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2023 1
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Page 1
Single-cell genomics and regulatory networks for 388 human brains.
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X; PsychENCODE Consortium‡; Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M; PsychENCODE Consortium. Emani PS, et al. Among authors: gerstein m, ni p. Science. 2024 May 24;384(6698):eadi5199. doi: 10.1126/science.adi5199. Epub 2024 May 24. Science. 2024. PMID: 38781369 Free PMC article.
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H; PsychENCODE Consortium†; Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ; PsychENCODE Consortium. Wen C, et al. Among authors: gerstein m. Science. 2024 May 24;384(6698):eadh0829. doi: 10.1126/science.adh0829. Epub 2024 May 24. Science. 2024. PMID: 38781368 Free PMC article.
GENCODE: reference annotation for the human and mouse genomes in 2023.
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron CG, Gonzalez JM, Hardy M, Harrison PW, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin FJ, Gómez LM, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt BM, Schreiber JM, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang YT, Yates A, Zafrulla Z, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Flicek P. Frankish A, et al. Among authors: gerstein m, ni p. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. Nucleic Acids Res. 2023. PMID: 36420896 Free PMC article.
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: gerstein m, ni p. Nucleic Acids Res. 2025 Jan 6;53(D1):D966-D975. doi: 10.1093/nar/gkae1078. Nucleic Acids Res. 2025. PMID: 39565199 Free PMC article.
An expanded reference catalog of translated open reading frames for biomedical research.
Chothani S, Ruiz-Orera J, Tierney JAS, Clauwaert J, Deutsch EW, Alba MM, Aspden JL, Baranov PV, Bazzini AA, Bruford EA, Brunet MA, Cardon T, Carvunis AR, Casola C, Choudhary JS, Dean K, Faridi P, Fierro-Monti I, Fournier I, Frankish A, Gerstein M, Hubner N, Jiang Y, Kellis M, Kok LW, Martinez TF, Menschaert G, Ni P, Orchard S, Roucou X, Rozowsky J, Salzet M, Siragusa M, Slavoff S, Swirski MI, Valen E, Vizcaino JA, Wacholder A, Wu W, Xie Z, Yang YT, Moritz RL, Mudge J, van Heesch S, Prensner JR, Rackham OJ. Chothani S, et al. Among authors: gerstein m, ni p. bioRxiv [Preprint]. 2025 Jul 7:2025.07.03.662928. doi: 10.1101/2025.07.03.662928. bioRxiv. 2025. PMID: 40672165 Free PMC article. Preprint.
Single-cell genomics and regulatory networks for 388 human brains.
Emani PS, Liu JJ, Clarke D, Jensen M, Warrell J, Gupta C, Meng R, Lee CY, Xu S, Dursun C, Lou S, Chen Y, Chu Z, Galeev T, Hwang A, Li Y, Ni P, Zhou X; PsychENCODE Consortium; Bakken TE, Bendl J, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Fullard JF, Gancz M, Garrido-Martín D, Gaynor-Gillett S, Grundman J, Hawken N, Henry E, Hoffman GE, Huang A, Jiang Y, Jin T, Jorstad NL, Kawaguchi R, Khullar S, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran JR, Nguyen E, Phalke N, Pjanic M, Pratt H, Quintero D, Rajagopalan AS, Riesenmy TR, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini KJ, Wamsley B, Wang G, Xia Y, Xiao S, Yang AC, Zheng S, Gandal MJ, Lee D, Lein ES, Roussos P, Sestan N, Weng Z, White KP, Won H, Girgenti MJ, Zhang J, Wang D, Geschwind D, Gerstein M. Emani PS, et al. Among authors: gerstein m, ni p. bioRxiv [Preprint]. 2024 Mar 30:2024.03.18.585576. doi: 10.1101/2024.03.18.585576. bioRxiv. 2024. Update in: Science. 2024 May 24;384(6698):eadi5199. doi: 10.1126/science.adi5199. PMID: 38562822 Free PMC article. Updated. Preprint.
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: gerstein m, ni p. bioRxiv [Preprint]. 2024 Oct 31:2024.10.29.620654. doi: 10.1101/2024.10.29.620654. bioRxiv. 2024. PMID: 39554180 Free PMC article. Preprint.
Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes.
Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Lu X, et al. Among authors: gerstein m, ni p. bioRxiv [Preprint]. 2024 Mar 19:2024.03.18.585480. doi: 10.1101/2024.03.18.585480. bioRxiv. 2024. Update in: Cell Rep. 2024 Jul 23;43(7):114376. doi: 10.1016/j.celrep.2024.114376. PMID: 38562714 Free PMC article. Updated. Preprint.
13 results