The Tri-lnstitutional Training Program in Computational Biology and Medicine (CBM) takes advantage of the outstanding educational and research resources of Cornell University in Ithaca, NY, the Weill Cornell Medical College in New York City, and the Sloan-Kettering Institute (the research arm of the Memorial Sloan- Kettering Cancer Center) to train computational biologists in the interdisciplinary approaches they need to solve the complex problems that characterize biology and medicine. The CBM training environment is designed to address the unique challenges of training scientists in this area and is characterized by: (i) coursework in both quantitative and biological sciences;(ii) research rotations to enable a well-informed thesis topic selection;(iii) journal clubs and research-in-progress series to enhance program cohesion and ensure fluency in relevant disciplines;(iv) thesis research in one of a diverse array of basic to translational computational and experimental laboratories;(v) both quantitative and biological mentorship in order to ensure training balance and breadth;(vi) encouragement to engage in hybrid computational/experimental projects to foster connections between theory and experiment. The enthusiastic support for the CBM program by the Tri-lnstitutional consortium has enabled the program to enroll and support 6 students annually. However, now that the program is well established and entering its sixth year, it is clear that it would benefit from an increase in its most vital component - outstanding students. To that end, the goal of this T32 proposal is to receive funding to increase our annual admission to 9 students. The justifications for such growth include: (i) an unmet demand by CBM faculty for students;(ii) the CBM applicant pool is deep enough to allow for an increase without either lowering quality or decreasing the percentage of admitted domestic students;and (iii) a national need to train more computational biologists. By enabling such growth, T32 funding would aid the CBM program in achieving its mission of training the next generation of scientist to use computational and analytical methods, often integrated with experimental and clinical studies, to solve complex interdisciplinary problems in biology. PERFORMANCE SITE(S) (organization, city, state) PHS 398 (Rev. 04/06) Page 2 Form Page 2 Principal Investigator/Program Director (Last, First, Middle): KEY PERSONNEL. See instructions. Use continuation pages as needed to provide the required information in the format shown below. Start with Principal Investigator(s). List all other key personnel in alphabetical order, last name first. Name eRA Commons User Name Organization Role on Project Christini, David J. dchristini Weill Cornell Med. Coll. Program Director Training Faculty OTHER SIGNIFICANT CONTRIBUTORS Name Gotto, Antonio, M.D., D. Phil. Skorton, David, M.D. Varmus, Harold DeLisi, Charles Kutzko, Philip Small, Gillian Terman, David Organization Weill Cornell Medical College Cornell University-Ithaca Sloan-Kettering Institute Boston University University of Iowa City University of New York Ohio State University Role on Project Executive Steering Committee Executive Steering Committee Executive Steering Committee External Advisory Board External Advisory Board External Advisory Board External Advisory Board Human Embryonic Stem Cells poundJ No D Yes If the proposed project Involves human embryonic stem cells, list below the registration number of the specific cell line(s) from the following list: http://stefncells.nih.QOV/reqistry/index.asp. Usecontinuation pages as needed. If a specific line cannot be referenced at this time, include a statement that one from the Registry will be used. Cell Line PHS 398 (Rev. 04/06) Page 3 Form Page 2-continued Number the following pages consecutively throughout the application. Do not use suffixessuch as 4a, 4b. Principal Investigator/Program Director: Key Personnel cont'd. Name ERA Commons User