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recount3: summaries and queries for large-scale RNA-seq expression and splicing.
Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. Wilks C, et al. Among authors: zhang d. Genome Biol. 2021 Nov 29;22(1):323. doi: 10.1186/s13059-021-02533-6. Genome Biol. 2021. PMID: 34844637 Free PMC article.
Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information.
Guelfi S, D'Sa K, Botía JA, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Quijada Leyton P, Gagliano Taliun SA, Nalls MA; International Parkinson’s Disease Genomics Consortium (IPDGC); UK Brain Expression Consortium (UKBEC); Small KS, Smith C, Ramasamy A, Hardy J, Weale ME, Ryten M. Guelfi S, et al. Among authors: d sa k, zhang d. Nat Commun. 2020 Feb 25;11(1):1041. doi: 10.1038/s41467-020-14483-x. Nat Commun. 2020. PMID: 32098967 Free PMC article.
Megadepth: efficient coverage quantification for BigWigs and BAMs.
Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B. Wilks C, et al. Among authors: zhang d. Bioinformatics. 2021 Sep 29;37(18):3014-3016. doi: 10.1093/bioinformatics/btab152. Bioinformatics. 2021. PMID: 33693500 Free PMC article.
IntroVerse: a comprehensive database of introns across human tissues.
García-Ruiz S, Gustavsson EK, Zhang D, Reynolds RH, Chen Z, Fairbrother-Browne A, Gil-Martínez AL, Botia JA, Collado-Torres L, Ryten M. García-Ruiz S, et al. Among authors: zhang d. Nucleic Acids Res. 2023 Jan 6;51(D1):D167-D178. doi: 10.1093/nar/gkac1056. Nucleic Acids Res. 2023. PMID: 36399497 Free PMC article.
Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage.
Chen Z, Zhang D, Reynolds RH, Gustavsson EK, García-Ruiz S, D'Sa K, Fairbrother-Browne A, Vandrovcova J; International Parkinson’s Disease Genomics Consortium (IPDGC); Hardy J, Houlden H, Gagliano Taliun SA, Botía J, Ryten M. Chen Z, et al. Among authors: d sa k, zhang d. Nat Commun. 2021 Apr 6;12(1):2076. doi: 10.1038/s41467-021-22262-5. Nat Commun. 2021. PMID: 33824317 Free PMC article.
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