T32-Funded Tri-Institutional Training Program in Computational Biology
The Tri-Institutional Training Program in Computational Biology and Medicine (CBM T32), funded by the National Institute of General Medical Sciences (NIGMS) of the NIH is a partnership of Cornell University in Ithaca, NY (CU-I), Weill Cornell Medicine in New York City (WCM), and Memorial Sloan-Kettering Cancer Center, in New York City (MSK). CBM trains computational biologists in the approaches they need to solve complex interdisciplinary biomedical problems. Established in 2003, this PhD Program has an expanding record of training success, including timely graduation and a strong record of placing graduates in research-related careers both in and outside academia. Support from the NIH T32 began in July 2009 and the grant is currently in its 10th year of support.
- Coursework in both quantitative and biological sciences;
- Research rotations to enable a well-informed thesis topic selection;
- Mentored thesis research in one of a diverse array of basic to translational laboratories;
- Opportunities for hybrid computational and research projects;
- Trainee Research-in-Progress seminar series to enhance program cohesion, foster fluency in relevant disciplines, and provide opportunities for scientific presentation practice;
- Training and mentorship in performing rigorous and reproducible scientific research;
- Programmatic enrichment activities, including an annual offsite retreat, lunches with visiting seminar speakers, fellowship and manuscript writing training, and annual refreshers in RCR and reproducible research practices;
- Active guidance and mentoring via annual formal meetings with program co-Directors, biannual thesis committee meetings that include career discussions, and annual IDPs;
- Exposure to various career paths for successful transition into the biomedical research workforce.
Expertise of Program Faculty
The 46 multidisciplinary participating faculty on the CBM T32 Training Grant are drawn from several departments at the three institutions. Their appointments to the CBM graduate faculty require the review and approval of the Tri-I Steering Committee. Criteria include the following:
- Have an existing appointment in a graduate field of the Weill Cornell Graduate School and/or Cornell University-Ithaca;
- Research interests fit into the major scientific categories that are the focus of the CBM program;
- Willingness to participate in teaching activities (including design of courses); participate actively in annual recruitment events; serve on program committees;
- Resources to fund a graduate student from grants or other laboratory support;
- Provide an environment that is conducive to effective mentoring of students and devote sufficient time and resources to assure a positive training experience;
- Offer guidance on career development and give trainees opportunities for networking at scientific conferences and other venues.
The major research interests of the CBM T32 faculty are included in five major categories listed below. Faculty appointments are from each of the Tri-I participating campuses:
Cancer Biology and Genomics
Large-scale and cutting-edge precision oncology efforts make the CBMa program a leader in cancer genomics and computational oncology:
Michael Berger (MSK) leads technological and computational developments for MSKIMPACT, the clinical sequencing assay that has now been deployed in over 18K tumors.
Olivier Elemento (WCM)develops computational methods for genomic, transcriptomic, and epigenomic analyses in hematopoietic and solid tumors.
Marcin Imielinski (WCM) develops novel algorithmic methods to understand structural variation in cancer genomes.
Alex Kentsis (MSK) is a cancer biologist and pediatric oncologist whose research leverages proteomics and functional genomics to improve anti-cancer therapies.
Ekta Khurana (WCM) develops computational approaches to predict the functional consequences of non-coding somatic variants in cancer genomes.
Dan Landau (WCM)is a computational biologist and oncologist who develops algorithmic approaches to study tumor evolution.
Elli Papaemmanuil (MSK) uses computational strategies to study how the genetic and clonal architecture of leukemias dictate clinical phenotype and outcome.
Nikolaus Schultz (MSK)leads the scientific and engineering team that develops the cBioPortal, one of the most widely used resources in cancer genomics.
Sohrab Shah (MSK) is a leading expert in computational cancer genomics and tumor evolution.
Barry Taylor (MSK) studies how somatic alterations in cancer genomes contribute to tumor phenotype and response to therapy.
Genomics and Gene Regulation
Development of computational and genomic strategies to dissect gene regulation, cellular phenotypes, and the genetics of human disease are major research strengths of the CBM program:
Ilana Brito (CU-I) uses both computational and experimental strategies to study the human microbiome and its impact on human health.
Andrew Clark (CU-I) is an internationally known population geneticist who studies the genetic basis of complex traits.
