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 model organism 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, Saccharomyces cerevisiae. 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.,