PeopleofSuperintelligence

Researcher

Anshul Kundaje

Anshul Kundaje is an associate professor of genetics and computer science at Stanford who develops deep learning models to explain how DNA controls gene activity. He completed his computer science PhD at Columbia in 2008, worked at Stanford, MIT and the Broad Institute, and joined Stanford's faculty in 2013. His work included the Roadmap Epigenomics Project, the 2017 DeepLIFT method for explaining neural network predictions, and the 2021 BPNet model for learning DNA-binding patterns. In 2025, he coauthored the ChromBPNet preprint, which separated experimental bias from regulatory DNA signals and helped interpret genetic variants linked to disease.

Works
723
Citations
72,416
h-index
88

Publication numbers from OpenAlex, as of 27 October 2026.

Timeline

  1. 2003–2008

    A doctorate at Columbia

    In 2008, he completes a PhD in computer science at Columbia University under Christina Leslie. His doctoral work uses boosting algorithms to model gene regulation in yeast.

  2. 2008–2013

    Postdoctoral work and Stanford faculty

    From 2008 to 2012, he conducts postdoctoral research in Stanford's Computer Science Department with Serafim Batzoglou and Arend Sidow, serving as lead data coordinator and primary integrative analyst for the human ENCODE consortium. In 2013, he works as a research scientist in MIT's Computer Science Department and at the Broad Institute of MIT and Harvard with Manolis Kellis's group. He joins Stanford's faculty in September 2013.

  3. 2014

    A Sloan Research Fellowship

    In 2014, he receives a Sloan Research Fellowship, which provides $50,000 for research costs.

  4. 2015

    The Roadmap Epigenomics Project

    In 2015, he leads computational analysis for the Roadmap Epigenomics Project and is a lead author of its main integrative analysis paper in Nature. The project maps regulatory features across adult and fetal human cells and tissues to help interpret the genetic basis of disease.

  5. 2016

    An NIH New Innovator Award

    In 2016, he wins the NIH Director's New Innovator Award. The award supports his work on deep neural networks to decode noncoding DNA and identify genetic variation associated with disease.

  6. 2017

    Explaining predictions with DeepLIFT

    In 2017, with Avanti Shrikumar and Peyton Greenside, he publishes DeepLIFT at the International Conference on Machine Learning. The method assigns contribution scores to input features to explain a neural network's prediction.

  7. 2019

    The Chen Award of Excellence

    In 2019, he receives the Chen Award of Excellence from the Human Genome Organization.

  8. 2021

    Reading DNA with BPNet

    In 2021, he coauthors BPNet, a deep learning model that predicts transcription-factor binding from DNA sequence at the level of individual bases. The team develops interpretation tools to identify DNA patterns and rules for cooperative binding.

  9. January 2025

    Introducing ChromBPNet

    In January 2025, he coauthors the ChromBPNet preprint with Anusri Pampari and colleagues. The deep learning model separates experimental enzyme bias from regulatory DNA signals and helps interpret genetic variants associated with traits and rare diseases.

  10. As of October 2026

    Associate professor at Stanford

    In October 2026, he is an associate professor of genetics and computer science at Stanford, where his lab develops machine learning models and interpretation frameworks for gene regulation and disease. He also co-chairs the Impact of Genomic Variation on Function consortium's steering committee and co-leads the Multi-omics in Health and Disease consortium's Data Analysis and Coordination Center.

Career

  1. NowStanford UniversityAssociate professor of genetics and computer science
  2. 2013–2015MIT CSAIL
  3. 2012–2015Massachusetts Institute of TechnologyResearch scientist
  4. Broad InstituteResearch scientist

Education

  1. 2008Columbia UniversityPhD in computer science

From the biography and OpenAlex affiliations (the years of papers that list the organization), so some years are approximate.

Colleagues

People named in this biography, and people with dated positions at the same organization in the same years.

Sources and credits

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  1. Spring 2013 | Department of Computer Science, Columbia University cs.columbia.edu. Checked 27 October 2026.
  2. Project maps human epigenome, discovers immune system role in Alzheimer's med.stanford.edu. Checked 27 October 2026.
  3. Four faculty members awarded Sloan Research Fellowships med.stanford.edu. Checked 27 October 2026.
  4. Seven researchers receive NIH grants for 'high-risk' work med.stanford.edu. Checked 27 October 2026.
  5. Learning Important Features Through Propagating Activation Differences proceedings.mlr.press. Checked 27 October 2026.
  6. Chen Awards - HUGO International hugo-international.org. Checked 27 October 2026.
  7. Anshul Kundaje's Profile | Stanford Profiles profiles.stanford.edu. Checked 27 October 2026.
  8. ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants - PMC pmc.ncbi.nlm.nih.gov. Checked 27 October 2026.
  9. Anshul Kundaje | Computer Science cs.stanford.edu. Checked 27 October 2026.