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Items: 23

1.

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk.

Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG.

Nat Genet. 2019 Jun;51(6):973-980. doi: 10.1038/s41588-019-0420-0. Epub 2019 May 27.

PMID:
31133750
2.

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
3.

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.

Zhou J, Theesfeld CL, Yao K, Chen KM, Wong AK, Troyanskaya OG.

Nat Genet. 2018 Aug;50(8):1171-1179. doi: 10.1038/s41588-018-0160-6. Epub 2018 Jul 16.

4.

Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder.

Krishnan A, Zhang R, Yao V, Theesfeld CL, Wong AK, Tadych A, Volfovsky N, Packer A, Lash A, Troyanskaya OG.

Nat Neurosci. 2016 Nov;19(11):1454-1462. doi: 10.1038/nn.4353. Epub 2016 Aug 1.

5.

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.

6.

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.

7.

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.

8.

Insulin-induced gene protein (INSIG)-dependent sterol regulation of Hmg2 endoplasmic reticulum-associated degradation (ERAD) in yeast.

Theesfeld CL, Hampton RY.

J Biol Chem. 2013 Mar 22;288(12):8519-30. doi: 10.1074/jbc.M112.404517. Epub 2013 Jan 10.

9.

The sterol-sensing domain (SSD) directly mediates signal-regulated endoplasmic reticulum-associated degradation (ERAD) of 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase isozyme Hmg2.

Theesfeld CL, Pourmand D, Davis T, Garza RM, Hampton RY.

J Biol Chem. 2011 Jul 29;286(30):26298-307. doi: 10.1074/jbc.M111.244798. Epub 2011 May 31.

10.

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.

11.

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.

12.

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.

13.

Opposing roles for actin in Cdc42p polarization.

Irazoqui JE, Howell AS, Theesfeld CL, Lew DJ.

Mol Biol Cell. 2005 Mar;16(3):1296-304. Epub 2004 Dec 22.

14.

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.

15.

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.

16.

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.

17.

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.

18.

A monitor for bud emergence in the yeast morphogenesis checkpoint.

Theesfeld CL, Zyla TR, Bardes EG, Lew DJ.

Mol Biol Cell. 2003 Aug;14(8):3280-91. Epub 2003 May 3.

19.

Determinants of Swe1p degradation in Saccharomyces cerevisiae.

McMillan JN, Theesfeld CL, Harrison JC, Bardes ES, Lew DJ.

Mol Biol Cell. 2002 Oct;13(10):3560-75.

20.

Septin-dependent assembly of a cell cycle-regulatory module in Saccharomyces cerevisiae.

Longtine MS, Theesfeld CL, McMillan JN, Weaver E, Pringle JR, Lew DJ.

Mol Cell Biol. 2000 Jun;20(11):4049-61.

21.

The morphogenesis checkpoint in Saccharomyces cerevisiae: cell cycle control of Swe1p degradation by Hsl1p and Hsl7p.

McMillan JN, Longtine MS, Sia RA, Theesfeld CL, Bardes ES, Pringle JR, Lew DJ.

Mol Cell Biol. 1999 Oct;19(10):6929-39.

22.

The role of actin in spindle orientation changes during the Saccharomyces cerevisiae cell cycle.

Theesfeld CL, Irazoqui JE, Bloom K, Lew DJ.

J Cell Biol. 1999 Sep 6;146(5):1019-32.

23.

Involvement of integrins alpha v beta 3 and alpha v beta 5 in ocular neovascular diseases.

Friedlander M, Theesfeld CL, Sugita M, Fruttiger M, Thomas MA, Chang S, Cheresh DA.

Proc Natl Acad Sci U S A. 1996 Sep 3;93(18):9764-9.

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