2023
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Liu Y, Zhao J, Adams T, Wang N, Schupp J, Wu W, McDonough J, Chupp G, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023, 24: 318. PMID: 37608264, PMCID: PMC10463720, DOI: 10.1186/s12859-023-05432-8.Peer-Reviewed Original Research
2022
CINS: 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 ResearchMeSH KeywordsAnimalsBayes TheoremCell CommunicationGene Expression ProfilingLigandsMiceSequence Analysis, RNASingle-Cell AnalysisConceptsCell type interactionsSingle-cell expression dataSingle-cell RNA-seq dataRNA-seq dataScRNA-seq experimentsCell-cell interactionsExpression dataCell typesMouse datasetsNetwork inferenceCell interactionsInteraction predictionNetwork analysisInference pipelineGenesCINSProteinInteractionBayesian network analysis
2021
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Muus C, Luecken M, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav E, Subramanian A, Smillie C, Jagadeesh K, Duong E, Fiskin E, Torlai Triglia E, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber A, Chung H, Montoro D, Adams T, Aliee H, Allon S, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui L, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon T, Cuoco M, Cuomo A, Deprez M, Duclos G, Fine D, Fischer D, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez A, Habermann A, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos T, Kuo C, Larsson L, Leney-Greene M, Lim K, Litviňuková M, Ludwig L, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr C, Mbano I, McAdams A, Nabhan A, Nyquist S, Penland L, Poirion O, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp J, Shea C, Shi X, Sinha R, Sit R, Slowikowski K, Slyper M, Smith N, Sountoulidis A, Strunz M, Sullivan T, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini K, Tucker N, Vernon K, Wadsworth M, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler C. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine 2021, 27: 546-559. PMID: 33654293, PMCID: PMC9469728, DOI: 10.1038/s41591-020-01227-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAlveolar Epithelial CellsAngiotensin-Converting Enzyme 2Cathepsin LCOVID-19Datasets as TopicDemographyFemaleGene Expression ProfilingHost-Pathogen InteractionsHumansLungMaleMiddle AgedOrgan SpecificityRespiratory SystemSARS-CoV-2Sequence Analysis, RNASerine EndopeptidasesSingle-Cell AnalysisVirus InternalizationConceptsSingle-cell RNA-sequencing studiesRNA-sequencing studiesSpecific expression patternsExpression programsKey immune functionsExpression patternsSARS-CoV-2 entry genesSpecific expressionAlveolar type 2 cellsMolecular pathwaysLung parenchyma samplesCoronavirus disease 2019 (COVID-19) transmissionDifferent tissuesCellular entryGenesRespiratory epithelial cellsAirway secretory cellsSecretory cellsTumor necrosis factorEntry genesExpression levelsType 2 cellsEpithelial cellsGut tissueSpecific subset
2017
Transcriptome profiles in sarcoidosis and their potential role in disease prediction
Schupp JC, Vukmirovic M, Kaminski N, Prasse A. Transcriptome profiles in sarcoidosis and their potential role in disease prediction. Current Opinion In Pulmonary Medicine 2017, 23: 487-492. PMID: 28590292, PMCID: PMC5637542, DOI: 10.1097/mcp.0000000000000403.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsGene Expression ProfilingGenome-Wide Association StudyHumansInterferon-gammaSarcoidosisSequence Analysis, RNASignal TransductionTh1 CellsTranscriptomeConceptsGenome-wide expression studiesWide expression studiesTranscriptome profilesTranscriptomic dataRNA sequencingExpression studiesGene expressionMolecular mechanismsLarge prospective followTh1 immune responseTranscriptomeNonnecrotizing granulomasProspective followSystemic diseaseDisease progressionTreatment outcomesImmune responseSarcoidosisPotential roleControl tissuesProgressive sarcoidosisKey roleDiseaseTranscriptomicsGranulomas