Charles Danko(CU-I)studies regulatory genomics through a combination of statistical modeling and the development of novel next generation sequencing assays.
Iwijn De Vlaminck (CU-I) develops novel measurement strategies for cell-free DNA and for single cell analyses.
Zhenglong Gu (CU-I) employs wet and dry lab activities to study the genetics of mitochondrial DNA in human adaptation and disease.
Iman Hajirasouliha (WCM) develops novel algorithmic and machine learning methods for genomics, metagenomics, and cancer genomics.
Scott Keeney (MSK) uses genomic and computational strategies to map molecular events in meiotic recombination.
AmnonKoren (CU-I) uses genomic approaches to study DNA replication timing and mutagenesis.
Eric Lai (MSK) explores genome-wide methods to study the role of small non-coding RNAs in developmental patterning.
Christina Leslie (MSK)develops machine learning and computational strategies to decipher the global regulation of gene expression in mammalian cells.
John Lis (CU-I)is studying the structure and regulation of gene promoters and develops novel genome-wide assays to dissect transcriptional regulation.
Christopher Mason (WCM) is a genomicist who deploys next-generation sequencing technologies to diverse problems in human disease, epigenomics and epitranscriptomics, metagenomics, and genomic analysis in space.
Christine Mayr (MSK)is molecular and cell biologist and a leading expert on alternative cleavage and polyadenylation and its functional consequences.
Philipp Messer (CU-I) develops novel computational and analytical approaches in evolutionary biology and population genetics.
Jason Mezey (CU-I & WCM)is a statistician and computational genomicist who studies the genetics and evolution of complex phenotypes and human disease.
Dana Pe’er (MSK) is a world-leading expert on the analysis of single cell transcriptomic and proteomic data and a key leader in the global Human Cell Atlas project.
Praveen Sethupathy (CU-I) uses experimental and computational strategies to study the role of non-coding RNAs in metabolic disease.
Andrea Ventura (MSK)is a cancer biologist with deep expertise in microRNA biology and CRISPR/Cas genome editing.
Amy Williams (CU-I) develops computational methods to study human genetic variation and evolution and the genetic basis of human disease.
Quantitative and Systems Biology
Analysis of the organization of cells into spatial structures, tissues and organs, involving quantitative experiments, mathematical modeling, and biological image analysis:
Zhirong Bao (MSK)uses 3D time-lapse microscopy to study cell dynamics, morphogenesis, and gene expression in the developing worm embryo.
David Christini (WCM)studies cardiac electrophysiological dynamics from the cellular to organ level using both computational and experimental approaches.
Thomas Fuchs (MSK)is an innovator in computational pathology, which seeks to use machine learning to automate and improve the analysis of pathology images.
Joao Xavier (MSK) uses quantitative experimental and computational methods to study the community behavior of bacteria, the spatial organization of tumors, and the microbiome.
Jennifer Zallen (MSK) is a developmental biologist who studies the generation of tissue structure through the collective behavior of cells. (HHMI Investigator)
Computational modeling and analysis tools to study the function of neurons and the brain is a vibrant area of CBM research, and one that interdigitates with several other program areas, from genomics to biophysics:
Emre Aksay (WCM) uses computational and experimental approaches to study neuronal temporal integration and its role in sensorimotor transformations, short-term memory behaviors, and decision-making problems. http://physiology.med.cornell.edu/faculty/profile.php?id=aksay
Daniel Gardner (WCM)focuses on the development of computational global resources in neuroinformatics.
Samie Jaffrey (WCM) utilizes experimental and computational approaches to study epitranscriptomic modification mRNA in neurons.
Nicholas Schiff (MSK) is a physician scientist who uses time series and circuit analysis methodologies to analyze patient records to illuminate the process of recovery of consciousness following brain injuries.
Hagen Tilgner (WCM)uses next-generation transcriptomics to study the brain and its diseases.
Jonathan Victor (WCM)is a physician scientist who combines mathematical, computational, and experimental approaches to study sensory processing.
Structural Biology & Biophysics
Computational and experimental studies of protein structure/function and protein-protein interactions are activities represented within this theme:
Olaf Anderson (WCM) studies the structure and function of ion channels and interactions between proteins and lipid bilayers. http://physiology.med.cornell.edu/faculty/profile.php?id=andersen
Scott Blanchard (WCM) studies structure/function relationships in macromolecular assemblies, including the ribosome and integral membrane proteins, in particular using innovative single molecule fluorescence techniques.
