Research Areas

Research Areas

By design, the Computational Biology and Medicine Program is not focused in one area of computational biology. Faculty in CBM engage in a wide range of research, as described here, providing students with diverse opportunities for thesis study. More information about the research of our graduate faculty can be found on the Faculty Directory page.

Scientific Expertise of Program Faculty

 

Cancer Biology and Genomics

Large-scale and cutting-edge precision oncology efforts make the CBM program a leader in cancer genomics and computational oncology. Michael Berger (MSK) is Co-Director for MSK’s Center for Molecular Oncology and leads technological and computational developments for MSK-IMPACT, the clinical sequencing assay that has now been deployed in over 70K tumors. Kivanc Birsoy (RU) uses high-throughput genetic screens together with computational analyses to study cancer metabolism. Jian Carrot-Zhang (MSK) develops advanced computational methods to link germline genetics to somatic phenotypes in cancer.   Olivier Elemento (WCM) is Director of the Englander Institute for Precision Medicine at WCM and develops computational methods for genomic, transcriptomic, and proteomic analyses of tumors for precision oncology. 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 genomic and epigenomic variation in cancer genomes. Ashley Laughney (WCM) studies the evolution of metastases and anti-tumor immunity using single-cell methods. Dan Landau (WCM) is a computational biologist and oncologist who develops algorithmic approaches and genomic technologies to study tumor evolution. Anna Nam (WCM) uses single-cell multi-omics to study hematopoietic neoplasms. Dawid Nowak (WCM) uses computational experimental methods including in vivo CRISPR-based lineage tracing to study the molecular and cellular events driving cancer progression and metastasis.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 Chief of the Computational Oncology Service at MSKCC and is a leading expert in computational cancer genomics and tumor evolution. Sanford Simon (RU) uses biophysical, cell biological, and genomic approaches to study a rare pediatric liver cancer. Tuomas Tammela  (MSK) studies the heterogeneity of cancer cells through genetically engineered mouse models, single-cell transcriptomics, lineage tracing and ablation, CRISPR/Cas technology, and advanced imaging techniques.Wesley Tansey (MSK) develops principled machine learning methods for analysis of tumor spatial expression profiling and cancer drug screening data.  Sohail Tavazoie (RU) is a physician-scientist who takes a systems biology approach to study the molecular and cell biological mechanisms underlying metastasis. Andrea Ventura (MSK) is a cancer biologist with deep expertise in microRNA biology and CRISPR/Cas genome editing..

Genomics and Gene Regulation

The 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, with both wet and dry labs working at the forefront of these fields. Eftychia Apostolou (WCM) uses somatic cell reprogramming together with genome-wide chromosome conformation capture assays as a system to decipher the role of 3D genomic architecture in regulating gene expression and cell identity. Doron Betel (WCM) carries out genomic and epigenomic analyses to study disease progression, response to therapy, stem cell differentiation, and neurological processes. Ilana Brito (CU-I) uses both computational and experimental strategies to study the human microbiome and its impact on human health. Junyue Cao (RU) develops highly scalable single-cell technologies to enable the transcriptomic or chromatin accessibility profiling of millions of single mammalian cells. Jean-Laurent Casanova (RU) is a physician-scientist and HHMI Investigator who studies the human genetic and immunological determinants of response to infectious diseases and led the COVID Human Genetic Effort, which made key discoveries about susceptibility to severe COVID. Andrew Clark (CU-I) is a 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. Kushal Dey (MSK) builds statistical and machine learning models that integrate genetics and genomics to decode the causal functional architecture of complex human diseases. Elaine Fuchs (RU) is an HHMI investigator who uses mammalian skin as a model for studying tissue stem cell biology. Iman Hajirasouliha  (WCM) is a computer scientist who develops novel algorithmic and machine learning methods for genomics, metagenomics, and cancer genomics. Steven Josefowicz  (WCM) uses mouse genetic systems and epigenomics to study signaling to chromatin in stimulation-induced gene expression programs. Christina Leslie  (MSK) develops machine learning and computational strategies to decipher the global regulation of gene expression in the immune system, cancer, and development. Jaehee Kim (CU-I) develops mathematical models to understand how evolutionary processes lead to observed patterns of genetic and phenotypic variation. Benjamin Kleaveland (WCM) is a physician-scientist who studies the function of non-coding RNAs using high-throughput molecular, biochemical, and computational approaches in mammalian cells and transgenic mice. Eric Lai (MSK) is a developmental biologist who uses genome-wide methods to study the role of small non-coding RNAs in developmental patterning. Caleb Lareau  (MSK) develops novel single-cell technologies and computational methods to study somatic evolution and the immune system. 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  (WCM/CU-I) is a statistician and computational genomicist who studies the genetics and evolution of complex phenotypes and human disease. Quaid Morris (MSK) develops novel machine learning and artificial intelligence methods to study cancer evolution and RNA-binding proteins involved in post-transcriptional regulation. Thomas Norman (MSK) develops Perturb-seq technologies, which combine CRISPRi/a screens with single-cell transcriptomics, and computational methods to analyze and model these data sets. Dana Pe’er  (MSK) is an HHMI Investigator and world-leading expert on the analysis of single-cell transcriptomic data and plays a leadership role in the Human Cell Atlas project. Viviana Risca (RU) studies the 3D architecture of chromatin using genomic and biophysical techniques. Jeremy Rock  (RU) develops and applies novel CRISPR-based tools to study Mycobacterium tuberculosis. Ruslan Soldatov (MSK) develops computational methods to analyze cell fate decisions and cancer evolution at single-cell resolution, building on his well-known RNA velocity work. Li Zhao (RU) uses population genomics and computational methods to study the evolution of de novo genes in Drosophila and humans.

