A yeast phenomic model for the gene interaction network modulating CFTR-ΔF508 protein biogenesis.

Louie RJ, Guo J, Rodgers JW, White R, Shah N, Pagant S, Kim P, Livstone M, Dolinski K, McKinney BA, Hong J, Sorscher EJ, Bryan J, Miller EA, Hartman JL 4th.

Genome Med. 2012 Dec 27;4(12):103. doi: 10.1186/gm404.

18.

The BioGRID interaction database: 2013 update.

Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, Stark C, Nixon J, Ramage L, Kolas N, O'Donnell L, Reguly T, Breitkreutz A, Sellam A, Chen D, Chang C, Rust J, Livstone M, Oughtred R, Dolinski K, Tyers M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D816-23. doi: 10.1093/nar/gks1158. Epub 2012 Nov 30.

19.

Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD).

Livstone MS, Oughtred R, Heinicke S, Vernot B, Huttenhower C, Durand D, Dolinski K.

Curr Protoc Bioinformatics. 2011 Mar;Chapter 6:Unit 6.11. doi: 10.1002/0471250953.bi0611s33.

20.

The BioGRID Interaction Database: 2011 update.

Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704. doi: 10.1093/nar/gkq1116. Epub 2010 Nov 11.

21.

Recurated protein interaction datasets.

Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.

Nat Methods. 2009 Dec;6(12):860-1. doi: 10.1038/nmeth1209-860. No abstract available.

PMID:
19935838
22.

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.

23.

Use and misuse of the gene ontology annotations.

Rhee SY, Wood V, Dolinski K, Draghici S.

Nat Rev Genet. 2008 Jul;9(7):509-15. doi: 10.1038/nrg2363. Epub 2008 May 13. Review.

PMID:
18475267
24.

The BioGRID Interaction Database: 2008 update.

Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, Dolinski K, Tyers M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D637-40. Epub 2007 Nov 13.

25.

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.

26.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

Heinicke S, Livstone MS, Lu C, Oughtred R, Kang F, Angiuoli SV, White O, Botstein D, Dolinski K.

PLoS One. 2007 Aug 22;2(8):e766.

27.

Orthology and functional conservation in eukaryotes.

Dolinski K, Botstein D.

Annu Rev Genet. 2007;41:465-507. Review.

PMID:
17678444
28.

Extracirculatory effects of noise of various frequency spectra in humans--effect of pink and blue noise on gastric myoelectrical activity and gastrointestinal passage of nutrients.

Kasicka-Jonderko A, Jonderko K, Dolinski K, Dolinski M, Kaminska M, Szymszal M, Dzielicki M, Blonska-Fajfrowska B.

J Smooth Muscle Res. 2007 Feb;43(1):25-42.

29.

Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains.

Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L.

PLoS One. 2007 Mar 28;2(3):e322.

30.

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.

31.

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis.

Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, Issel-Tarver L, Schwartz K, Sethuraman A, Botstein D, Cherry JM; Saccharomyces Genome Database Project.

Yeast. 2006 Sep;23(12):857-65.

32.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN, Tyers M.

J Biol. 2006;5(4):11. doi: 10.1186/jbiol36. Epub 2006 Jun 8.

33.

Discovery of biological networks from diverse functional genomic data.

Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG.

Genome Biol. 2005;6(13):R114. Epub 2005 Dec 19.

34.

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.

35.

Changing perspectives in yeast research nearly a decade after the genome sequence.

Dolinski K, Botstein D.

Genome Res. 2005 Dec;15(12):1611-9. Review.

36.

How reproducible is cutaneous electrogastrography? An in-depth evidence-based study.

Jonderko K, Kasicka-Jonderko A, Krusiec-Swidergoł B, Dzielicki M, Strój L, Doliński M, Doliński K, Błońska-Fajfrowska B.

Neurogastroenterol Motil. 2005 Dec;17(6):800-9.

PMID:
16336495
37.

Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures.

Brauer MJ, Saldanha AJ, Dolinski K, Botstein D.

Mol Biol Cell. 2005 May;16(5):2503-17. Epub 2005 Mar 9.

38.

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.

39.

Saccharomyces genome database: underlying principles and organisation.

Dwight SS, Balakrishnan R, Christie KR, Costanzo MC, Dolinski K, Engel SR, Feierbach B, Fisk DG, Hirschman J, Hong EL, Issel-Tarver L, Nash RS, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Weng S, Botstein D, Cherry JM.

Brief Bioinform. 2004 Mar;5(1):9-22.

40.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Christie KR, Weng S, Balakrishnan R, Costanzo MC, Dolinski K, Dwight SS, Engel SR, Feierbach B, Fisk DG, Hirschman JE, Hong EL, Issel-Tarver L, Nash R, Sethuraman A, Starr B, Theesfeld CL, Andrada R, Binkley G, Dong Q, Lane C, Schroeder M, Botstein D, Cherry JM.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D311-4.

41.

The Gene Ontology (GO) database and informatics resource.

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61.

42.

A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae).

Troyanskaya OG, Dolinski K, Owen AB, Altman RB, Botstein D.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8348-53. Epub 2003 Jun 25.

43.

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins.

Weng S, Dong Q, Balakrishnan R, Christie K, Costanzo M, Dolinski K, Dwight SS, Engel S, Fisk DG, Hong E, Issel-Tarver L, Sethuraman A, Theesfeld C, Andrada R, Binkley G, Lane C, Schroeder M, Botstein D, Michael Cherry J.

Nucleic Acids Res. 2003 Jan 1;31(1):216-8.

44.

Saccharomyces Genome Database.

Issel-Tarver L, Christie KR, Dolinski K, Andrada R, Balakrishnan R, Ball CA, Binkley G, Dong S, Dwight SS, Fisk DG, Harris M, Schroeder M, Sethuraman A, Tse K, Weng S, Botstein D, Cherry JM.

Methods Enzymol. 2002;350:329-46. No abstract available.

PMID:
12073322
45.

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).

Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM.

Nucleic Acids Res. 2002 Jan 1;30(1):69-72.

46.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

47.

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data.

Ball CA, Jin H, Sherlock G, Weng S, Matese JC, Andrada R, Binkley G, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Schroeder M, Botstein D, Cherry JM.

Nucleic Acids Res. 2001 Jan 1;29(1):80-1.

48.

Integrating functional genomic information into the Saccharomyces genome database.

Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM.

Nucleic Acids Res. 2000 Jan 1;28(1):77-80.

50.

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