2024
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-artUCSCProteomicsTranscriptionGenesSpecies
2014
Comparative analysis of the transcriptome across distant species
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species. Nature 2014, 512: 445-448. PMID: 25164755, PMCID: PMC4155737, DOI: 10.1038/nature13424.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCaenorhabditis elegansChromatinCluster AnalysisDrosophila melanogasterGene Expression ProfilingGene Expression Regulation, DevelopmentalHistonesHumansLarvaModels, GeneticMolecular Sequence AnnotationPromoter Regions, GeneticPupaRNA, UntranslatedSequence Analysis, RNATranscriptome