Kara Dolinski, Ph.D. Director, Genome Databases Group Assistant Director, Lewis-Sigler Institute for Integrative Genomics Princeton University Carl Icahn Laboratory Room 142 Princeton, NJ 08544 [email protected]

Education Duke University: 1993-1998 Ph.D. in Genetics, May 1998.

Carnegie Mellon University: 1988-1992 B.S. Degree with University Honors in Technical Writing and Editing, May, 1992.

Positions and Employment 1992-1993 Lab technician, laboratory of Elizabeth Jones, Carnegie Mellon University 1993-1998 Graduate student, laboratory of Joseph Heitman, Duke University 1998-2003 Curator, Saccharomyces Genome Database, Stanford University 2001-2003 Scientific Programmer and Head Curator, Saccharomyces Genome Database, Stanford University 2003-present Director, Genomic Databases Lewis Sigler Institute for Integrative Genomics, Princeton University 2010-present Assistant Director, Lewis Sigler Institute for Integrative Genomics, Princeton University

Service and Professional Memberships 1994-present Member, Genetics Society of America. Member of the Organizing Committee for Genetics Society of America Yeast Genetics and Molecular Biology meeting, Princeton, 2011. Member of the Organizing Committee for the XXth International Conference on Yeast Genetics and Molecular Biology, Prague, 2001.

2005-present Member, International Biocurator Society; Organized the 1st International Biocurator Meeting, Asilomar Conference Center, Pacific Grove, CA, 2005, which laid the groundwork for the formation of the Biocurator Professional Society.

2005-present Ad-hoc reviewer for NIH proposals under the NHGRI, NCRR, NCATS, and the Office of the Director.

Ongoing Research Support Source: NIH (PI: Tyers, co-Investigator: Dolinski) ID: R01OD010929 Title: BioGRID: An Open Integrated Resource for Biological Interaction Data Total Period: 5/15/07-5/31/2021 Major Goals: We propose to expand the capabilities of BioGRID and Osprey by i) developing advanced network visualization tools, ii) enhancing the BioGRID database’s features and compatibility, iii) curating interactions for additional organisms, iv) curating post-translational modifications and v) construction higher order pathway interactions from gold standard interaction data. Note: M. Tyers at the Samuel Lunenfeld Research Institute in Toronto, Canada is PI and K. Dolinski is co-Investigator, PI on the subcontract at Princeton.

Source: NIH (PI: Garret Fitzgerald) ID: 1U54HL117798 Title: Personalization of Therapeutic Efficacy and Risk Total Period: 7/1/12-6/30/17 Major Goals: The Princeton Curation Core will interact directly with every other Core in this GLUE proposal, serving to facilitate not just data exchange and integration but communication in general across the individual groups. The Curation Core will be responsible for working with the data generators and analysts to combine and integrate these very diverse data to make the sum more powerful than the parts. Specific roles will be data annotation, quality control, and analysis, as well as software tool and interface design and development. Note: Kara Dolinski is the PI for core D, Curation.

Completed Research Support

Source: NIH (PI: Dolinski) ID: R24OD011194 Title: Systematic data curation and integration to link models of human disease Total Period: 9/14/11-7/31/15 Major Goals: We will collect a unique and extensive set of protein and gene interactions from models that are relevant to human disease, as well as their interactions with chemicals (drugs) and their effect on specific functions. These data will allow the prediction of new disease network functions using specialized algorithms, which will lead to a better understanding of human disease and facilitate the discovery of new drugs. Note: M. Tyers at the Samuel Lunenfeld Research Institute in Toronto, Canada is Co- Investigator.

Source: NIH (PI: D. Botstein) ID: P50 GM071508 Title: Center for Quantitative Biology Total Period: 9/1/04-8/31/14 Major Goals: The overarching goal of the proposed Center for Quantitative Biology remains to instantiate at Princeton a research and teaching environment, presented by advances in computation and genomics, to practice a usefully quantitative biological science, sometimes referred to as “systems biology”. Note: This is a multi-investigator grant (29 faculty members). K. Dolinski provides administrative oversight for this grant and also participates in the Computational Core / Bioinformatics projects.