John Chodera (MSK) uses rigorous physical models to study the effect of small molecular therapeutics on biomolecular macromolecules and to understand the functional and therapeutic consequences of somatic mutations.
David Eliezer (WCM) applies NMR spectroscopy to problems in non-native structural biology, including in molecular aggregations involved in neurodegenerative disease.
Harel Weinstein (WCM) develops and applies methods in computational biophysics to study diverse biological processes triggered by molecular recognition and leading to signal transduction.
Haiyuan Yu (CU-I) uses high throughput experimental and computational strategies to map and model the protein-protein interactome.
CBM T32 Program Activities for Trainees
- Annual symposium: Students organize an annual CBM symposium/retreat that brings together faculty and students from the three institutions. The 2-day event features an invited keynote speaker (selected and invited by students), oral presentations by senior students, posters by junior students, and student and faculty sessions to discuss programmatic issues. In addition to offering students an opportunity to present their work in a formal scientific forum to their peers and faculty, the symposium serves as a vehicle for cross-campus student and faculty interactions to help build program cohesion. It also offers those students interested in organization and leadership a chance to do so, as they organize the entire program.
- Research-in-Progress series: Students are required to attend the CBM Research-in-Progress series, in which students in their research years present their work to their peers. These take place about once a month during the academic year. In addition to keeping students informed of their peers’ projects and providing the presenters with useful feedback for their research, these sessions are useful in helping students develop the presentation skills so critical to success in science. Importantly, these sessions are videoconferenced between Ithaca and NYC to maintain cohesion between students at the two locations.
- Journal clubs and Seminar series: CBM students attend journal clubs affiliated with their individual laboratories and/or departments. There are numerous seminar series at the three institutions for the students to attend. Listed below are a few that have computational biology focuses (there are many others relevant to particular biological interest areas):
- Cornell Biophysics Colloquia (CU-I)
- Problems and Perspectives in Computational Molecular Biology (CU-I)
- Tri-I NYC Computational Biology Seminar Series (WCMC & SKI)
- Institute for Computational Biology Seminar Series (WCMC)
- Physiology, Biophysics, and Systems Biology Seminar Series (WCMC & SKI)
- Systems Biology Discussion Group at the New York Academy of Sciences (NYC)
CBM 2T32GM083937 Appointees
July 1, 2009-June 30, 2019
|Dana Pe’er||Integrative spatial and time course models for single cell RNA-seq data|
|Christopher Mason||Validation of targeted exome capture protocols. Single cell sequencing and analysis of AML/MDS patient samples. Analysis of whole genome essentiality screens in cancer cell lines.|
|Christopher Mason||Developing best practices for analyzing meta-genomic data; build web interfact to visualize data|
|Christina Leslie||Mutations in FOXA1 identified in patient cohorts and recapitulated in mouse prostate organoids.|
|Christina Mayr||Single-cell landscape of differential polyadenylation site utilization|
|Olivier Elemento||Quantitative modeling for drug development and therapeutic target discovery|
|Christina Leslie; Andrea Ventura||Examining gene expression and regulation in mucosal associated in variant T cells; using CRISPR
screens to evaluate the function of topologically associating domains.
|Dan Landau||Development of computational and experimental genomic tools to investigate the phenomenon of cancer evolution. Awarded a NYSTEM fellowship, October 2018|
|Seidman, Daniel||7/1/18-6/30/19||Amy Williams||Designing tool for construction of phylogenetic trees including structural variant mutations and for fast inference of IBD Segments in Unphased Data|
|Kim, Minsoo||7/1/17-6/30/18||Sohrab Shah||Characterize variants in mtDNA of single cell whole genome sequenced ovarian and breast cancers using Direct Library Preparation+ method|
|Marderstein, Andrew||7/1/17-6/30/18||Andrew Clark; Olivier Elemento||Development of statistical and computational methods for understanding the genetic basis of complex phenotypes|
|Gyan, Kofi||7/1/16-6/30/17||Marcin Imielinski; David Lyden||Leveraging the transcriptome and epigenome to infer cell type of origin.
