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Arxiv|August 13, 2025
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNAAman Patel, Arpita Singhal, Austin Wang, et al.
Biorxiv : the Preprint Server for Biology|September 16, 2024
Flexible use of conserved motif vocabularies constrains genome access in cell type evolutionChew Chai, Jesse Gibson, Pengyang Li, et al.
Biorxiv : the Preprint Server for Biology|June 10, 2024
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosageSahin Naqvi, Seungsoo Kim, Saman Tabatabaee, et al.
Cell Genomics|February 28, 2025
Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosageSahin Naqvi, Seungsoo Kim, Saman Tabatabaee, et al.
Journal of Medical Systems|September 1, 2021
Patient Experience Surveys Reveal Gender-Biased Descriptions of Their Care ProvidersDylan Haynes, Anusri Pampari, Christina Topham, et al.
Cell Genomics|October 24, 2022
Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseasesSean K Wang, Surag Nair, Rui Li, et al.
Biorxiv : the Preprint Server for Biology|October 24, 2023
Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotencySurag Nair, Mohamed Ameen, Laksshman Sundaram, et al.
Developmental Cell|August 9, 2023
Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activationKaelan J Brennan, Melanie Weilert, Sabrina Krueger, et al.
Biorxiv : the Preprint Server for Biology|January 20, 2025
ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variantsAnusri Pampari, Anna Shcherbina, Evgeny Z Kvon, et al.
Science Advances|May 23, 2024
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elementsHenry E Pratt, Gregory Andrews, Nicole Shedd, et al.
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