GENCODE 2025: reference gene annotation for human and mouse
Mudge J, Carbonell-Sala S, Diekhans M, Martinez J, Hunt T, Jungreis I, Loveland J, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés L, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James B, Jiang Y, Johnson R, Kaur G, Kay M, Mangan R, Maquedano M, Gómez L, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner M, Uszczynska-Ratajczak B, Wass E, Yang Y, Zhang D, Finn R, Gerstein M, Guigó R, Hubbard T, Kellis M, Kundaje A, Paten B, Tress M, Birney E, Martin F, Frankish A. GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Research 2024, gkae1078. PMID: 39565199, DOI: 10.1093/nar/gkae1078.Peer-Reviewed Original ResearchGene annotationLong-read transcriptome sequencingMulti-genome alignmentsRibo-Seq experimentsUCSC Genome BrowserState-of-the-art proteomicsGenome browserRibo-seqSpecies genomesMouse genomeTranscriptome sequencingGENCODEGenomeAnnotation workflowAnnotationSequencePangenomeMiceGenesetsState-of-the-artUCSCProteomicsTranscriptionGenesSpeciesSpatially 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 M, Fan R. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell 2024, 187: 6760-6779.e24. PMID: 39353436, PMCID: PMC11568911, DOI: 10.1016/j.cell.2024.09.001.Peer-Reviewed Original ResearchRNA biologyWhole-transcriptome sequencingMicroRNA regulatory networkSplicing dynamicsDeterministic barcodingRNA speciesRNA processingRNA variantsFFPE tissuesRegulatory networksTranscriptome sequencingSpliced isoformsNon-malignant cellsTumor clonal architecturesClonal architectureGene expressionCellular dynamicsRNAArchival formalin-fixed paraffin-embedded tissueMalignant subclonesFormalin-fixed paraffin-embedded (FFPEFFPE samplesParaffin-embedded (FFPEBiologyHuman lymphomas