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A compendium of RNA-binding motifs for decoding gene regulation.
Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR. Ray D, et al. Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311. Nature. 2013. PMID: 23846655 Free PMC article.
Deep learning in biomedicine.
Wainberg M, Merico D, Delong A, Frey BJ. Wainberg M, et al. Among authors: Frey BJ. Nat Biotechnol. 2018 Oct;36(9):829-838. doi: 10.1038/nbt.4233. Epub 2018 Sep 6. Nat Biotechnol. 2018. PMID: 30188539
Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism.
Kemaladewi DU, Maino E, Hyatt E, Hou H, Ding M, Place KM, Zhu X, Bassi P, Baghestani Z, Deshwar AG, Merico D, Xiong HY, Frey BJ, Wilson MD, Ivakine EA, Cohn RD. Kemaladewi DU, et al. Among authors: Frey BJ. Nat Med. 2017 Aug;23(8):984-989. doi: 10.1038/nm.4367. Epub 2017 Jul 17. Nat Med. 2017. PMID: 28714989
C2H2 zinc finger proteins greatly expand the human regulatory lexicon.
Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. Najafabadi HS, et al. Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18. Nat Biotechnol. 2015. PMID: 25690854
MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.
Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, Barbosa-Morais NL, Burge CB, Moffat J, Frey BJ, Nagy A, Ellis J, Wrana JL, Blencowe BJ. Han H, et al. Nature. 2013 Jun 13;498(7453):241-5. doi: 10.1038/nature12270. Epub 2013 Jun 5. Nature. 2013. PMID: 23739326 Free PMC article.
A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation.
Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. Aznarez I, et al. Genome Res. 2008 Aug;18(8):1247-58. doi: 10.1101/gr.073155.107. Epub 2008 May 2. Genome Res. 2008. PMID: 18456862 Free PMC article.
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.
C Yuen RK, Merico D, Bookman M, L Howe J, Thiruvahindrapuram B, Patel RV, Whitney J, Deflaux N, Bingham J, Wang Z, Pellecchia G, Buchanan JA, Walker S, Marshall CR, Uddin M, Zarrei M, Deneault E, D'Abate L, Chan AJ, Koyanagi S, Paton T, Pereira SL, Hoang N, Engchuan W, Higginbotham EJ, Ho K, Lamoureux S, Li W, MacDonald JR, Nalpathamkalam T, Sung WW, Tsoi FJ, Wei J, Xu L, Tasse AM, Kirby E, Van Etten W, Twigger S, Roberts W, Drmic I, Jilderda S, Modi BM, Kellam B, Szego M, Cytrynbaum C, Weksberg R, Zwaigenbaum L, Woodbury-Smith M, Brian J, Senman L, Iaboni A, Doyle-Thomas K, Thompson A, Chrysler C, Leef J, Savion-Lemieux T, Smith IM, Liu X, Nicolson R, Seifer V, Fedele A, Cook EH, Dager S, Estes A, Gallagher L, Malow BA, Parr JR, Spence SJ, Vorstman J, Frey BJ, Robinson JT, Strug LJ, Fernandez BA, Elsabbagh M, Carter MT, Hallmayer J, Knoppers BM, Anagnostou E, Szatmari P, Ring RH, Glazer D, Pletcher MT, Scherer SW. C Yuen RK, et al. Among authors: Frey BJ. Nat Neurosci. 2017 Apr;20(4):602-611. doi: 10.1038/nn.4524. Epub 2017 Mar 6. Nat Neurosci. 2017. PMID: 28263302 Free PMC article.
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