Author

Anshul Kundaje

Stanford University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 3 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:deep learning· 3 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Research Focus:differential expression· 2 Organism:mouse· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Alexander Davis· 1 shared Alexis Battle· 1 shared Amit BlumbergiD· 1 shared Anastasiia MasaltsevaiD· 1 shared Boxiong Deng· 1 shared Chad J. MungeriD· 1 shared Charles G. DankoiD· 1 shared Chelsea Nnebe· 1 shared

Activity by Year

2015-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 9 mutual co-author links

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1 shared paperSynthetic Biology

Alexander Davis

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Author profile →

4 papers

Recent·Most cited

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

Tri C. Nguyen, Hunter D. King, Dulguun Amgalan, Olga Pushkarev, Yanyan Alexandra Mo, Chad J. Munger, Chloe McCreery, Revant Gupta, Tony Zeng, Ronghao Zhou, Stephanie D. Conley, Surya Prakash Rao Batta, Maya U. Sheth, Eugenio Mattei, Anastasiia Masaltseva, , Jesse M. Engreitz

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

bioRxiv · Nov 5, 2026 · PreprintGenomics

Deep learning-guided design of cell type-specific AAV promoters

Sean K. Wang, Boxiong Deng, Surag Nair, 任肖白, Jiaying Li, J Tijerina, Praveen Prakhar, Ziming Luo, Chelsea Nnebe, Samuel H. Kim, Yimin Zhou, Sahil Hemant Shah, Alexander Davis, Rohan Mahajan, Yilin Qiao, , Sui Wang

This study designs cell type-specific AAV promoters using deep learning, outperforming rational approaches in mouse retinal cells and showing promise for human applications.

bioRxiv · Jan 14, 2026 · PreprintSynthetic Biology

Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution

Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar

The paper uses deep sequencing to analyze mtDNA transcription in human and metazoan organisms, revealing conserved pausing sites and divergence across species.

Genome Research · Jan 3, 2017Peer-reviewedGenomics

Impact of the X chromosome and sex on regulatory variation

Kimberly R Kukurba, Princy Parsana, Kevin S Smith, Zachary Zappala, David A Knowles, Marie-Julie Favé, Xin Li, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Anshul Kundaje, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, , Stephen B Montgomery

This study examines how the X chromosome and sex influence gene regulation and disease by analyzing gene expression and regulatory variation in whole blood from 922 individuals.

bioRxiv · Aug 7, 2015Genomics