Source: NIH (PI: Tyers, PI on subcontract: Dolinski) ID: R01 RR024031 Title: BioGRID: An Open Resource for Biological Interactions and Network Analysis Period: 03/05/07-02/28/11 Major Goals: Cellular behavior is dictated by complex networks of protein interactions, which are reflected in dense networks of genetic interactions. High throughput determination of interactions and phenotypes affords the potential of systems-level understanding of biological responses. However, these approaches are hampered by a dearth of software tools to manage, integrate and query the wealth of interaction data described in the literature. To fill this gap, we have developed a freely available, public database called the BioGRID (www.thebiogrid.org) that serves as a repository of interaction data and provides the requisite tools that enable researchers to query the data collection and to analyze and visualize interaction networks.

Source: NIH (PI: Blake, PI on subcontract: Dolinski) ID: P41 HG002273 - Subcontract Title: Gene Ontology Consortium Period: 08/01/09-02/28/11 Major Goals: Our objective is to provide the scientific community with a consistent, robust information environment for describing, sharing, integrating and comparing the functional roles of genes within and across all organisms. The Gene Ontology (GO) Consortium is an international collaboration of database and genome annotation groups who have joined together to establish standards for describing gene products and to provide tools and support for the consistent application of these standards for functional annotations that facilitate and enable biological research. The subcontract to Princeton is focused on GO annotation of large protein families, and the identification of orthologs within these families.

Source: NIH (PI: Cherry, PI on subcontract: Dolinski) ID: P41HG001315 - Subcontract Title: Genomic Database for the yeast Saccharomyces Period: 08/01/09-07/31/11 Major Goals: The goal of the Saccharomyces Genome Database (SGD) is to continue the design, development, and implementation of a database containing comprehensive annotated information about the genome of the budding yeast, . The subcontract to Princeton focuses on the design and implementation of a more powerful expression analysis tool, and the continuing collection of functional genomics data sets.

Source: NIH (PI: Botstein, co-Investigator: Dolinski) ID: R01 HG003471 Title: Integrating and Disseminating Functional Genomics Data Period: 11/1/04-10/31/08 Major Goals: To devise and implement systems that make possible continuing integration of the information contained within genomic data sets, including gene expression, two-hybrid, synthetic lethality, and systematic deletion studies and to make integrated information accessible to the research community through the Saccharomyces Genome Database (SGD) and later in the Generic Model Organism Database (GMOD).

