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
2021
Transcriptomics of the depressed and PTSD brain
Zhang J, Kaye AP, Wang J, Girgenti MJ. Transcriptomics of the depressed and PTSD brain. Neurobiology Of Stress 2021, 15: 100408. PMID: 34703849, PMCID: PMC8524242, DOI: 10.1016/j.ynstr.2021.100408.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsHigh-throughput transcriptomic methodsSingle-cell RNA sequencingCell RNA sequencingLarge genomic datasetsCommon molecular pathwaysTranscriptomic approachTranscriptional programsTranscriptome studiesStress adaptationTranscriptomic methodsRNA sequencingGenomic datasetsSurvival mechanismMolecular pathwaysOrganismsPTSD brainsTranscriptomeTranscriptomicsAdaptationNeurobiology of stressStressSequencingPathwayCentral questionNeurobiologists