Quantitative and Systems Biology 

Another major research theme is the analysis of the organization of cells into tissues and biological systems such as the immune system, involving quantitative experiments and mathematical modeling, as well as computational and experimental studies of protein structure/function and molecular interactions. Zhirong Bao  (MSK) uses 3D time-lapse microscopy to study cell dynamics, morphogenesis, and gene expression in the developing worm embryo. 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. Benjamin Greenbaum  (MSK) uses methods from statistical physics to the effect of innate immune responses on viral evolution and the role of neoantigens in tumor evolution. Jim Hudspeth  (RU) is an HHMI Investigator who studies the mechanosensory mechanisms of hearing and regenerative treatments for hearing loss. Jan Krumsiek (WCM) uses metabolomic and multi-omic computational analyses to decipher metabolic changes in human disease. Jiankun Lyu (RU) develops novel algorithms to screen vast chemical libraries to identify small molecule ligands of biological targets. Daniel Mucida (RU) is an HHMI Investigator who studies immune activity and tolerance in the intestinal mucosa, including using novel systems immunology strategies. Crina Nimagean (WCM) is a structural biologist who uses cryo-EM to determine high-resolution structures of ion channels in different conformations and lipid environments. Michel Nussenzweig (RU) is an HHMI Investigator and renowned immunologist who studies B cell affinity maturation and develops antibody-based therapies for HIV and SARS-CoV-2 infection. Charles Rice (RU) is a Nobel laureate who studies innate immune responses to limit viral replication with colloborative work encompassing genomic technologies and immunopeptidomics. Mary Teruel (WCM) uses quantitative biology approaches including in vitro live cell imaging to study adipocyte differentiation, with applications to diabetes and obesity. Gabriel Victora (RU) is an HMMI Investigator who studies the biology of how antibodies are generated in response to infection and immunization, including through novel systems biology methods. Fei Wang (WCM) develops data-driven methods to integrate electronic health records with molecular data for human disease phenotyping and drug discovery. Joao Xavier  (MSK) uses quantitative experimental and computational methods to study the community behavior of bacteria, the spatial organization of tumors, and the microbiome. Haiyuan Yu  (CU-I) uses high-throughput experimental and computational strategies to map and model the protein-protein interactome.

Computational Neuroscience

The use of computational modeling and analysis to study the function of neurons and the brain is a vibrant area of CBM research that interdigitates with several other Program areas, from genomics to systems biology. 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. Winrich Freiwald (RU) combines computational and experimental strategies to model how the brain processes visual cues from faces.  Samie Jaffrey  (WCM) utilizes experimental and computational approaches to study epitranscriptomic modification of mRNA in neurons. Daniel Lee (CTech) focuses on understanding computational principles underlying biological systems and how to apply this knowledge to build autonomous robots, bridging neuroscience and AI. Hagen Tilgner  (WCM) uses next-generation transcriptomics to study the brain and its diseases. Mert Sabuncu (CTech) develops machine learning and other computational strategies to exploit large-scale biomedical imaging data with applications in neuroscience and neurology. Jonathan Victor (WCM) is a physician scientist who combines mathematical, computational, and experimental approaches to study sensory processing. Thomas Vierbuchen (MSK) uses directed differentiation of human and mouse pluripotent stem cells together with genomics and systems genetics approaches to study mechanisms of neuronal cell fate specification and function.

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