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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2002 4
2003 2
2004 3
2005 3
2006 3
2007 3
2008 10
2009 6
2010 10
2011 13
2012 14
2013 10
2014 13
2015 9
2016 9
2017 13
2018 11
2019 14
2020 14
2021 6
2022 6
2023 9
2024 8
2025 10
2026 1

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189 results

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Page 1
An expanded registry of candidate cis-regulatory elements.
Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Khandpekar M, Ganna M, Choudhury E, Swofford R, Phan H, Ramirez CC, Campbell M, Likhite M, Farrell NP, Weimer AK, Pampari A, Ramalingam V, Reese F, Borsari B, Yu X, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Colubri A, Beer MA, Guigó R, Gerstein MB, Engreitz JM, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z. Moore JE, et al. Among authors: bernstein be. Nature. 2026 Jan 7. doi: 10.1038/s41586-025-09909-9. Online ahead of print. Nature. 2026. PMID: 41501460
In vivo CRISPR screening in head and neck cancer reveals Uchl5 as an immunotherapy target.
Fu C, Saddawi-Konefka R, Chinai JM, Kim SY, Kammula AV, Perera JJ, Jiang A, Tiwari P, Kistler EN, Tang S, Luna SM, Colvin KJ, Dubrot J, Anderson S, Fetterman RA, Chuong CL, Lane-Reticker SK, Cheruiyot CK, Muscato AJ, Alipour Z, Adkins DR, Griffin GK, Bernstein BE, Egloff AM, Yates KB, Chernock RD, Gutkind JS, Uppaluri R, Manguso RT. Fu C, et al. Among authors: bernstein be. Nat Commun. 2025 Sep 29;16(1):8572. doi: 10.1038/s41467-025-63592-y. Nat Commun. 2025. PMID: 41022734 Free PMC article.
Loss of NOTCH2 creates a TRIM28-dependent vulnerability in small cell lung cancer.
Hong D, Lyu Y, Nayak R, Becker JS, Booker MA, Masuzawa K, Devos Z, Wang T, Saito S, Liu Q, Li Y, Li Z, Knelson EH, Thai T, Duplaquet L, Laimon YN, Roberti De Oliveira G, Signoretti S, Doench JG, Barbie DA, Tolystorukov MY, Qi J, Bernstein BE, Ge Y, Oser MG. Hong D, et al. Among authors: bernstein be. Dev Cell. 2025 Dec 15;60(24):3462-3479.e13. doi: 10.1016/j.devcel.2025.07.023. Epub 2025 Aug 26. Dev Cell. 2025. PMID: 40865518
Mutant IDH silences GSX2 to reprogram neural progenitor cell fate and promote gliomagenesis.
Xiao Y, Shi DD, Guo L, Neumann E, Levitt MM, Kaphle P, Shipman T, Li H, Cai F, Ramirez DMO, Zacharias LG, Chen Z, Lin M, Puliyappadamba VT, Chen T, Savani MR, Peña S, Wansapura J, Mathews TP, Mishra P, Kim YJ, Raj P, Richardson TE, Xu J, Mack SC, Rahme GJ, Bernstein BE, DeBerardinis RJ, Tirosh I, Suvà ML, Xu L, Abdullah KG, McBrayer SK. Xiao Y, et al. Among authors: bernstein be. bioRxiv [Preprint]. 2025 Aug 13:2025.08.12.667486. doi: 10.1101/2025.08.12.667486. bioRxiv. 2025. PMID: 40832272 Free PMC article. Preprint.
The Somatic Mosaicism across Human Tissues Network.
Coorens THH, Oh JW, Choi YA, Lim NS, Zhao B, Voshall A, Abyzov A, Antonacci-Fulton L, Aparicio S, Ardlie KG, Bell TJ, Bennett JT, Bernstein BE, Blanchard TG, Boyle AP, Buenrostro JD, Burns KH, Chen F, Chen R, Choudhury S, Doddapaneni HV, Eichler EE, Evrony GD, Faith MA, Fazzio TG, Fulton RS, Garber M, Gehlenborg N, Germer S, Getz G, Gibbs RA, Hernandez RG, Jin F, Korbel JO, Landau DA, Lawson HA, Lennon NJ, Li H, Li Y, Loh PR, Marth G, McConnell MJ, Mills RE, Montgomery SB, Natarajan P, Park PJ, Satija R, Sedlazeck FJ, Shao DD, Shen H, Stergachis AB, Underhill HR, Urban AE, VonDran MW, Walsh CA, Wang T, Wu TP, Zong C, Lee EA, Vaccarino FM; Somatic Mosaicism across Human Tissues Network. Coorens THH, et al. Among authors: bernstein be. Nature. 2025 Jul;643(8070):47-59. doi: 10.1038/s41586-025-09096-7. Epub 2025 Jul 2. Nature. 2025. PMID: 40604182 Free PMC article. Review.
Programs, origins and immunomodulatory functions of myeloid cells in glioma.
Miller TE, El Farran CA, Couturier CP, Chen Z, D'Antonio JP, Verga J, Villanueva MA, Gonzalez Castro LN, Tong YE, Saadi TA, Chiocca AN, Zhang Y, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE. Miller TE, et al. Among authors: bernstein be. Nature. 2025 Apr;640(8060):1072-1082. doi: 10.1038/s41586-025-08633-8. Epub 2025 Feb 26. Nature. 2025. PMID: 40011771 Free PMC article.
Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles.
Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB; ENCODE Imputation Challenge Participants. Schreiber JM, et al. Among authors: bernstein be. Genome Biol. 2025 Feb 13;26(1):31. doi: 10.1186/s13059-025-03494-w. Genome Biol. 2025. PMID: 39948633 Free PMC article. No abstract available.
Multi-locus CRISPRi targeting with a single truncated guide RNA.
Moore MM, Wekhande S, Issner R, Collins A, Cruz AJ, Liu YV, Javed N, Casaní-Galdón S, Buenrostro JD, Epstein CB, Mattei E, Doench JG, Bernstein BE, Shoresh N, Najm FJ. Moore MM, et al. Among authors: bernstein be. Nat Commun. 2025 Feb 4;16(1):1357. doi: 10.1038/s41467-025-56144-x. Nat Commun. 2025. PMID: 39905017 Free PMC article.
A multi-modal transformer for cell type-agnostic regulatory predictions.
Javed N, Weingarten T, Sehanobish A, Roberts A, Dubey A, Choromanski K, Bernstein BE. Javed N, et al. Among authors: bernstein be. Cell Genom. 2025 Feb 12;5(2):100762. doi: 10.1016/j.xgen.2025.100762. Epub 2025 Jan 29. Cell Genom. 2025. PMID: 39884279 Free PMC article.
189 results