2025
Adaptation to Volumetric Compression Drives an Apoptosis-Resistant and Invasive Phenotype in Liver Cancer.
Gong X, Ogino N, Leite M, Zhang D, Chen Z, Nguyen R, Liu R, Kruglov E, Flores K, Cabral A, Moreira de M Mendes G, Ehrlich B, Mak M. Adaptation to Volumetric Compression Drives an Apoptosis-Resistant and Invasive Phenotype in Liver Cancer. Cancer Research 2025 PMID: 40387600, DOI: 10.1158/0008-5472.can-24-0859.Peer-Reviewed Original ResearchEpithelial-to-mesenchymal transition genesLiver cancerResistance to apoptosisCell state transitionsProliferation of tumor cellsYAP nuclear translocationCancer cell invasionIntracellular calcium signalingLiver cancer developmentTranscriptional dynamicsRac1 activationCellular protrusionsInhibiting Rac1Apoptosis-resistantTranscriptional changesInvasive phenotypeIntracellular calciumTumor cellsCell invasionNuclear translocationCancer developmentCalcium signalingTransition genesCancer cellsLiver-specific markers
2024
Gene trajectory inference for single-cell data by optimal transport metrics
Qu R, Cheng X, Sefik E, Stanley III J, Landa B, Strino F, Platt S, Garritano J, Odell I, Coifman R, Flavell R, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nature Biotechnology 2024, 43: 258-268. PMID: 38580861, PMCID: PMC11452571, DOI: 10.1038/s41587-024-02186-3.Peer-Reviewed Original ResearchGene dynamicsGene programTrajectory inferenceBiological processesCell-cell graphDynamics of genesCell trajectory inferenceSingle-cell RNA sequencingSingle-cell dataCell state transitionsMyeloid lineage maturationDynamics of biological processesGene distributionRNA sequencingPseudotemporal orderingGene processingTrajectories of cellsGenesActivity of biological processesTechnical noiseGroups of cellsLineage maturationCellsConstruct cellsSequence
2023
Automated time-lapse data segmentation reveals in vivo cell state dynamics
Genuth M, Kojima Y, Jülich D, Kiryu H, Holley S. Automated time-lapse data segmentation reveals in vivo cell state dynamics. Science Advances 2023, 9: eadf1814. PMID: 37267354, PMCID: PMC10413672, DOI: 10.1126/sciadv.adf1814.Peer-Reviewed Original ResearchConceptsCell statesSingle-cell RNA sequencing dataCell state dynamicsCell behaviorEmbryonic development proceedsCell state transitionsRNA sequencing dataCollective cell behaviorIndividual cell behaviorsZebrafish tailbudLeft-right asymmetryCell tracking dataCollective cell motionGene expressionSequencing dataMolecular processesIndividual embryosDevelopment proceedsEmbryosCell motionParallel identificationBilateral symmetryReproducible patternTailbudState transitions
2022
Control of cell state transitions
Rukhlenko O, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher N, Kolch W, Kholodenko B. Control of cell state transitions. Nature 2022, 609: 975-985. PMID: 36104561, PMCID: PMC9644236, DOI: 10.1038/s41586-022-05194-y.Peer-Reviewed Original ResearchConceptsCell state transitionsCell fateCell statesCell fate transitionsCell fate decisionsSingle-cell dataNew biological insightsFate transitionsMovement of cellsFate decisionsWaddington landscapePhenotypic dataBiological insightsOmics datasetsOmics dataCellular modelMechanistic modelLandscape1FateCellsDevelopment pathwaysLandscapeBiologyState transitionsTherapeutic interventions
2019
Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
Craig M, Kaveh K, Woosley A, Brown AS, Goldman D, Eton E, Mehta RM, Dhawan A, Arai K, Rahman MM, Chen S, Nowak MA, Goldman A. Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer. PLOS Computational Biology 2019, 15: e1007278. PMID: 31449515, PMCID: PMC6709889, DOI: 10.1371/journal.pcbi.1007278.Peer-Reviewed Original ResearchMeSH KeywordsAdaptation, PhysiologicalCarcinoma, Non-Small-Cell LungCell Line, TumorCell ProliferationCoculture TechniquesComputational BiologyComputer SimulationCRISPR-Cas SystemsDEAD-box RNA HelicasesDrug Resistance, MultipleDrug Resistance, NeoplasmHumansLung NeoplasmsModels, BiologicalMutationRibonuclease IIIConceptsCancer cellsCell state transitionsWild-type cellsCooperative adaptationNon-small cell lung cancer cellsInterspecies competitionCell lung cancer cellsCRISPR/Drug-sensitive cellsLung cancer cellsNSCLC patient samplesDruggable targetsDrug pressureMutantsFlow cytometry dataPhenotypic heterogeneitySensitive cells
2010
Antiviral Response Dictated by Choreographed Cascade of Transcription Factors
Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, tenOever BR, Sealfon SC, Kleinstein SH. Antiviral Response Dictated by Choreographed Cascade of Transcription Factors. The Journal Of Immunology 2010, 184: 2908-2917. PMID: 20164420, PMCID: PMC2856074, DOI: 10.4049/jimmunol.0903453.Peer-Reviewed Original ResearchMeSH KeywordsConserved SequenceDendritic CellsGene Expression Regulation, ViralGenes, OverlappingHumansMonocytesMultigene FamilyNewcastle disease virusOligonucleotide Array Sequence AnalysisPredictive Value of TestsPromoter Regions, GeneticReproducibility of ResultsTranscription FactorsUp-RegulationConceptsCell state transitionsRegulatory networksTranscription factorsGenetic programMost individual genesNovel transcription factorSpecific transcription factorsSingle regulatory networkAntiviral responseGene expression changesCurrent biological knowledgeActivation of RIGChoreographed cascadePromoter analysisIndividual genesGenetic regulatory networksMaster regulatorExpression changesBiological knowledgeExpression kineticsImmune evasion genesAntiviral roleImmune antagonistsHost immune systemNewcastle disease virus
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