2024
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis
Liu T, Long W, Cao Z, Wang Y, He C, Zhang L, Strittmatter S, Zhao H. CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. Briefings In Bioinformatics 2024, 26: bbae626. PMID: 39592241, PMCID: PMC11596696, DOI: 10.1093/bib/bbae626.Peer-Reviewed Original ResearchSystems biology dissection of PTSD and MDD across brain regions, cell types, and blood
Daskalakis N, Iatrou A, Chatzinakos C, Jajoo A, Snijders C, Wylie D, DiPietro C, Tsatsani I, Chen C, Pernia C, Soliva-Estruch M, Arasappan D, Bharadwaj R, Collado-Torres L, Wuchty S, Alvarez V, Dammer E, Deep-Soboslay A, Duong D, Eagles N, Huber B, Huuki L, Holstein V, Logue M, Lugenbühl J, Maihofer A, Miller M, Nievergelt C, Pertea G, Ross D, Sendi M, Sun B, Tao R, Tooke J, Wolf E, Zeier Z, Berretta S, Champagne F, Hyde T, Seyfried N, Shin J, Weinberger D, Nemeroff C, Kleinman J, Ressler K, Nievergelt C, Maihofer A, Atkinson E, Chen C, Choi K, Coleman J, Daskalakis N, Duncan L, Polimanti R, Aaronson C, Amstadter A, Andersen S, Andreassen O, Arbisi P, Ashley-Koch A, Austin S, Avdibegoviç E, Babić D, Bacanu S, Baker D, Batzler A, Beckham J, Belangero S, Benjet C, Bergner C, Bierer L, Biernacka J, Bierut L, Bisson J, Boks M, Bolger E, Brandolino A, Breen G, Bressan R, Bryant R, Bustamante A, Bybjerg-Grauholm J, Bækvad-Hansen M, Børglum A, Børte S, Cahn L, Calabrese J, Caldas-de-Almeida J, Chatzinakos C, Cheema S, Clouston S, Colodro-Conde L, Coombes B, Cruz-Fuentes C, Dale A, Dalvie S, Davis L, Deckert J, Delahanty D, Dennis M, Desarnaud F, DiPietro C, Disner S, Docherty A, Domschke K, Dyb G, Kulenović A, Edenberg H, Evans A, Fabbri C, Fani N, Farrer L, Feder A, Feeny N, Flory J, Forbes D, Franz C, Galea S, Garrett M, Gelaye B, Gelernter J, Geuze E, Gillespie C, Goleva S, Gordon S, Goçi A, Grasser L, Guindalini C, Haas M, Hagenaars S, Hauser M, Heath A, Hemmings S, Hesselbrock V, Hickie I, Hogan K, Hougaard D, Huang H, Huckins L, Hveem K, Jakovljević M, Javanbakht A, Jenkins G, Johnson J, Jones I, Jovanovic T, Karstoft K, Kaufman M, Kennedy J, Kessler R, Khan A, Kimbrel N, King A, Koen N, Kotov R, Kranzler H, Krebs K, Kremen W, Kuan P, Lawford B, Lebois L, Lehto K, Levey D, Lewis C, Liberzon I, Linnstaedt S, Logue M, Lori A, Lu Y, Luft B, Lupton M, Luykx J, Makotkine I, Maples-Keller J, Marchese S, Marmar C, Martin N, Martínez-Levy G, McAloney K, McFarlane A, McLaughlin K, McLean S, Medland S, Mehta D, Meyers J, Michopoulos V, Mikita E, Milani L, Milberg W, Miller M, Morey R, Morris C, Mors O, Mortensen P, Mufford M, Nelson E, Nordentoft M, Norman S, Nugent N, O'Donnell M, Orcutt H, Pan P, Panizzon M, Pathak G, Peters E, Peterson A, Peverill M, Pietrzak R, Polusny M, Porjesz B, Powers A, Qin X, Ratanatharathorn A, Risbrough V, Roberts A, Rothbaum A, Rothbaum B, Roy-Byrne P, Ruggiero K, Rung A, Runz H, Rutten B, de Viteri S, Salum G, Sampson L, Sanchez S, Santoro M, Seah C, Seedat S, Seng J, Shabalin A, Sheerin C, Silove D, Smith A, Smoller J, Sponheim S, Stein D, Stensland S, Stevens J, Sumner J, Teicher M, Thompson W, Tiwari A, Trapido E, Uddin M, Ursano R, Valdimarsdóttir U, Van Hooff M, Vermetten E, Vinkers C, Voisey J, Wang Y, Wang Z, Waszczuk M, Weber H, Wendt F, Werge T, Williams M, Williamson D, Winsvold B, Winternitz S, Wolf C, Wolf E, Xia Y, Xiong Y, Yehuda R, Young K, Young R, Zai C, Zai G, Zervas M, Zhao H, Zoellner L, Zwart J, deRoon-Cassini T, van Rooij S, van den Heuvel L, Stein M, Ressler K, Koenen K. Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood. Science 2024, 384: eadh3707. PMID: 38781393, PMCID: PMC11203158, DOI: 10.1126/science.adh3707.Peer-Reviewed Original ResearchConceptsMajor depressive disorderPosttraumatic stress disorderMedial prefrontal cortexStudies of posttraumatic stress disorderStress-related disordersHippocampal dentate gyrusDorsolateral PFCPrefrontal cortexDepressive disorderStress disorderBrain regionsCentral nucleusDentate gyrusGenome-wide association studiesSynaptic regulationMolecular pathologyMultiomics studiesStress hormonesGene network analysisDisordersCell typesNon-neuronal cell typesSingle nucleus RNA sequencingGenomic structureFine-mappingClustering-aided prediction of outcomes in patients with idiopathic pulmonary fibrosis
Wang L, Wu P, Liu Y, Patel D, Leonard T, Zhao H. Clustering-aided prediction of outcomes in patients with idiopathic pulmonary fibrosis. Respiratory Research 2024, 25: 383. PMID: 39443991, PMCID: PMC11515489, DOI: 10.1186/s12931-024-03015-6.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisProgression of idiopathic pulmonary fibrosisMatrix metalloproteinase-9IPF-PRO RegistryClinical factorsC-indexPulmonary fibrosisBlood biomarkersMedian Follow-UpVascular cell adhesion protein 1Area under the curveHarrell's C-indexSurfactant protein DPredictive of outcomeClinical characteristicsComposite outcomeFollow-upCarcinoembryonic antigenCox regressionMetalloproteinase-9Disease progressionProtein DAverage C-indexPatientsCirculating proteins
2023
Statistical assessment of biomarker replicability using MAJAR method
Xie Y, Zhai S, Jiang W, Zhao H, Mehrotra D, Shen J. Statistical assessment of biomarker replicability using MAJAR method. Statistical Methods In Medical Research 2023, 32: 1961-1972. PMID: 37519295, DOI: 10.1177/09622802231188519.Peer-Reviewed Original ResearchConceptsBayesian false discovery rateDifferent data generation processesNovel statistical frameworkExtensive simulation studyExpectation-maximization algorithmStatistical frameworkComputational efficiencyGWAS summary statistics dataSimulation studyData generation processStatistical assessmentSimulation resultsStatistical powerFalse discovery rateResponse predictionSummary statistics dataDiscovery rateSample sizeLimited powerOutliersAlgorithmGeneration processRobustnessPowerSmall sample size
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