World's Best Scientists 2026 revealed!

D-Index & Metrics

Genetics

D-Index
83
Citations
58998
World Ranking
1384
National Ranking
655

Research.com Recognitions

  • 2014 - Fellow of Alfred P. Sloan Foundation

Overview

Anshul Kundaje is affiliated with Stanford University in the United States. Their work primarily spans the field of Biochemistry, Genetics, and Molecular Biology, with a significant focus on Molecular Biology. Additional subfields of study include Genetics, Immunology, Cancer Research, and Pathology and Forensic Medicine.

The research topics covered by Kundaje encompass a variety of areas within genomics and molecular biology. Key topics include:

  • Genomics and Chromatin Dynamics
  • RNA Research and Splicing
  • RNA and protein synthesis mechanisms
  • Single-cell and spatial transcriptomics
  • Genomics and Phylogenetic Studies
  • RNA modifications and cancer
  • CRISPR and Genetic Engineering

Kundaje has published extensively in multiple scientific venues. Frequent publication venues include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Zenodo (CERN European Organization for Nuclear Research)
  • Nature Genetics
  • Nature
  • Cell

Notable recent papers authored or co-authored by Kundaje showcase a focus on genomic regulation, transcription factor modeling, and single-cell resolution studies. These papers include:

  • Genome-wide enhancer maps link risk variants to disease genes, 2021, Nature
  • Base-resolution models of transcription-factor binding reveal soft motif syntax, 2021, Nature Genetics
  • GENCODE: reference annotation for the human and mouse genomes in 2023, 2022, Nucleic Acids Research
  • Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution, 2021, Cell
  • Transparency and reproducibility in artificial intelligence, 2020, Nature

Kundaje frequently collaborates with a set of co-authors, including:

  • William J. Greenleaf
  • Georgi K. Marinov
  • Surag Nair
  • Anna Shcherbina
  • M Snyder

Recognition includes being named a Fellow of the Alfred P. Sloan Foundation in 2014, reflecting engagement within the scientific community.

Best Publications

  • Integrative analysis of 111 reference human epigenomes

    Anshul Kundaje;Wouter Meuleman;Wouter Meuleman;Jason Ernst

  • An integrated encyclopedia of DNA elements in the human genome

    Ian Dunham;Anshul Kundaje;Shelley F. Aldred;Patrick J. Collins

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

    Jill E. Moore;Michael J. Purcaro;Henry E. Pratt;Charles B. Epstein

  • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

    Stephen G. Landt;Georgi K. Marinov;Anshul Kundaje;Pouya Kheradpour

  • Opportunities and obstacles for deep learning in biology and medicine.

    Travers Ching;Daniel S. Himmelstein;Brett K. Beaulieu-Jones;Alexandr A. Kalinin

  • Learning important features through propagating activation differences

    Avanti Shrikumar;Peyton Greenside;Anshul Kundaje

  • A comparative encyclopedia of DNA elements in the mouse genome

    Feng Yue;Feng Yue;Yong Cheng;Alessandra Breschi;Jeff Vierstra

  • An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

    M Ryan Corces;Alexandro E Trevino;Emily G Hamilton;Peyton G Greenside

  • Architecture of the human regulatory network derived from ENCODE data

    Mark B Gerstein;Anshul Kundaje;Manoj Hariharan;Stephen G Landt

  • A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    Richard M. Myers;John Stamatoyannopoulos;Michael Snyder;Ian Dunham

  • The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

    Haley M. Amemiya;Anshul Kundaje;Alan P. Boyle

  • Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

    Jie Wang;Jiali Zhuang;Sowmya Iyer;Sowmya Iyer;XinYing Lin

  • Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

    M Ryan Corces;Jason D Buenrostro;Jason D Buenrostro;Beijing Wu;Peyton G Greenside

  • Defining functional DNA elements in the human genome

    Manolis Kellis;Barbara Wold;Michael P. Snyder;Bradley E. Bernstein

  • Integrative annotation of chromatin elements from ENCODE data

    Michael M. Hoffman;Jason Ernst;Jason Ernst;Jason Ernst;Steven P. Wilder;Anshul Kundaje;Anshul Kundaje

  • Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

    Suna Onengut-Gumuscu;Wei-Min Chen;Oliver Burren;Nick J Cooper

  • Opportunities and challenges for transcriptome-wide association studies.

    Michael Wainberg;Nasa Sinnott-Armstrong;Nicholas Mancuso;Alvaro N. Barbeira

  • Not Just a Black Box: Learning Important Features Through Propagating Activation Differences

    Avanti Shrikumar;Peyton Greenside;Anna Shcherbina;Anshul Kundaje

  • Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

    Elizabeta Gjoneska;Andreas R. Pfenning;Hansruedi Mathys;Gerald Quon

  • Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

    Suna Onengut-Gumuscu;Wei-Min Chen;Oliver Burren;Emily Farber

Frequent Co-Authors

Michael Snyder
Michael Snyder Stanford University
William J. Greenleaf
William J. Greenleaf Stanford University
Howard Y. Chang
Howard Y. Chang Amgen (United States)
Mark Gerstein
Mark Gerstein Yale University
Michael C. Bassik
Michael C. Bassik Stanford University
Zhiping Weng
Zhiping Weng University of Massachusetts Chan Medical School
Bradley E. Bernstein
Bradley E. Bernstein Broad Institute
Christina S. Leslie
Christina S. Leslie Memorial Sloan Kettering Cancer Center
Job Dekker
Job Dekker University of Massachusetts Chan Medical School

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