Name Guckenheimer, John RFG2CORNELL Sander, Chris sanderchris Weinstein, Harel hweinstein Aksay, Emre Eaksay Altan-Bonnet, Gregoire ALTANBOGMSKCC Anderson, Olaf Sparre osparrea Ballon, Douglas DBallon Bao, Zhirong Begg, Colin BEGGCOLIN Bdskey, Adele Boskeya Bustamante, Carlos Campagne, Fabien FCAMPAGNE Clancy, Colleen cclancy Clark, Andrew AC347CORNELL Eliezer, David deliezer Gardner, Daniel dangardner Gilmour, Robert rfg2cornell Klein, Robert kleinrj Lai, Eric Leslie, Christina Linster, Christiane CI243cornell Lipson, Hod Mezey, Jason Michor, Franziska Nirenberg, Sheila NIRENBERG2 Rand, Richard Schwager, Steve Sethna, James Shalloway, David DIS2CORNELL Siepel, Adam Siggia, Eric SIGGIAE Strogatz, Steven van der Meulen, Marjolein MCVANDERMEULEN Victor, Jonathan jdvicto Vilar, Jose Wright, Timothy tmwright Zallen, Jennifer Organization Cornell-Ithaca Sloan-Kettering Institute Weill Cornell Med.Coll. Sloan-Kettering Institute Weill Cornell Med.Coll. Weill Cornell Med.Coll. Sloan-Kettering Institute Sloan-Kettering Institute Weill Cornell Med.Coll. Cornell-Ithaca Weill Cornell Med.Coll. Weill Cornell Med.Coll. Cornell-Ithaca Weill Cornell Med.Coll. Weill Cornell Med.Coll. Cornell-Ithaca Sloan-Kettering Institute Sloan-Kettering Institute Sloan-Kettering Institute Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Sloan-Kettering Institute Weill Cornell Med.Coll. Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Cornell-Ithaca Weill Cornell Med.Coll. Sloan-Kettering Institute Weill Cornell Med.Coll. Sloan-Kettering Institute Christini, David, J. Role on Project Training Faculty; Member, Internal Advisory Committee Training Faculty; Member, Internal Advisory Committee Training Faculty; Member, Internal Advisory Committee Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Training Faculty Institutional Training TOC Program Director/Principal Investigator Christini, David J. Substitute Page (Last, first, middle): Type the name of the program director/principal investigator at the top of each printed page and each continuation page. (For type specifications, see PHS 398 Instructions.) INSTITUTIONAL RESEARCH TRAINING INCLUDING RUTH L. KIRSCHSTEIN NATIONAL RESEARCH SERVICE AWARD TABLE OF CONTENTS (Substitute Page) Page Numbers Face Page (Form Page 1) 1 Description,
| Strobel, Eric J; Yu, Angela M; Lucks, Julius B (2018) High-throughput determination of RNA structures. Nat Rev Genet 19:615-634 |
| Ricketts, Camir; Popic, Victoria; Toosi, Hosein et al. (2018) Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees. Curr Protoc Bioinformatics 62:e49 |
| Mohammed, Jaaved; Flynt, Alex S; Panzarino, Alexandra M et al. (2018) Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res 28:52-65 |
| Carlson, Paul D; Evans, Molly E; Yu, Angela M et al. (2018) SnapShot: RNA Structure Probing Technologies. Cell 175:600-600.e1 |
| Pyenson, Nora C; Gayvert, Kaitlyn; Varble, Andrew et al. (2017) Broad Targeting Specificity during Bacterial Type III CRISPR-Cas Immunity Constrains Viral Escape. Cell Host Microbe 22:343-353.e3 |
| Weizman, Orr-El; Adams, Nicholas M; Schuster, Iona S et al. (2017) ILC1 Confer Early Host Protection at Initial Sites of Viral Infection. Cell 171:795-808.e12 |
| Spencer, Alison K; Schaumberg, Andrew J; Zallen, Jennifer A (2017) Scaling of cytoskeletal organization with cell size inDrosophila. Mol Biol Cell 28:1519-1529 |
| Schaumberg, Andrew J; Sirintrapun, S Joseph; Al-Ahmadie, Hikmat A et al. (2017) DeepScope: Nonintrusive Whole Slide Saliency Annotation and Prediction from Pathologists at the Microscope. Comput Intell Methods Bioinform Biostat (2016) 10477:42-58 |
| Kotini, Andriana G; Chang, Chan-Jung; Chow, Arthur et al. (2017) Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia. Cell Stem Cell 20:315-328.e7 |
| Liang, Siqi; Tippens, Nathaniel D; Zhou, Yaoda et al. (2017) iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations. Genome Biol 18:10 |
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