2022
Microenvironmental sensing by fibroblasts controls macrophage population size
Zhou X, Franklin RA, Adler M, Carter TS, Condiff E, Adams TS, Pope SD, Philip NH, Meizlish ML, Kaminski N, Medzhitov R. Microenvironmental sensing by fibroblasts controls macrophage population size. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2205360119. PMID: 35930670, PMCID: PMC9371703, DOI: 10.1073/pnas.2205360119.Peer-Reviewed Original ResearchConceptsCell typesDensity-dependent gene expressionTGF-β target genesDiverse cell typesActin-dependent mechanismLineage-specific growth factorsDistinct cell typesGrowth factor availabilityActivation of YAP1Different cell typesExpression programsMicroenvironmental sensingTranscriptional coactivatorTarget genesGene expressionPopulation sizeFactor availabilityPopulation numbersTissue environmentTissue integrityHippoProliferation of macrophagesYAP1Animal tissuesMechanical forces
2018
Reconstructing differentiation networks and their regulation from time series single-cell expression data
Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Research 2018, 28: 383-395. PMID: 29317474, PMCID: PMC5848617, DOI: 10.1101/gr.225979.117.Peer-Reviewed Original ResearchTranscription factorsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataDiverse cell populationsGene expression levelsDifferent cell typesStages of organogenesisCell fateDescendant cellsDifferentiation networkExpression similarityKey regulatorRegulatory informationExpression dataCell typesProgenitor cellsCell trajectoriesExpression levelsCell populationsDevelopmental dataCellsLineagesOrganogenesisRegulator