NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
Zhang J, Liu J, McGillivray P, Yi C, Lochovsky L, Lee D, Gerstein M. NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. BMC Bioinformatics 2020, 21: 474. PMID: 33092526, PMCID: PMC7580035, DOI: 10.1186/s12859-020-03758-1.Peer-Reviewed Original ResearchConceptsDNase I hypersensitive sitesMutation rate heterogeneityDNA elementsCancer whole genome sequencesMutational hotspotsMutation burden analysisFunctional genomics dataNon-coding regionsGene regulatory networksWhole Genomes (PCAWG) projectWhole genome sequencesBackground mutation rateBurden analysisChromatin organizationReplication timingGenome sequenceRegulatory networksTranscription factorsHypersensitive sitesGenomic featuresRate heterogeneityGenome ProjectGenomic dataIntegrative methodGamma-Poisson mixture modelExpanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583: 699-710. PMID: 32728249, PMCID: PMC7410828, DOI: 10.1038/s41586-020-2493-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinDatabases, GeneticDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA Replication TimingGenomeGenome, HumanGenomicsHistonesHumansMiceMice, TransgenicMolecular Sequence AnnotationRegistriesRegulatory Sequences, Nucleic AcidRNA-Binding ProteinsTranscription, GeneticTransposasesConceptsMouse genomeCandidate cis-regulatory elementsCis-regulatory elementsDNA Elements (ENCODE) projectMouse fetal developmentChromatin structureGene regulationRespective genomesCellular contextDNA elementsDNA methylationENCODE dataTranscription factorsRNA transcriptionWeb-based serverGenomeExpansive resourceRNAEncyclopediaProteinFetal developmentChromatinTranscriptionHumansMethylation