Currently funded by an NSF fellowship
|Appointees||Appointment Period(s)||Mentor(s)||Research Interests
|Elkhader, Jamal||7/1/15-6/30/16||Olivier Elemento||Application of machine learning methods in identifying drug indications|
|Gorelick, Alexander||7/1/15-6/30/16||Barry Taylor||Toward understanding the interaction among multiple co-incident mutations in cancer pathogenesis and therapy|
|La, Konnor||7/1/15-6/30/16||Nikolaus Schultz||Dysfunctional mitochondria and their role in cancer progression|
|Yu, Angela||7/1/15-6/30/16||Julius Lucks||Computationally reconstructing RNA folding pathways from cotranscriptional SHAPE-seq|
|Behr, Julie||7/1/14-6/30/15||Marcin Imielinski||Chromatin conformation changes in rearranged cancer genomes|
|Doane, Ashley||7/1/14-6/30/15||Olivier Elemento||Transcriptional reprogramming in B-cell development and lymphomagenesis.
Currently funded by an NIH F31 fellowship
|Fass, Joshua||7/1/14-6/30/15||John Chodera||Active sampling methods for drug design|
|Thomas Fuchs||Genotype and histological phenotype relationships in cancer, with automated therapy optimization.
Currently funded by an NIH F31 fellowship
|Tippens, Nathaniel||7/1/14-6/30/15||John Lis; Haiyuan Yu||Functional sequence architecture of transcribed regulatory elements|
|Torok, Justin||7/1/14-6/30/15||Ashish Raj/Yi Wang||Linear model of dementia progression to determine the brain regions of atrophy origination|
|Appointees 7/1/09-6/30/14||Year PhD Awarded||Mentor||Current Position|
|Barker, Brandon||2014||Zhenglong Gu||Computational Scientist, Center for Advanced Computing, Cornell University|
|Behr, Julie||TBD||Marcin Imielinski||Current Student|
|Bomash, Illya||2013||Sheila Nirenberg||Managing Data Scientist, Knewton, Inc.|
|Braiman, Chananel||2018||Nicholas Schiff||TBA|
|Brooks, Sarah||Terminal Masters Degree 2018||Jason Mezey||TBA|
|Carty, Mark||2016||Christina Leslie||Postdoctoral Fellow, Princeton University|
|Cerami, Ethan||2011||Chris Sander||Director, Knowledge Systems Group, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute|
|Chang, Diana||2014||Keinan, Alon||Scientist, Bioinformatics, Genentech|
|Cheng, Yu-Kang||2012||Franziska Michor||Software Engineer, Google|
|Davidson, Natalie||Thesis Defense: 12/18||Gunnar Ratsch||TBA|
|Dukler, Noah||Thesis Defense: 12/18||Adam Siepel||TBA|
|Fairchild, Lauren||2018||Christina Leslie||TBA|
|Gayvert, Kaitlyn||2017||Olivier Elemento||Associate Director of Informatics, Fractal Therapeutics|
|Hunter-Zinck, Haley||2014||Andrew Clark||Health Scientist Specialist, VA Healthcare Systems|
|Melman, Tamar||2018||Jonathan Victor||TBA|
|Meyer, Michael||2016||Haiyuan Yu||Senior Scientist, 4Catalyzer Medical Devices Industry|
|Madhukar, Neel||2017||Olivier Elemento||CEO/Co-Founder, OneThree Biotech; Startup Postdoc, Runway, Jacobs Institute|
|Mohammed, Jaaved||2016||Eric Lai/Adam Siepel||Postdoctoral Fellow, Stanford University|
|Pipes, Lenore||2017||Christopher Mason; Adam Siepel||Postdoctoral Fellow, University of California, Berkeley|
|Reeves, Darryl||2016||Christopher Mason||Assistant Professor, Long Island University|
|Saletore, Yogesh||2015||Christopher Mason||Bioinformatics Specialist, Talis Biomedical Corporation|
|Shenker, Solomon||2016||Eric Lai||Senior Scientist, KSQ Therapeutics, Inc.|
|Vijay, Priyanka||2017||Christopher Mason||Senior Scientist, AbbVie, Inc|
|Wang, Yiping||TBD||Zhenglong Gu||Current Student|
|Zawack, Kelson||2017||James Booth; Yrjo Grohn||Postdoctoral Fellow, Yale University|