2021
Inference and analysis of cell-cell communication using CellChat
Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using CellChat. Nature Communications 2021, 12: 1088. PMID: 33597522, PMCID: PMC7889871, DOI: 10.1038/s41467-021-21246-9.Peer-Reviewed Original ResearchConceptsSingle-cell RNA sequencing dataCell-cell communicationEffective systems-level analysesDatabase of interactionsRNA sequencing dataIntercellular communication networksContext-specific pathwaysCellChatDiverse tissuesIntercellular communicationSystem-level analysisSignaling linkNetwork analysisPathwayCellsMolecular complexesCofactorComplexesReceptors
2019
Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage
Uderhardt S, Martins A, Tsang J, Lämmermann T, Germain R. Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage. Cell 2019, 177: 541-555.e17. PMID: 30955887, PMCID: PMC6474841, DOI: 10.1016/j.cell.2019.02.028.Peer-Reviewed Original ResearchConceptsTissue-resident macrophagesTissue homeostasisDiverse tissuesCell deathOrgan architectureIndividual cellsNeutrophil swarmsResident macrophagesDense swarmsLocal cell injuryIntravital imagingLocal disruptionParenchymal cell deathDynamic intravital imagingInescapable consequenceCell damageCell injuryHomeostasisMacrophagesCascadeInflammatory damageDamageCellsAccumulationDisruption
2017
Stomach and Bone
Kitay AM, Geibel JP. Stomach and Bone. Advances In Experimental Medicine And Biology 2017, 1033: 97-131. PMID: 29101653, DOI: 10.1007/978-3-319-66653-2_6.Peer-Reviewed Original ResearchConceptsBone metabolismGastric acid secretionCalcium-sensing receptorVitamin DParathyroid glandsAcid secretionGastrointestinal organsTherapeutic implicationsEndocrine modulatorsCalcium homeostasisDiseaseStomachOrgansMetabolismImportant playersIntermediary organDiverse tissuesDysfunctionCaSRPTHCalcitoninKidneySecretionIntestineReceptorsGenetic effects on gene expression across human tissues
Aguet F, Brown A, Castel S, Davis J, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segrè A, Strober B, Zappala Z, Cummings B, Gelfand E, Hadley K, Huang K, Lek M, Li X, Nedzel J, Nguyen D, Noble M, Sullivan T, Tukiainen T, MacArthur D, Getz G, Addington A, Guan P, Koester S, Little A, Lockhart N, Moore H, Rao A, Struewing J, Volpi S, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Mash D, Davis D, Sobin L, Barcus M, Branton P, Abell N, Balliu B, Delaneau O, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Han B, He A, Hormozdiari F, Li X, Liu B, Kang E, McDowell I, Ongen H, Palowitch J, Peterson C, Quon G, Ripke S, Saha A, Shabalin A, Shimko T, Sul J, Teran N, Tsang E, Zhang H, Zhou Y, Bustamante C, Cox N, Guigó R, Kellis M, McCarthy M, Conrad D, Eskin E, Li G, Nobel A, Sabatti C, Stranger B, Wen X, Wright F, Ardlie K, Dermitzakis E, Lappalainen T, Aguet F, Ardlie K, Cummings B, Gelfand E, Getz G, Hadley K, Handsaker R, Huang K, Kashin S, Karczewski K, Lek M, Li X, MacArthur D, Nedzel J, Nguyen D, Noble M, Segrè A, Trowbridge C, Tukiainen T, Abell N, Balliu B, Barshir R, Basha O, Battle A, Bogu G, Brown A, Brown C, Castel S, Chen L, Chiang C, Conrad D, Cox N, Damani F, Davis J, Delaneau O, Dermitzakis E, Engelhardt B, Eskin E, Ferreira P, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Guigo R, Hall I, Han B, He Y, Hormozdiari F, Howald C, Kyung Im H, Jo B, Yong Kang E, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy M, McDowell