Publications1-53

1 Islamaj Dogan, R., Kim, S., Chatr-Aryamontri, A., Chang, C. S., Oughtred, R., Rust, J., Wilbur, W. J., Comeau, D. C., Dolinski, K. & Tyers, M. The BioC- BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. Database (Oxford). 2017;2017. PMCID: PMC5225395. 2 Chatr-Aryamontri, A., Oughtred, R., Boucher, L., Rust, J., Chang, C., Kolas, N. K., O'Donnell, L., Oster, S., Theesfeld, C., Sellam, A., Stark, C., Breitkreutz, B. J., Dolinski, K. & Tyers, M. The BioGRID interaction database: 2017 update. Nucleic Acids Res. 2017;45(D1):D369-D379. PMCID: PMC5210573. 3 Sun, S., Yang, F., Tan, G., Costanzo, M., Oughtred, R., Hirschman, J., Theesfeld, C. L., Bansal, P., Sahni, N., Yi, S., Yu, A., Tyagi, T., Tie, C., Hill, D. E., Vidal, M., Andrews, B. J., Boone, C., Dolinski, K. & Roth, F. P. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res. 2016;26(5):670-680. PMCID: PMC4864455. 4 Oughtred, R., Chatr-aryamontri, A., Breitkreutz, B. J., Chang, C. S., Rust, J. M., Theesfeld, C. L., Heinicke, S., Breitkreutz, A., Chen, D., Hirschman, J., Kolas, N., Livstone, M. S., Nixon, J., O'Donnell, L., Ramage, L., Winter, A., Reguly, T., Sellam, A., Stark, C., Boucher, L., Dolinski, K. & Tyers, M. Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. Cold Spring Harb Protoc. 2016;2016(1):pdb prot088880. 5 Oughtred, R., Chatr-aryamontri, A., Breitkreutz, B. J., Chang, C. S., Rust, J. M., Theesfeld, C. L., Heinicke, S., Breitkreutz, A., Chen, D., Hirschman, J., Kolas, N., Livstone, M. S., Nixon, J., O'Donnell, L., Ramage, L., Winter, A., Reguly, T., Sellam, A., Stark, C., Boucher, L., Dolinski, K. & Tyers, M. BioGRID: A Resource for Studying Biological Interactions in Yeast. Cold Spring Harb Protoc. 2016;2016(1):pdb top080754. 6 Kim, S., Islamaj Dogan, R., Chatr-Aryamontri, A., Chang, C. S., Oughtred, R., Rust, J., Batista-Navarro, R., Carter, J., Ananiadou, S., Matos, S., Santos, A., Campos, D., Oliveira, J. L., Singh, O., Jonnagaddala, J., Dai, H. J., Su, E. C., Chang, Y. C., Su, Y. C., Chu, C. H., Chen, C. C., Hsu, W. L., Peng, Y., Arighi, C., Wu, C. H., Vijay-Shanker, K., Aydin, F., Husunbeyi, Z. M., Ozgur, A., Shin, S. Y., Kwon, D., Dolinski, K., Tyers, M., Wilbur, W. J. & Comeau, D. C. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database (Oxford). 2016;2016. PMCID: PMC5009341. 7 Greene, C. S., Krishnan, A., Wong, A. K., Ricciotti, E., Zelaya, R. A., Himmelstein, D. S., Zhang, R., Hartmann, B. M., Zaslavsky, E., Sealfon, S. C., Chasman, D. I., FitzGerald, G. A., Dolinski, K., Grosser, T. & Troyanskaya, O. G. Understanding multicellular function and disease with human tissue-specific networks. Nat Genet. 2015;47(6):569-576. PMCID: PMC4828725. 8 Dolinski, K. & Troyanskaya, O. G. Implications of Big Data for cell biology. Mol Biol Cell. 2015;26(14):2575-2578. PMCID: PMC4501356. 9 Chatr-Aryamontri, A., Breitkreutz, B. J., 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, M. S., Dolinski, K. & Tyers, M. The BioGRID interaction database: 2015 update. Nucleic Acids Res. 2015;43(Database issue):D470-478. PMCID: PMC4383984. 10 Sadowski, I., Breitkreutz, B. J., Stark, C., Su, T. C., Dahabieh, M., Raithatha, S., Bernhard, W., Oughtred, R., Dolinski, K., Barreto, K. & Tyers, M. The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. Database (Oxford). 2013;2013:bat026. PMCID: PMC3653121. 11 Dolinski, K., Chatr-Aryamontri, A. & Tyers, M. Systematic curation of protein and genetic interaction data for computable biology. BMC Biol. 2013;11:43. PMCID: PMC3626917. 12 Dolinski, K. & Botstein, D. Automating the construction of gene ontologies. Nat Biotechnol. 2013;31(1):34-35. 