2024
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Duan Z, Xu S, Srinivasan S, Hwang A, Lee C, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings In Bioinformatics 2024, 25: bbae096. PMID: 38493342, PMCID: PMC10944576, DOI: 10.1093/bib/bbae096.Peer-Reviewed Original ResearchConceptsA/B compartmentsEpigenetic dataChromatin interaction frequenciesCell type-specific mannerChromatin conformational changesGenome binsGenomic regionsChromatin conformationEukaryotic DNAChromatin compartmentsDynamic compartmentalizationRepressed stateGenetic blueprintTranscriptional programsTranscriptional changesChromatinConformational changesComplex tissuesInteraction frequencyCompartmentGenomeChromosomeStructural heterogeneityDNAA/B
2012
Architecture of the human regulatory network derived from ENCODE data
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O’Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489: 91-100. PMID: 22955619, PMCID: PMC4154057, DOI: 10.1038/nature11245.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineDNAEncyclopedias as TopicGATA1 Transcription FactorGene Expression ProfilingGene Regulatory NetworksGenome, HumanGenomicsHumansK562 CellsMolecular Sequence AnnotationOrgan SpecificityPhosphorylationPolymorphism, Single NucleotideProtein Interaction MapsRegulatory Sequences, Nucleic AcidRNA, UntranslatedSelection, GeneticTranscription FactorsTranscription Initiation SiteConceptsTranscription factorsRegulatory networksHuman transcriptional regulatory networkHuman regulatory networkSpecific genomic locationsTranscription-related factorsState of genesTranscriptional regulatory networksAllele-specific activityPersonal genome sequencesGenomic locationStrong selectionGenome sequenceENCODE dataGenomic informationInformation-flow bottlenecksRegulatory informationConnected network componentsCombinatorial fashionInfluences expressionHuman biologyBinding informationNetwork motifsCo-associationGenes
2009
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology 2009, 27: 66-75. PMID: 19122651, PMCID: PMC2924752, DOI: 10.1038/nbt.1518.Peer-Reviewed Original Research