Author

Aman Patel

Stanford UniversityORCID 0000-0003-2113-3251Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Assay:ATAC-seq· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:scRNA-seq· 2 Research Focus:variant effect prediction· 2 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1

Frequent Co-Authors

Anshul Bharat KundajeiD· 3 shared Anusri PampariiD· 2 shared Bo WangiD· 1 shared Brennan D. McDonaldiD· 1 shared Chew ChaiiD· 1 shared Christy LuongiD· 1 shared Howard Y. ChangiD· 1 shared Jesse Gibson· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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3 shared papersGenomics

Anshul Bharat KundajeORCID

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3 papers

Recent·Most cited

Evolutionary BiologyNature Ecology & EvolutionPeer-reviewedSep 8, 2026

Flexible use of conserved motif vocabularies constrains genome access in cell type evolution

Chew Chai, Jesse Gibson, Pengyang Li…·Bo Wang

The paper shows that conserved motif vocabularies constrain genome access in cell type evolution across species.

8 citationstop 5%

multiple speciesscRNA-seq

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GenomicsbioRxivPreprintJul 12, 2026

✦ In-depth digest

ARSENAL: Learning Transferable Regulatory DNA Representations with Targeted Short-Context Language Models

Aman Patel, Anshul Bharat Kundaje

A 350 bp masked DNA language model trained on ENCODE cCREs with a frequency-domain regularizer recovers TF motifs zero-shot, scores regulatory variants, improves ChromBPNet inputs, and guides sequence design.

DOI 10.64898/2026.02.05.703637

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GenomicsCell GenomicsPeer-reviewedJul 27, 2022

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases

Sean K. Wang, Surag Nair, Rui Li…·Howard Y. Chang

The paper uses a single-cell multiome atlas of the human retina and deep learning to identify causal noncoding variants in eye diseases.

88 citationstop 1%

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