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Associate Professor and Principal Investigator

Anshul Kundaje

Anshul Kundaje is an Assistant Professor of Genetics and Computer Science at Stanford University. The Kundaje lab develops statistical and machine learning methods for large-scale integrative analysis of functional genomic data to decode regulatory elements and pathways across diverse cell types and tissues and understand their role in cellular function and disease. Anshul completed his Ph.D. in Computer Science in 2008 from Columbia University. As a postdoc at Stanford University from 2008-2012 and a research scientist at MIT and the Broad Institute from 2012-2014, he led the integrative analysis efforts for two of the largest functional genomics consortia - The Encyclopedia of DNA Elements (ENCODE) and The Roadmap Epigenomics Project. Dr. Kundaje is a recipient of the 2019 Chen Award of Excellence from the Human Genome Organization, 2016 NIH Director’s New Innovator Award and The 2014 Alfred Sloan Foundation Fellowship. Anshul is also a member of the NIH Director's Advisory Committee for Artificial Intelligence in Biomedical Research and the NHGRI Genomic Data Science Working Group.

2012-2013, I was a Research Scientist in Manolis Kellis' lab at MIT and The Broad Institute studying epigenomic and chromatin state dynamics across organisms, cell-types and individuals as part of the Roadmap Epigenomics Project and the mod/ENCODE (Encyclopedia for DNA elements) consortium. 

2008 - 2012, I was a Postdoctoral Research Associate with Serafim Batzoglou and Arend Sidow in the Computer Science Dept. at Stanford University. I served as one of the lead data coordinators and computational analysts for the ENCODE consortium. My primary focus was on deciphering heterogeneity of regulatory interactions in the human genome. I also developed ENCODE's ChIP-seq statistical data analysis pipeline.2003-2008, I was a graduate student (PhD.) in Christina Leslie's lab in the Computer Science Dept. at Columbia University in New York. I developed Machine Learning methods for modeling transcriptional gene regulation in yeast and worm. 2002-2003, I briefly worked at the IBM T.J. Watson Research Center in the Functional Genomics and Systems Biology group under Gustavo Stolovitzky. I developed one of the first statistical noise models for massively parallel sequencing data (MPSS) in a collaboration with The Institute of Systems Biology and Lynx Therapeutics.In a past life, I was an Electrical Engineer (B.E from Mumbai University, 2001 and M.S. from Columbia University, 2002) and worked on computer networks and voice over IP with Henning Schulzrinne.



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