I, Mohammadi P, Monlong J, Montgomery S, Muñoz-Aguirre M, Ndungu A, Nicolae D, Nobel A, Oliva M, Ongen H, Palowitch J, Panousis N, Papasaikas P, Park Y, Parsana P, Payne A, Peterson C, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott A, Shabalin A, Sodaei R, Stephens M, Stranger B, Strober B, Sul J, Tsang E, Urbut S, van de Bunt M, Wang G, Wen X, Wright F, Xi H, Yeger-Lotem E, Zappala Z, Zaugg J, Zhou Y, Akey J, Bates D, Chan J, Chen L, Claussnitzer M, Demanelis K, Diegel M, Doherty J, Feinberg A, Fernando M, Halow J, Hansen K, Haugen E, Hickey P, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya M, Lee K, Billy Li J, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano M, Molinie B, Montgomery S, Nelson J, Neri F, Oliva M, Park Y, Pierce B, Rinaldi N, Rizzardi L, Sandstrom R, Skol A, Smith K, Snyder M, Stamatoyannopoulos J, Stranger B, Tang H, Tsang E, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Nierras C, Branton P, Carithers L, Guan P, Moore H, Rao A, Vaught J, Gould S, Lockart N, Martin C, Struewing J, Volpi S, Addington A, Koester S, Little A, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Davis D, Mash D, Undale A, Smith A, Tabor D, Roche N, McLean J, Vatanian N, Robinson K, Sobin L, Barcus M, Valentino K, Qi L, Hunter S, Hariharan P, Singh S, Um K, Matose T, Tomaszewski M, Barker L, Mosavel M, Siminoff L, Traino H, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion S, Zerbino D, Craft B, Goldman M, Haeussler M, Kent W, Lee C, Paten B, Rosenbloom K, Vivian J, Zhu J. Genetic effects on gene expression across human tissues. Nature 2017, 550: 204-213. PMID: 29022597, PMCID: PMC5776756, DOI: 10.1038/nature24277.Peer-Reviewed Original ResearchConceptsGene expression levelsGenetic effectsExpression levelsGenotype-Tissue Expression (GTEx) projectLocal genetic variationMajority of genesHuman genetic traitsDisease-associated variationMolecular functionsGene regulationHuman genomeHuman tissuesExpression projectGenetic variationGenetic basisDiverse tissuesGene expressionTissue specificityGenetic traitsCellular mechanismsGenesFunctional propertiesGenomeTissueLociTissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson J, Chen C, Lopes-Ramos C, Kuijjer M, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics 2017, 18: 437. PMID: 28974199, PMCID: PMC5627434, DOI: 10.1186/s12859-017-1847-x.Peer-Reviewed Original ResearchConceptsRNA-seq data setsRNA-seqGenotype-Tissue ExpressionRNA-seq processingGenome-wide transcriptional profilingRNA-seq studiesRNA-seq dataGene filteringDownstream analysisRNA sequencingTranscriptional profilesDiverse tissuesAnalytical pipelineR packageQuality controlSignificant analytical challengeSoftware pipelineGenesRNAMulti-group studyNormalization stepAnalytical challengesResultsWeTissueExpression
2016
Hardwiring Stem Cell Communication through Tissue Structure
Xin T, Greco V, Myung P. Hardwiring Stem Cell Communication through Tissue Structure. Cell 2016, 164: 1212-1225. PMID: 26967287, PMCID: PMC4805424, DOI: 10.1016/j.cell.2016.02.041.Peer-Reviewed Original Research
2009
The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect
