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Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.
Bai Z, Zhang D, Gao Y, Tao B, Zhang D, Bao S, Enninful A, Wang Y, Li H, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Bai Z, et al. Among authors: gerstein m, zhang d. Cell. 2024 Nov 14;187(23):6760-6779.e24. doi: 10.1016/j.cell.2024.09.001. Epub 2024 Sep 30. Cell. 2024. PMID: 39353436 Free PMC article.
Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT.
Fan R, Baysoy A, Tian X, Zhang F, Renauer P, Bai Z, Shi H, Zhang D, Li H, Tao B, Yang M, Enninful A, Gao F, Wang G, Zhang W, Tran T, Patterson N, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly J, Pruett-Miller S, Wang D, Xu M, Gerstein M, Chi H, Chen S. Fan R, et al. Among authors: gerstein m, zhang d. Res Sq [Preprint]. 2025 May 8:rs.3.rs-6481967. doi: 10.21203/rs.3.rs-6481967/v1. Res Sq. 2025. PMID: 40386382 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: gerstein m, zhang d. Nucleic Acids Res. 2025 Jan 6;53(D1):D966-D975. doi: 10.1093/nar/gkae1078. Nucleic Acids Res. 2025. PMID: 39565199 Free PMC article.
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, zhang d. bioRxiv [Preprint]. 2024 Oct 31:2024.10.29.620654. doi: 10.1101/2024.10.29.620654. bioRxiv. 2024. PMID: 39554180 Free PMC article. Preprint.
Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues.
Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Bai Z, et al. Among authors: gerstein m, zhang d. bioRxiv [Preprint]. 2024 Feb 8:2024.02.06.579143. doi: 10.1101/2024.02.06.579143. bioRxiv. 2024. Update in: Cell. 2024 Nov 14;187(23):6760-6779.e24. doi: 10.1016/j.cell.2024.09.001. PMID: 38370833 Free PMC article. Updated. Preprint.
ASTRO: Automated Spatial-Transcriptome whole RNA Output.
Zhang D, Chu Z, Huo Y, Jiang Y, Chen Y, Bai Z, Fan R, Lu J, Gerstein M. Zhang D, et al. Among authors: gerstein m. Bioinformatics. 2026 Jan 3;42(2):btaf688. doi: 10.1093/bioinformatics/btaf688. Bioinformatics. 2026. PMID: 41495477 Free PMC article.