2019
Integrating multiomics longitudinal data to reconstruct networks underlying lung development
Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multiomics longitudinal data to reconstruct networks underlying lung development. American Journal Of Physiology - Lung Cellular And Molecular Physiology 2019, 317: l556-l568. PMID: 31432713, PMCID: PMC6879899, DOI: 10.1152/ajplung.00554.2018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, NewbornChildChild, PreschoolDNA MethylationEpigenesis, GeneticFemaleGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Regulatory NetworksHigh-Throughput Nucleotide SequencingHumansImmunity, InnateInfantInfant, NewbornLungMaleMiceMice, Inbred C57BLMicroRNAsOrganogenesisProteomicsPulmonary AlveoliRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsSingle-cell RNA-seq dataLung developmentDynamic regulatory networksOmics data setsRNA-seq dataIndividual cell typesHuman lung developmentRegulatory networksDNA methylationLaser capture microdissectionEpigenetic changesExpression trajectoriesKey pathwaysCell typesActive pathwaysCapture microdissectionRegulatorKey eventsInnate immunityNew insightsSpecific key eventsPathwayComprehensive understandingProteomicsMethylation
2018
iDREM: Interactive visualization of dynamic regulatory networks
Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLOS Computational Biology 2018, 14: e1006019. PMID: 29538379, PMCID: PMC5868853, DOI: 10.1371/journal.pcbi.1006019.Peer-Reviewed Original ResearchConceptsDynamic regulatory networksRegulatory networksHigh-throughput time series dataInteraction dataProtein-DNA interaction dataSingle-cell RNA-seqTime series gene expression dataStatic datasetsInteractive visualizationGene expression dataData typesRNA-seqTime series dataBiological processesExpression dataMiRNA expressionNetworkSeries dataImportant challengeNew versionDevelopmental dataNovel hypothesisUnified modelMultiple labsRecent years
2013
Reconstructing dynamic microRNA-regulated interaction networks
Schulz MH, Pandit KV, Cardenas C, Ambalavanan N, Kaminski N, Bar-Joseph Z. Reconstructing dynamic microRNA-regulated interaction networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 15686-15691. PMID: 23986498, PMCID: PMC3785769, DOI: 10.1073/pnas.1303236110.Peer-Reviewed Original ResearchConceptsTranscription factorsGene expressionDynamic Regulatory Events MinerTemporal gene expressionDynamic regulatory networksSpecific developmental phasesMRNA expression dataLung developmentRegulatory networksMiRNA targetsInteraction networksImportant miRNAsExpression dataMiRNAsAdditional miRNAsLung differentiationDevelopmental phasesMiRNAPostnatal lung developmentProgression pathwaysProliferation assaysExpressionRegulationMRNA expressionMicroRNAs