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 is an Associate Director for MSKCC’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 18K tumors. Olivier Elemento is Director of the Englander Institute for Precision Medicine at WCM and develops computational methods for genomic, transcriptomic, and epigenomic analyses in hematopoietic and solid tumors. Marcin Imielinski develops novel algorithmic methods to understand structural variation in cancer genomes. Alex Kentsis is a cancer biologist and pediatric oncologist whose research leverages proteomics and functional genomics to improve anti-cancer therapies. Ekta Khurana develops computational approaches to predict the functional consequences of non-coding somatic variants in cancer genomes. Dan Landau is a computational biologist and oncologist who develops algorithmic approaches to study tumor evolution. Elli Papaemmanuil uses computational strategies to study how the genetic and clonal architecture of leukemias dictate clinical phenotype and outcome. Nikolaus Schultz leads the scientific and engineering team that develops the cBioPortal, one of the most widely used resources in cancer genomics. Sohrab Shah is Chief of the newly formed Computational Oncology Service at MSKCC and is a leading expert in computational cancer genomics and tumor evolution.  Barry Taylor is an Associate Director of the Center for Molecular Oncology at MSKCC and studies how somatic alterations in cancer genomes contribute to tumor phenotype and response to therapy. (10 faculty)

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. Ilana Brito uses both computational and experimental strategies to study the human microbiome and its impact on human health. Andrew Clark is an internationally known population geneticist who studies the genetic basis of complex traits. Charles Danko studies regulatory genomics through a combination of statistical modeling and the development of novel next-generation sequencing assays. Iwijn De Vlaminck develops novel measurement strategies for cell-free DNA and for single cell analyses. Zhenglong Gu is an evolutionary biologist with both wet and dry lab activities to study the genetics of mitochondrial DNA in human adaptation and disease. Iman Hajirasouliha is a computer scientist who develops novel algorithmic and machine learning methods for genomics, metagenomics, and cancer genomics. Christina Leslie develops machine learning and computational strategies to decipher the global regulation of gene expression in mammalian cells. Scott Keeney is one of the foremost experts on meiosis and uses genomic and computational strategies to map molecular events in meiotic recombination. Amnon Koren used genomic approaches to study DNA replication timing and mutagenesis. Eric Lai is a developmental biologist who uses genome-wide methods to study the role of small non-coding RNAs in developmental patterning. John Lis is an internationally known molecular biologist who studies the structure and regulation of gene promoters and develops novel genome-wide assays to dissect transcriptional regulation. Christopher Mason 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 is molecular and cell biologist and a leading expert on alternative cleavage and polyadenylation and its functional consequences. Philipp Messer develops novel computational and analytical approaches in evolutionary biology and population genetics. Jason Mezey is a statistician and computational genomicist who studies the genetics and evolution of complex phenotypes and human disease. Dana Pe’er 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 uses experimental and computational strategies to study the role of non-coding RNAs in metabolic disease. Andrea Ventura is a cancer biologist with deep expertise in microRNA biology and CRISPR/Cas genome editing. Amy Williams develops computational methods to study human genetic variation and evolution and the genetic basis of human disease. (19 faculty)

Quantitative and Systems Biology 

Another major research theme is the analysis of the organization of cells into spatial structures, tissues and organs, involving quantitative experiments, mathematical modeling, and biological image analysis. Zhirong Bao uses 3D time-lapse microscopy to study cell dynamics, morphogenesis, and gene expression in the developing worm embryo. David Christini studies cardiac electrophysiological dynamics from the cellular to organ level using both computational and experimental approaches. Thomas Fuchs is an innovator in computational pathology, which seeks to use machine learning to automate and improve the analysis of pathology images. Joao Xavier uses quantitative experimental and computational methods to study the community behavior of bacteria, the spatial organization of tumors, and the microbiome. Jennifer Zallen is a developmental biologist who studies the generation of tissue structure through the collective behavior of cells. (5 faculty)

Computational Neuroscience

The use of 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 uses computational and experimental approaches to study neuronal temporal integration and its role in sensorimotor transformations, short-term memory behaviors, and decision making problems. Daniel Gardner focuses on the development of computational global resources in neuroinformatics. Samie Jaffrey utilizes experimental and computational approaches to study epitranscriptomic modification mRNA in neurons. Nicholas Schiff 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 uses next-generation transcriptomics to study the brain and its diseases. Jonathan Victor is a physician-scientist who combines mathematical, computational, and experimental approaches to study sensory processing. (6 faculty)

Structural Biology and Biophysics

Computational and experimental studies of protein structure/function and protein-protein interactions are activities represented within this theme. Olaf Anderson studies the structure and function of ion channels and interactions between proteins and lipid bilayers. Scott Blanchard studies structure/function relationships in macromolecular assemblies, including the ribosome and integral membrane proteins, in particular using innovative single molecule fluorescence techniques. John Chodera 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 applies NMR spectroscopy to problems in non-native structural biology, including in molecular aggregations involved in neurodegenerative disease. Harel Weinstein is Chair of the Physiology, Biophysics and Systems Biology department at WCM and develops and applies methods in computational biophysics to study diverse biological processes triggered by molecular recognition and leading to signal transduction. Haiyuan Yu uses high-throughput experimental and computational strategies to map and model the protein-protein interactome. (6 faculty)

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