2022
Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
Raredon M, Yang J, Kothapalli N, Lewis W, Kaminski N, Niklason L, Kluger Y. Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES. Bioinformatics 2022, 39: btac775. PMID: 36458905, PMCID: PMC9825783, DOI: 10.1093/bioinformatics/btac775.Peer-Reviewed Original ResearchConceptsCell-cell interactionsCell-cell signalingSingle-cell resolutionSingle-cell dataLocal cellular microenvironmentSingle-cell levelSpatial transcriptomics dataCell clustersExtracellular signalingTranscriptomic dataGene expression valuesSpatial transcriptomicsSignaling mechanismCellular microenvironmentNicheExpression valuesSupplementary dataSignalingTranscriptomicsComprehensive visualizationBioinformaticsInteractionCINS: Cell Interaction Network inference from Single cell expression data
Yuan Y, Cosme C, Adams TS, Schupp J, Sakamoto K, Xylourgidis N, Ruffalo M, Li J, Kaminski N, Bar-Joseph Z. CINS: Cell Interaction Network inference from Single cell expression data. PLOS Computational Biology 2022, 18: e1010468. PMID: 36095011, PMCID: PMC9499239, DOI: 10.1371/journal.pcbi.1010468.Peer-Reviewed Original ResearchConceptsCell type interactionsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataScRNA-seq experimentsCell-cell interactionsExpression dataCell typesMouse datasetsNetwork inferenceCell interactionsInteraction predictionNetwork analysisInference pipelineGenesCINSProteinInteractionBayesian network analysisComputation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome
Raredon MSB, Yang J, Garritano J, Wang M, Kushnir D, Schupp JC, Adams TS, Greaney AM, Leiby KL, Kaminski N, Kluger Y, Levchenko A, Niklason LE. Computation and visualization of cell–cell signaling topologies in single-cell systems data using Connectome. Scientific Reports 2022, 12: 4187. PMID: 35264704, PMCID: PMC8906120, DOI: 10.1038/s41598-022-07959-x.Peer-Reviewed Original Research
2019
Single-cell connectomic analysis of adult mammalian lungs
Raredon MSB, Adams TS, Suhail Y, Schupp JC, Poli S, Neumark N, Leiby KL, Greaney AM, Yuan Y, Horien C, Linderman G, Engler AJ, Boffa DJ, Kluger Y, Rosas IO, Levchenko A, Kaminski N, Niklason LE. Single-cell connectomic analysis of adult mammalian lungs. Science Advances 2019, 5: eaaw3851. PMID: 31840053, PMCID: PMC6892628, DOI: 10.1126/sciadv.aaw3851.Peer-Reviewed Original ResearchConceptsTissue homeostasisMammalian lungSingle-cell RNA sequencing techniquesAdult mammalian lungRNA sequencing techniquesCell-cell interactionsSequencing techniquesKey pathwaysAlveolar type IFunctional roleCell typesCell populationsRegenerative medicineHomeostatic mechanismsHomeostasisFine architectureFunctional lung tissueIncomplete understandingMajor roleType ITissueRegulationPathwayAlveolar cell populationsDistal lung
1999
A Mechanism for Regulating Pulmonary Inflammation and Fibrosis: The Integrin αvβ6 Binds and Activates Latent TGF β1
Munger J, Huang X, Kawakatsu H, Griffiths M, Dalton S, Wu J, Pittet J, Kaminski N, Garat C, Matthay M, Rifkin D, Sheppard D. A Mechanism for Regulating Pulmonary Inflammation and Fibrosis: The Integrin αvβ6 Binds and Activates Latent TGF β1. Cell 1999, 96: 319-328. PMID: 10025398, DOI: 10.1016/s0092-8674(00)80545-0.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsAntigens, NeoplasmBleomycinCHO CellsCricetinaeEpithelial CellsEsophagusHumansIntegrinsKeratinocytesLigandsMiceMice, KnockoutPeptide FragmentsProtein BindingProtein PrecursorsProteinsPulmonary FibrosisTransforming Growth Factor betaTransforming Growth Factor beta1Tumor Cells, CulturedConceptsLatency-associated peptideIntegrin alpha v beta 6Alpha v beta 6 integrinAlpha v beta 6Beta gene productsTGF beta 1Latent TGF-β1TGF-beta functionGrowth factor-beta (TGF-beta) family membersPulmonary inflammationExaggerated inflammationPulmonary fibrosisTGF-β1Beta 6Alpha vBeta 1Beta family membersInflammationFibrosisFamily membersNovel mechanismExtracellular activationVivoActivationIntegrins