2023
Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
Chen X, Wang Y, Cappuccio A, Cheng W, Zamojski F, Nair V, Miller C, Rubenstein A, Nudelman G, Tadych A, Theesfeld C, Vornholt A, George M, Ruffin F, Dagher M, Chawla D, Soares-Schanoski A, Spurbeck R, Ndhlovu L, Sebra R, Kleinstein S, Letizia A, Ramos I, Fowler V, Woods C, Zaslavsky E, Troyanskaya O, Sealfon S. Author Correction: Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nature Computational Science 2023, 3: 805-805. PMID: 38177788, PMCID: PMC10766523, DOI: 10.1038/s43588-023-00523-1.Peer-Reviewed Original ResearchMapping disease regulatory circuits at cell-type resolution from single-cell multiomics data
Chen X, Wang Y, Cappuccio A, Cheng W, Zamojski F, Nair V, Miller C, Rubenstein A, Nudelman G, Tadych A, Theesfeld C, Vornholt A, George M, Ruffin F, Dagher M, Chawla D, Soares-Schanoski A, Spurbeck R, Ndhlovu L, Sebra R, Kleinstein S, Letizia A, Ramos I, Fowler V, Woods C, Zaslavsky E, Troyanskaya O, Sealfon S. Mapping disease regulatory circuits at cell-type resolution from single-cell multiomics data. Nature Computational Science 2023, 3: 644-657. PMID: 37974651, PMCID: PMC10653299, DOI: 10.1038/s43588-023-00476-5.Peer-Reviewed Original ResearchCell-type resolutionRegulatory circuitsMethicillin resistanceTransposase-accessible chromatin sequencingDisease-associated transcription factorsOmics data typesSingle-cell dataSingle-cell RNA sequencingGene expression changesChromatin sitesMethicillin-susceptible S. aureus infectionsChromatin sequencingTranscription factorsRNA sequencingStaphylococcus aureus sepsisMultiomics dataExpression analysisExpression changesBloodstream infectionsBacterial sepsisCD14 monocytesSequencePredictive valueHierarchical Bayesian approachUninfected controls
2022
Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
Duren Z, Chang F, Naqing F, Xin J, Liu Q, Wong W. Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. Genome Biology 2022, 23: 114. PMID: 35578363, PMCID: PMC9109353, DOI: 10.1186/s13059-022-02682-2.Peer-Reviewed Original ResearchConceptsGene expressionChromatin accessibility dataCis-regulatory potentialCis-regulatory elementsCis-regulatory networksProfile of gene expressionNetwork inference accuracyGWAS variantsChromatin accessibilityRegulatory networksMultiomics dataChromatinRegulatory analysisExpressionGWASInflammatory bowel diseaseBowel diseaseVariantsAccess data
2021
Multiomics Analysis and Systems Biology Integration Identifies the Roles of IL-9 in Keratinocyte Metabolic Reprogramming
Marathe S, Dhamija B, Kumar S, Jain N, Ghosh S, Dharikar J, Srinivasan S, Das S, Sawant A, Desai S, Khan F, Syiemlieh A, Munde M, Nayak C, Gandhi M, Kumar A, Srivastava S, Venkatesh K, Barthel S, Purwar R. Multiomics Analysis and Systems Biology Integration Identifies the Roles of IL-9 in Keratinocyte Metabolic Reprogramming. Journal Of Investigative Dermatology 2021, 141: 1932-1942. PMID: 33667432, DOI: 10.1016/j.jid.2021.02.013.Peer-Reviewed Original ResearchConceptsMetabolic reprogrammingHuman primary keratinocytesIL-9Production of tricarboxylic acid cycle intermediatesRedirection of metabolic fluxIntegration of multiomics dataCentral carbohydrate metabolismElectron transport chain proteinsPrimary keratinocytesHigh-throughput quantitative proteomicsTricarboxylic acid cycle intermediatesStable isotope metabolomicsNuclear magnetic resonance-based metabolomicsElectron transport chainSystems-level analysisIL-9-producing T cellsPathogenesis of inflammatory disordersMetabolic fluxIncreased glucose consumptionIL-9 signalingTransport chainQuantitative proteomicsMultiomics dataCycle intermediatesMultiomics analysis
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