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 an Associate 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 18K tumors. Kivanc Birsoy (RU) studies how metabolic pathways in mammalian cells are rewired by their nutrient environment and how metabolic liabilities in disease can be therapeutically exploited. Olivier Elemento(WCM) 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 (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. 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 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 Chief of the newly formed Computational Oncology Service at MSK and is a leading expert in computational cancer genomics and tumor evolution. 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. Sohail Tavazoie (RU) employs computational and experimental methods to understand mechanisms underlying cancer progression and gene regulation. Barry Taylor (MSK) is an Associate Director of the Center for Molecular Oncology at MSK and studies how somatic alterations in cancer genomes contribute to tumor phenotype and response to therapy. 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. 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. Elaine Fuchs (RU) exploits high-throughput technologies to elucidate the mechanisms by which tissue stem cells respond to their environment to make and repair tissues and how these processes go awry in cancer. Zhenglong Gu (CU-I) 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 (WCM) is a computer scientist who develops novel algorithmic and machine learning methods for genomics, metagenomics, and cancer genomics. Amnon Koren (CU-I) uses genomic approaches to study the causes and consequences of DNA replication timing. Christina Leslie (MSK) develops machine learning and computational strategies to decipher the global regulation of gene expression in mammalian cells. Eric Lai (MSK) is a developmental biologist who uses genome-wide methods to study the role of small non-coding RNAs in developmental patterning. John Lis (CU-I) 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 (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. 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. Viviana Risca (RU) studies three-dimensional chromatin structure at high resolution and the biophysical mechanisms that regulation DNA accessibility and transcription. Praveen Sethupathy (CU-I) uses experimental and computational strategies to study the role of non-coding RNAs in metabolic disease. Amy Williams (CU-I) develops computational methods to study human genetic variation and evolution and the genetic basis of human disease. Li Zhao (RU) studies the evolution and function of de novo genes and the genetic basis of adaptive evolution in flies and human.
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 (MSK) uses 3D time-lapse microscopy to study cell dynamics, morphogenesis, and gene expression in the developing worm embryo. Jean-Laurent Casanova (RU) studies the human genetics of infectious disease by combining experimental and mathematical approaches. 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.
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 (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) investigates the computational principles of complex neural circuits used for information processing 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. Marcelo Magnasco (RU) carries out research in computational and cognitive neuroscience. Nicholas Schiff (WCM) 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. Alipasha Vaziri (RU) develops and applies new optical tools for large-scale, high-speed, and single-cell resolution interrogation of neuroactivity across model systems. 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 fundamental mechanisms of neuronal cell fate specification and function.
Structural Biology and 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. Olga Boudker (WCM) is an HHMI investigator and structural biologist who studies glutamate transporters in synaptic signaling. 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. James Hudspeth (RU) investigates process of hearing using membrane biophysics, cellular mechanics, and developmental biology. Crina Nimigean (WCM) is a structural biologist who uses cryo-EM to determine high-resolution structures of ion channels in different conformations and lipid environments. Simon Sanford (RU) carries out computational and biophysical studies of cellular functions as well as studies of childhood cancer. Harel Weinstein (WCM) 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 (CU-I) uses high-throughput experimental and computational strategies to map and model the protein-protein interactome.