13 Chatr-Aryamontri, A., Breitkreutz, B. J., 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. The BioGRID interaction database: 2013 update. Nucleic Acids Res. 2013;41(Database issue):D816-823. PMCID: PMC3531226. 14 Louie, R. J., Guo, J., Rodgers, J. W., White, R., Shah, N., Pagant, S., Kim, P., Livstone, M., Dolinski, K., McKinney, B. A., Hong, J., Sorscher, E. J., Bryan, J., Miller, E. A. & Hartman, J. L. t. A yeast phenomic model for the gene interaction network modulating CFTR-DeltaF508 protein biogenesis. Genome Med. 2012;4(12):103. PMCID: PMC3906889. 15 Stark, C., Breitkreutz, B. J., Chatr-Aryamontri, A., Boucher, L., Oughtred, R., Livstone, M. S., Nixon, J., Van Auken, K., Wang, X., Shi, X., Reguly, T., Rust, J. M., Winter, A., Dolinski, K. & Tyers, M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011;39(Database issue):D698-704. PMCID: PMC3013707. 16 Livstone, M. S., Oughtred, R., Heinicke, S., Vernot, B., Huttenhower, C., Durand, D. & Dolinski, K. Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD). Curr Protoc Bioinformatics. 2011;Chapter 6:Unit 6 11. PMCID: PMC3763948. 17 Engel, S. R., Balakrishnan, R., Binkley, G., Christie, K. R., Costanzo, M. C., Dwight, S. S., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Hong, E. L., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R., Oughtred, R., Park, J., Skrzypek, M. S., Weng, S., Wong, E. D., Dolinski, K., Botstein, D. & Cherry, J. M. Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res. 2010;38(Database issue):D433-436. PMCID: PMC2808950. 18 Salwinski, L., Licata, L., Winter, A., Thorneycroft, D., Khadake, J., Ceol, A., Aryamontri, A. C., Oughtred, R., Livstone, M., Boucher, L., Botstein, D., Dolinski, K., Berardini, T., Huala, E., Tyers, M., Eisenberg, D., Cesareni, G. & Hermjakob, H. Recurated protein interaction datasets. Nat Methods. 2009;6(12):860-861. 19 Rhee, S. Y., Wood, V., Dolinski, K. & Draghici, S. Use and misuse of the gene ontology annotations. Nat Rev Genet. 2008;9(7):509-515. 20 Hong, E. L., Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Krieger, C. J., Livstone, M. S., Miyasato, S. R., Nash, R. S., Oughtred, R., Skrzypek, M. S., Weng, S., Wong, E. D., Zhu, K. K., Dolinski, K., Botstein, D. & Cherry, J. M. Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008;36(Database issue):D577-581. PMCID: PMC2238894. 21 Breitkreutz, B. J., Stark, C., Reguly, T., Boucher, L., Breitkreutz, A., Livstone, M., Oughtred, R., Lackner, D. H., Bahler, J., Wood, V., Dolinski, K. & Tyers, M. The BioGRID Interaction Database: 2008 update. Nucleic Acids Res. 2008;36(Database issue):D637-640. PMCID: PMC2238873. 22 Schacherer, J., Ruderfer, D. M., Gresham, D., Dolinski, K., Botstein, D. & Kruglyak, L. Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One. 2007;2(3):e322. PMCID: PMC1829191. 23 Nash, R., Weng, S., Hitz, B., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Livstone, M. S., Oughtred, R., Park, J., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Dolinski, K., Botstein, D. & Cherry, J. M. Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res. 2007;35(Database issue):D468-471. PMCID: PMC1669759. 24 Heinicke, S., Livstone, M. S., Lu, C., Oughtred, R., Kang, F., Angiuoli, S. V., White, O., Botstein, D. & Dolinski, K. The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. PLoS One. 2007;2(8):e766. PMCID: PMC1942082. 25 Dolinski, K. & Botstein, D. Orthology and functional conservation in eukaryotes. Annu Rev Genet. 2007;41:465-507. 26 Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hon, G. C., Myers, C. L., Parsons, A., Friesen, H., Oughtred, R., Tong, A., Stark, C., Ho, Y., Botstein, D., Andrews, B., Boone, C., Troyanskya, O. G., Ideker, T., Dolinski, K., Batada, N. N. & Tyers, M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006;5(4):11. PMCID: PMC1561585. 