Thomson T, Lin H. The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect. Annual Review Of Cell And Developmental Biology 2009, 25: 355-376. PMID: 19575643, PMCID: PMC2780330, DOI: 10.1146/annurev.cellbio.24.110707.175327.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPIWI proteinsGermline stem cell maintenanceStem cell maintenanceSmall noncoding RNAsGermline determinationAGO proteinsGermline developmentMetazoan speciesPiRNA speciesPIWI subfamiliesSmall RNAsIntergenic sequencesPosttranscriptional regulationCell maintenanceRNA precursorsNoncoding RNAsPiwi familyDiverse functionsDiverse tissuesRNANovel mechanismProteinBiogenesisSpeciesDifferentiation of Neural Progenitor Cells in a Microfluidic Chip‐Generated Cytokine Gradient
Park J, Kim S, Woo D, Lee E, Kim J, Lee S. Differentiation of Neural Progenitor Cells in a Microfluidic Chip‐Generated Cytokine Gradient. Stem Cells 2009, 27: 2646-2654. PMID: 19711444, DOI: 10.1002/stem.202.Peer-Reviewed Original ResearchConceptsCell typesNeural progenitorsHuman embryonic stem cellsEarly embryonic developmentStem cellsEmbryonic stem cellsCytokine gradientsEnriched populationNeural progenitor cellsPrimitive stem cellsEmbryonic developmentSignaling moleculesDiverse tissuesCell body clustersProgenitor cellsNeurite bundlesGrowth factorProgenitorsCell-friendly microenvironmentCellsDifferentiationExogenous cytokinesImportant roleBody clustersSpatial gradients
2008
Regulation of the Noradrenaline Neurotransmitter Phenotype by the Transcription Factor AP-2β*
Hong S, Lardaro T, Oh M, Huh Y, Ding Y, Kang U, Kirfel J, Buettner R, Kim K. Regulation of the Noradrenaline Neurotransmitter Phenotype by the Transcription Factor AP-2β*. Journal Of Biological Chemistry 2008, 283: 16860-16867. PMID: 18424435, PMCID: PMC2423267, DOI: 10.1074/jbc.m709106200.Peer-Reviewed Original ResearchConceptsAP-2betaNervous systemDopamine beta-hydroxylaseCentral nervous systemPeripheral nervous systemNA neuronsSympathetic developmentNeonatal lethalityNull miceLocus coeruleusNeurotransmitter phenotypeSympathetic gangliaPharmacological treatmentMouse embryosBeta-hydroxylaseAP-2NoradrenalineAP-2 factorsMiceNeuronal developmentPhenotypic specificityCell typesFamily transcription factorsDiverse tissuesTranscription factors
2003
Mitochondrial uncoupling protein 2 in the central nervous system: neuromodulator and neuroprotector
Horvath TL, Diano S, Barnstable C. Mitochondrial uncoupling protein 2 in the central nervous system: neuromodulator and neuroprotector. Biochemical Pharmacology 2003, 65: 1917-1921. PMID: 12787871, DOI: 10.1016/s0006-2952(03)00143-6.Peer-Reviewed Original ResearchConceptsMitochondrial membrane potentialInner membraneRole of UCP2Normal neuronal functionDiverse tissuesUnknown functionProtein 2Functional significanceImportant playersCentral nervous systemNeuronal functionProteinMembrane potentialNervous systemUCP2Disease statesUCPBrown adipose tissueNew avenuesMitochondriaTissueAdipose tissueUCP1Better understandingUncoupler
1998
Neuroprotective versus neurodestructive effects of NO‐related species
Lipton S, Choi Y, Sucher N, Chen H. Neuroprotective versus neurodestructive effects of NO‐related species. BioFactors 1998, 8: 33-40. PMID: 9699006, DOI: 10.1002/biof.5520080107.Peer-Reviewed Original ResearchConceptsNMDA receptorsCentral nervous systemNMDA receptor subunitsNeuronal injuryNeurodestructive effectsNervous systemRedox modulationReceptor subunitsNitric oxideExcessive Ca2Protective actionChannel activitySuperoxide anionNO groupReceptorsS-nitrosylationGroupDiverse tissuesNeuroprotectionInjuryBrain
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