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Anshul Kundaje

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Articles 179
Citations 19672
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Recent Articles
1.
Rios Coronado P, Zhou J, Fan X, Zanetti D, Naftaly J, Prabala P, et al.
Cell . 2025 Mar; PMID: 40049164
Coronary arteries have a specific branching pattern crucial for oxygenating heart muscle. Among humans, there is natural variation in coronary anatomy with respect to perfusion of the inferior/posterior left heart,...
2.
Marderstein A, Kundu S, Padhi E, Deshpande S, Wang A, Robb E, et al.
bioRxiv . 2025 Mar; PMID: 40027628
Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal common and...
3.
Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard J, et al.
Cell Genom . 2025 Feb; 5(3):100780. PMID: 40020686
Deep learning models have advanced our ability to predict cell-type-specific chromatin patterns from transcription factor (TF) binding motifs, but their application to perturbed contexts remains limited. We applied transfer learning...
4.
Zaslavsky M, Craig E, Michuda J, Sehgal N, Ram-Mohan N, Lee J, et al.
Science . 2025 Feb; 387(6736):eadp2407. PMID: 39977494
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system's own record of antigen exposures encoded by...
5.
Adli M, Przybyla L, Burdett T, Burridge P, Cacheiro P, Chang H, et al.
Nature . 2025 Feb; 638(8050):351-359. PMID: 39939790
Recent advances in functional genomics and human cellular models have substantially enhanced our understanding of the structure and regulation of the human genome. However, our grasp of the molecular functions...
6.
Zhu Y, Lee H, White S, Weimer A, Monte E, Horning A, et al.
Nat Cancer . 2025 Jan; 6(2):404. PMID: 39865177
No abstract available.
7.
Pampari A, Shcherbina A, Kvon E, Kosicki M, Nair S, Kundu S, et al.
bioRxiv . 2025 Jan; PMID: 39829783
Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (TF) binding and chromatin accessibility at...
8.
Kundaje A, Pollard K, Ma J, Chang X, Chen M, Rohs R
Mol Cell . 2025 Jan; 85(2):193-198. PMID: 39824161
In recent years, computational methods and artificial intelligence approaches have proven uniquely suited for studying patterns in molecular biology. In this focus issue, we spoke with researchers about using these...
9.
Moore J, Pratt H, Fan K, Phalke N, Fisher J, Elhajjajy S, et al.
bioRxiv . 2025 Jan; PMID: 39763870
Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated...
10.
Ma X, Conley S, Kosicki M, Bredikhin D, Cui R, Tran S, et al.
medRxiv . 2024 Nov; PMID: 39606363
Congenital heart defects (CHD) arise in part due to inherited genetic variants that alter genes and noncoding regulatory elements in the human genome. These variants are thought to act during...