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Representations of lipid nanoparticles using large language models for transfection efficiency prediction.
Bioinformatics. 2024 May 29:btae342. doi: 10.1093/bioinformatics/btae342. Online ahead of print.
Bioinformatics. 2024.
PMID: 38810107
Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency.
Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A.
Nair S, et al. Among authors: balsubramani a.
bioRxiv [Preprint]. 2023 Oct 21:2023.10.04.560808. doi: 10.1101/2023.10.04.560808.
bioRxiv. 2023.
PMID: 37873116
Free PMC article.
Preprint.
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Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A.
Ameen M, et al. Among authors: balsubramani a.
Cell. 2022 Dec 22;185(26):4937-4953.e23. doi: 10.1016/j.cell.2022.11.028.
Cell. 2022.
PMID: 36563664
Free PMC article.
Item in Clipboard
Accelerating in silico saturation mutagenesis using compressed sensing.
Schreiber J, Nair S, Balsubramani A, Kundaje A.
Schreiber J, et al. Among authors: balsubramani a.
Bioinformatics. 2022 Jul 11;38(14):3557-3564. doi: 10.1093/bioinformatics/btac385.
Bioinformatics. 2022.
PMID: 35678521
Free PMC article.
Item in Clipboard
Domain-adaptive neural networks improve cross-species prediction of transcription factor binding.
Cochran K, Srivastava D, Shrikumar A, Balsubramani A, Hardison RC, Kundaje A, Mahony S.
Cochran K, et al. Among authors: balsubramani a.
Genome Res. 2022 Mar;32(3):512-523. doi: 10.1101/gr.275394.121. Epub 2022 Jan 18.
Genome Res. 2022.
PMID: 35042722
Free PMC article.
Item in Clipboard
A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.
Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A.
Wainberg M, et al. Among authors: balsubramani a.
Nat Genet. 2021 May;53(5):638-649. doi: 10.1038/s41588-021-00840-z. Epub 2021 Apr 15.
Nat Genet. 2021.
PMID: 33859415
Free PMC article.
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The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network.
Rozenblatt-Rosen O, et al.
Cell. 2020 Apr 16;181(2):236-249. doi: 10.1016/j.cell.2020.03.053.
Cell. 2020.
PMID: 32302568
Free PMC article.
Review.
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