Anshul Kundaje

About

Anshul Kundaje is an Assistant Professor of Genetics and of Computer Science at Stanford University. He is affiliated with the Center for Artificial Intelligence in Medicine & Imaging (AIMI). His research focuses on the application of artificial intelligence and computational methods to medicine and imaging, contributing to the advancement of healthcare through innovative data-driven approaches. His work involves integrating genetics, computer science, and AI to develop new tools and insights in biomedical research and clinical practice.

Research topics

• Biology
• Genetics
• Computational biology
• Medicine
• Computer Science
• Bioinformatics
• Pathology
• Data Mining
• Cell biology
• Cancer research

Selected publications

• Expanded encyclopaedias of DNA elements in the human and mouse genomes

  Nature · 2020 · 2538 citations

  data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the…

  DOI

• Genome-wide enhancer maps link risk variants to disease genes

  Nature · 2021 · 736 citations

  DOI

• The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

  Cell · 2020 · 581 citations

  Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinic…

  DOI

• CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities

  Nature · 2020 · 330 citations

  DOI

• Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

  Nature Genetics · 2022 · 315 citations

  To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles and single-cell transcriptomes from 1,000 to 10,000 cells per sample for 48 polyps, 27 normal tissues and 6 CRCs collected from patients with or without germline APC mutations. A large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigeneti…

  DOI

Recent grants

• NIH Grant DP2GM12348501

  NIH · $2.4M · 2021

• Predicting context-specific molecular and phenotypic effects of genetic variation through the lens of the cis-regulatory code

  NIH · $3.2M · 2021–2026

• SOFTWARE FOR LARGE-SCALE INFERENCE OF THE GENETICS OF LIFESTYLE MEASURES, BIOMARKERS, AND COMMON AND RARE DISEASES

  NIH · $2.0M · 2018–2023

Frequent coauthors

• Jenny Chang‐Claude

  117 shared

• Loı̈c Le Marchand

  Cancer Center of Hawaii

  113 shared

• William J. Greenleaf

  107 shared

• Vı́ctor Moreno

  Universitat de Barcelona

  99 shared

• Hermann Brenner

  TU Bergakademie Freiberg

  93 shared

• Andrew T. Chan

  Brigham and Women's Hospital

  92 shared

• Joshua W. K. Ho

  University of Hong Kong

  91 shared

• M Snyder

  85 shared

Education

• Ph.D., Genetics and Computer Science

  Stanford University

  2013

• M.S., Computer Science

  Stanford University

  2009

• B.S., Computer Science

  University of Pennsylvania

  2007

Similar researchers at Stanford University

• Ronald Davish-183
• Robert Harringtonh-169