27 Hirschman, J. E., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hong, E. L., Livstone, M. S., Nash, R., Park, J., Oughtred, R., Skrzypek, M., Starr, B., Theesfeld, C. L., Williams, J., Andrada, R., Binkley, G., Dong, Q., Lane, C., Miyasato, S., Sethuraman, A., Schroeder, M., Thanawala, M. K., Weng, S., Dolinski, K., Botstein, D. & Cherry, J. M. Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res. 2006;34(Database issue):D442-445. PMCID: PMC1347479. 28 Fisk, D. G., Ball, C. A., Dolinski, K., Engel, S. R., Hong, E. L., Issel-Tarver, L., Schwartz, K., Sethuraman, A., Botstein, D., Cherry, J. M. & Saccharomyces Genome Database, P. Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast. 2006;23(12):857-865. PMCID: PMC3040122. 29 Myers, C. L., Robson, D., Wible, A., Hibbs, M. A., Chiriac, C., Theesfeld, C. L., Dolinski, K. & Troyanskaya, O. G. Discovery of biological networks from diverse functional genomic data. Genome Biol. 2005;6(13):R114. PMCID: PMC1414113. 30 Dolinski, K. & Botstein, D. Changing perspectives in yeast research nearly a decade after the genome sequence. Genome Res. 2005;15(12):1611-1619. 31 Brauer, M. J., Saldanha, A. J., Dolinski, K. & Botstein, D. Homeostatic adjustment and metabolic remodeling in glucose-limited yeast cultures. Mol Biol Cell. 2005;16(5):2503-2517. PMCID: PMC1087253. 32 Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R., Oughtred, R., Skrzypek, M., Theesfeld, C. L., Binkley, G., Dong, Q., Lane, C., Sethuraman, A., Weng, S., Botstein, D. & Cherry, J. M. Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Res. 2005;33(Database issue):D374-377. PMCID: PMC539977. 33 Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., Richter, J., Rubin, G. M., Blake, J. A., Bult, C., Dolan, M., Drabkin, H., Eppig, J. T., Hill, D. P., Ni, L., Ringwald, M., Balakrishnan, R., Cherry, J. M., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R. S., Sethuraman, A., Theesfeld, C. L., Botstein, D., Dolinski, K., Feierbach, B., Berardini, T., Mundodi, S., Rhee, S. Y., Apweiler, R., Barrell, D., Camon, E., Dimmer, E., Lee, V., Chisholm, R., Gaudet, P., Kibbe, W., Kishore, R., Schwarz, E. M., 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, C. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32(Database issue):D258-261. PMCID: PMC308770. 34 Dwight, S. S., Balakrishnan, R., Christie, K. R., Costanzo, M. C., Dolinski, K., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J., Hong, E. L., Issel-Tarver, L., Nash, R. S., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Weng, S., Botstein, D. & Cherry, J. M. Saccharomyces genome database: underlying principles and organisation. Brief Bioinform. 2004;5(1):9-22. PMCID: PMC3037832. 35 Christie, K. R., Weng, S., Balakrishnan, R., Costanzo, M. C., Dolinski, K., Dwight, S. S., Engel, S. R., Feierbach, B., Fisk, D. G., Hirschman, J. E., Hong, E. L., Issel-Tarver, L., Nash, R., Sethuraman, A., Starr, B., Theesfeld, C. L., Andrada, R., Binkley, G., Dong, Q., Lane, C., Schroeder, M., Botstein, D. & Cherry, J. M. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2004;32(Database issue):D311-314. PMCID: PMC308767. 36 Weng, S., Dong, Q., Balakrishnan, R., Christie, K., Costanzo, M., Dolinski, K., Dwight, S. S., Engel, S., Fisk, D. G., Hong, E., Issel-Tarver, L., Sethuraman, A., Theesfeld, C., Andrada, R., Binkley, G., Lane, C., Schroeder, M., Botstein, D. & Michael Cherry, J. Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Res. 2003;31(1):216-218. PMCID: PMC165501. 37 Troyanskaya, O. G., Dolinski, K., Owen, A. B., Altman, R. B. & Botstein, D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci U S A. 2003;100(14):8348-8353. PMCID: PMC166232. 