Anshul Kundaje
Associate Professor of Genetics and of Computer Science
Develops deep learning models of gene regulation from functional genomics data.
Anshul Kundaje's lab at Stanford works on genomics & computational biology. 84 papers since 2023, 24 at top venues, mostly Nature and Cell. Applications close .
At a glance
- papers, 2023–2026
- 22/ year
- at T1 venues
- 29%
- PhD students
- —
- MS students
- —
- alumni listed
- —
Papers by yearfrom the lab homepage, 2023–2026
- 13 papers2026 · T1 6 · collecting
- 25 papers2025 · T1 9
- 23 papers2024 · T1 5
- 23 papers2023 · T1 4
T1 venuesOtherVenues: Nature, Cell, Nature Communications, Science, Nucleic Acids Research
Research focuspaper titles that use each topic's words
- gene13 papers
- Genomics & computational biology9 papers
- gene regulation1 paper
- regulation1 paper
- develops deep0 papers
Paper list
From the lab homepage.
202613 papers
- Nature (T1)An encyclopedia of human enhancer-gene regulatory interactions. (opens in a new tab)
- Nature (T1)An expanded registry of candidate cis-regulatory elements. (opens in a new tab)
- Nature geneticsDecoding common and rare noncoding variant effects across cellular and developmental contexts. (opens in a new tab)
- Nature ecology & evolutionFlexible use of conserved motifs constrains genome access in cell type evolution. (opens in a new tab)
- BMC medicineGenetic risk factors modulate the association between physical activity and colorectal cancer. (opens in a new tab)
- Nature geneticsMapping enhancer-gene regulatory interactions from single-cell data. (opens in a new tab)
- Nature (T1)Multiomics and deep learning dissect regulatory syntax in human development. (opens in a new tab)
- Nature Communications (T1)Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models. (opens in a new tab)
- Nature Communications (T1)Prediction and functional interpretation of inter-chromosomal genome architecture from DNA sequence with TwinC. (opens in a new tab)
- Molecular cellRibo-Tweezer: Rapid removal of ribosomal proteins reveals additional layers of post-transcriptional gene regulation. (opens in a new tab)
- Cell reportsSingle-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration. (opens in a new tab)
- Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive OncologyTGF-β-pathway-based polygenic risk score modifies the association between red meat intake and colorectal cancer risk: Application of a novel pathway-based PRS method. (opens in a new tab)
202525 papers
- Cell genomicsA cell and transcriptome atlas of human arterial vasculature. (opens in a new tab)
- Communications medicineAchieving inclusive healthcare through integrating education and research with AI and personalized curricula. (opens in a new tab)
- PLOS ONEAn updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome. (opens in a new tab)
- MOLECULAR CELLArtificial intelligence in molecular biology
- Nature cancerAuthor Correction: Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. (opens in a new tab)
- PNAS (T1)Cell type-specific purifying selection of synonymous mitochondrial DNA variation. (opens in a new tab)
- Cell (T1)CXCL12 drives natural variation in coronary artery anatomy across diverse populations. (opens in a new tab)
- —Deep learning guided design of cell type-specific AAV promoters
- Science (T1)Disease diagnostics using machine learning of B cell and T cell receptor sequences. (opens in a new tab)
- Molecular systems biologyEpigenomic landscape of single vascular cells reflects developmental origin and disease risk loci. (opens in a new tab)
- Nature (T1)GREGoR: accelerating genomics for rare diseases. (opens in a new tab)
- Nature (T1)In vivo mapping of mutagenesis sensitivity of human enhancers. (opens in a new tab)
202423 papers
- Developmental cellAn SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity. (opens in a new tab)
- DIGITAL DISCOVERYApplication of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes (opens in a new tab)
- Nature cell biologyAuthor Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). (opens in a new tab)
- GENOME BIOLOGYCAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods (opens in a new tab)
- EpidemiologyCharacterization of additive gene-environment interactions for colorectal cancer risk. (opens in a new tab)
- —DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
- Nature (T1)Deciphering the impact of genomic variation on function. (opens in a new tab)
- —Deep Learning the Cis-Regulatory Code of Epigenomic Rewiring By Fusion Transcription Factors in Pediatric Leukemia (opens in a new tab)
- Cell (T1)Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders (opens in a new tab)
- Nature Communications (T1)Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. (opens in a new tab)
- Nucleic Acids ResearchGENCODE 2025: reference gene annotation for human and mouse. (opens in a new tab)
- British journal of cancerGenetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk. (opens in a new tab)
202323 papers
- Cancer researchA genetic locus within the FMN1/GREM1 gene region interacts with body mass index in colorectal cancer risk. (opens in a new tab)
- Nature cell biologyAdvances and prospects for the Human BioMolecular Atlas Program (HuBMAP). (opens in a new tab)
- Nature geneticsAuthor Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. (opens in a new tab)
- Genome biologyCasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping. (opens in a new tab)
- Nature agingChromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging. (opens in a new tab)
- Developmental cellChromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. (opens in a new tab)
- Journal of the National Cancer InstituteGenome-Wide Analyses Characterize Shared Heritability Among Cancers and Identify Novel Cancer Susceptibility Regions. (opens in a new tab)
- Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive OncologyGenome-wide gene-environment interaction analyses to understand the relationship between red meat and processed meat intake and colorectal cancer risk. (opens in a new tab)
- The American journal of clinical nutritionGenome-wide interaction analysis of folate for colorectal cancer risk. (opens in a new tab)
- Methods in molecular biologyGenome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. (opens in a new tab)
- Nature (T1)Identification of constrained sequence elements across 239 primate genomes. (opens in a new tab)
- Nature (T1)Latent human herpesvirus 6 is reactivated in CAR T cells. (opens in a new tab)
Where alumni went
Alumni are not listed on the lab homepage.
Apply to StanfordFall 2027
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