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204 results

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Page 1
Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart.
Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A; Birth Defects Research Laboratory; Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Ma XR, et al. Among authors: kundaje a. medRxiv [Preprint]. 2024 Nov 22:2024.11.20.24317557. doi: 10.1101/2024.11.20.24317557. medRxiv. 2024. PMID: 39606363 Free PMC article. Preprint.
Mapping enhancer-gene regulatory interactions from single-cell data.
Sheth MU, Qiu WL, Rosa Ma X, Gschwind AR, Jagoda E, Tan AS, Einarsson H, Gorissen BL, Dubocanin D, McGinnis CS, Amgalan D, Satpathy AT, Jones TR, Steinmetz LM, Kundaje A, Ustun B, Engreitz JM, Andersson R. Sheth MU, et al. Among authors: kundaje a. bioRxiv [Preprint]. 2024 Nov 24:2024.11.23.624931. doi: 10.1101/2024.11.23.624931. bioRxiv. 2024. PMID: 39605382 Free PMC article. Preprint.
GENCODE 2025: reference gene annotation for human and mouse.
Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, Maquedano M, Gómez LM, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Birney E, Martin FJ, Frankish A. Mudge JM, et al. Among authors: kundaje a. Nucleic Acids Res. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Online ahead of print. Nucleic Acids Res. 2024. PMID: 39565199
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.
Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Mądry T, Jungreis I, Arnan C, Lagarde J, Borsari B, Sisu C, Jiang Y, Bennett R, Berry A, Cerdán-Vélez D, Cochran K, Vara C, Davidson C, Donaldson S, Dursun C, González-López S, Gopal Das S, Hardy M, Hollis Z, Kay M, Montañés JC, Ni P, Nurtdinov R, Palumbo E, Pulido-Quetglas C, Suner MM, Yu X, Zhang D, Loveland JE, Albà MM, Diekhans M, Tanzer A, Mudge JM, Flicek P, Martin FJ, Gerstein M, Kellis M, Kundaje A, Paten B, Tress ML, Johnson R, Uszczynska-Ratajczak B, Frankish A, Guigó R. Kaur G, et al. Among authors: kundaje a. bioRxiv [Preprint]. 2024 Oct 31:2024.10.29.620654. doi: 10.1101/2024.10.29.620654. bioRxiv. 2024. PMID: 39554180 Free PMC article. Preprint.
Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis.
Esplin ED, Hanson C, Wu S, Horning AM, Barapour N, Nevins SA, Jiang L, Contrepois K, Lee H, Guha TK, Hu Z, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Becker WR, Bahmani B, Khan A, Michael B, Weimer AK, Esplin DG, Shen J, Lancaster S, Monte E, Karathanos TV, Ladabaum U, Longacre TA, Kundaje A, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. Esplin ED, et al. Among authors: kundaje a. Nat Cancer. 2024 Nov;5(11):1737-1753. doi: 10.1038/s43018-024-00831-z. Epub 2024 Oct 30. Nat Cancer. 2024. PMID: 39478120 Free PMC article.
Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis.
Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. Zhu Y, et al. Among authors: kundaje a. Nat Cancer. 2024 Nov;5(11):1697-1712. doi: 10.1038/s43018-024-00823-z. Epub 2024 Oct 30. Nat Cancer. 2024. PMID: 39478119 Free PMC article.
An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity.
Levin-Konigsberg R, Mitra K, Spees K, Nigam A, Liu K, Januel C, Hivare P, Arana SM, Prolo LM, Kundaje A, Leonetti MD, Krishnan Y, Bassik MC. Levin-Konigsberg R, et al. Among authors: kundaje a. Dev Cell. 2024 Oct 21:S1534-5807(24)00604-X. doi: 10.1016/j.devcel.2024.10.003. Online ahead of print. Dev Cell. 2024. PMID: 39476838
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders.
Zhou B, Arthur JG, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo JXJ, Lee H, Nachun DC, Purmann C, Monte EM, Weimer AK, Qu PP, Shi M, Jiang L, Yang X, Fullard JF, Bendl J, Girdhar K, Kim M, Chen X; PsychENCODE Consortium; Greenleaf WJ, Duncan L, Ji HP, Zhu X, Song G, Montgomery SB, Palejev D, Zu Dohna H, Roussos P, Kundaje A, Hallmayer JF, Snyder MP, Wong WH, Urban AE. Zhou B, et al. Among authors: kundaje a. Cell. 2024 Nov 14;187(23):6687-6706.e25. doi: 10.1016/j.cell.2024.09.014. Epub 2024 Sep 30. Cell. 2024. PMID: 39353437
204 results