38 Issel-Tarver, L., Christie, K. R., Dolinski, K., Andrada, R., Balakrishnan, R., Ball, C. A., Binkley, G., Dong, S., Dwight, S. S., Fisk, D. G., Harris, M., Schroeder, M., Sethuraman, A., Tse, K., Weng, S., Botstein, D. & Cherry, J. M. Saccharomyces Genome Database. Methods Enzymol. 2002;350:329-346. 39 Dwight, S. S., Harris, M. A., Dolinski, K., Ball, C. A., Binkley, G., Christie, K. R., Fisk, D. G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., Botstein, D. & Cherry, J. M. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 2002;30(1):69-72. PMCID: PMC99086. 40 Ball, C. A., Jin, H., Sherlock, G., Weng, S., Matese, J. C., Andrada, R., Binkley, G., Dolinski, K., Dwight, S. S., Harris, M. A., Issel-Tarver, L., Schroeder, M., Botstein, D. & Cherry, J. M. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2001;29(1):80-81. PMCID: PMC29796. 41 Ball, C. A., Dolinski, K., Dwight, S. S., Harris, M. A., Issel-Tarver, L., Kasarskis, A., Scafe, C. R., Sherlock, G., Binkley, G., Jin, H., Kaloper, M., Orr, S. D., Schroeder, M., Weng, S., Zhu, Y., Botstein, D. & Cherry, J. M. Integrating functional genomic information into the Saccharomyces genome database. Nucleic Acids Res. 2000;28(1):77-80. PMCID: PMC102447. 42 Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M. & Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-29. PMCID: PMC3037419. 43 Scholz, C., Maier, P., Dolinski, K., Heitman, J. & Schmid, F. X. R73A and H144Q mutants of the yeast mitochondrial cyclophilin Cpr3 exhibit a low prolyl isomerase activity in both peptide and protein-folding assays. FEBS Lett. 1999;443(3):367- 369. 44 Dolinski, K. J. & Heitman, J. Hmo1p, a high mobility group 1/2 homolog, genetically and physically interacts with the yeast FKBP12 prolyl isomerase. Genetics. 1999;151(3):935-944. PMCID: PMC1460526. 45 Chervitz, S. A., Hester, E. T., Ball, C. A., Dolinski, K., Dwight, S. S., Harris, M. A., Juvik, G., Malekian, A., Roberts, S., Roe, T., Scafe, C., Schroeder, M., Sherlock, G., Weng, S., Zhu, Y., Cherry, J. M. & Botstein, D. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Res. 1999;27(1):74-78. PMCID: PMC148101. 46 Dolinski, K. J., Cardenas, M. E. & Heitman, J. CNS1 encodes an essential p60/Sti1 homolog in Saccharomyces cerevisiae that suppresses cyclophilin 40 mutations and interacts with Hsp90. Mol Cell Biol. 1998;18(12):7344-7352. PMCID: PMC109316. 47 Dolinski, K., Ball, C. A., Chervitz, S. A., Dwight, S. S., Harris, M. A., Roberts, S., Roe, T., Cherry, J. M. & Botstein, D. Expanding yeast knowledge online. Yeast. 1998;14(16):1453-1469. PMCID: PMC3037831. 48 Chervitz, S. A., Aravind, L., Sherlock, G., Ball, C. A., Koonin, E. V., Dwight, S. S., Harris, M. A., Dolinski, K., Mohr, S., Smith, T., Weng, S., Cherry, J. M. & Botstein, D. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science. 1998;282(5396):2022-2028. PMCID: PMC3057080. 49 Scholz, C., Schindler, T., Dolinski, K., Heitman, J. & Schmid, F. X. Cyclophilin active site mutants have native prolyl isomerase activity with a protein substrate. FEBS Lett. 1997;414(1):69-73. 50 Dolinski, K., Scholz, C., Muir, R. S., Rospert, S., Schmid, F. X., Cardenas, M. E. & Heitman, J. Functions of FKBP12 and mitochondrial cyclophilin active site residues in vitro and in vivo in Saccharomyces cerevisiae. Mol Biol Cell. 1997;8(11):2267-2280. PMCID: PMC25707. 51 Dolinski, K., Muir, S., Cardenas, M. & Heitman, J. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1997;94(24):13093- 13098. PMCID: PMC24268. 52 Hemenway, C. S., Dolinski, K., Cardenas, M. E., Hiller, M. A., Jones, E. 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