Chao Cheng
PhD CandidateAbout
Research
Publications
2024
UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors
Yang D, Geng T, Harrison A, Cahoon J, Xing J, Jiao B, Wang M, Cheng C, Hill R, Wang H, Vella A, Cheng G, Wang Y, Wang P. UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors. Nature Communications 2024, 15: 780. PMID: 38278841, PMCID: PMC10817939, DOI: 10.1038/s41467-024-45141-1.Peer-Reviewed Original ResearchConceptsUbiquitin protein ligase E3 component N-recognin 5RIG-IImmune response to RNA virusesResponse to RNA virusesRetinoic acid-inducible gene ILysine 63-linked ubiquitinationAntiviral immune responseRNA virus infectionViral RNA sensorsKnockout cell linesInitiation of antiviral immune responsesBoost antiviral immune responseImmune responsePosttranslational regulationTranscriptional brakeGene IEpigenetic repressorsRNA virusesDe-SUMOylationRNA sensorsUbiquitinWild type littermatesIncreased viral replicationTRIM28Transcription
2023
Binding peptide generation for MHC Class I proteins with deep reinforcement learning
Chen Z, Zhang B, Guo H, Emani P, Clancy T, Jiang C, Gerstein M, Ning X, Cheng C, Min M. Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinformatics 2023, 39: btad055. PMID: 36692135, PMCID: PMC9907221, DOI: 10.1093/bioinformatics/btad055.Peer-Reviewed Original Research
2022
Is the Product Method More Efficient Than the Difference Method for Assessing Mediation?
Cheng C, Spiegelman D, Li F. Is the Product Method More Efficient Than the Difference Method for Assessing Mediation? American Journal Of Epidemiology 2022, 192: 84-92. PMID: 35921210, PMCID: PMC10144745, DOI: 10.1093/aje/kwac144.Peer-Reviewed Original ResearchStructure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series
Zeng X, Lin Z, Uddin M, Zhou B, Cheng C, Zhang J, Freyberg Z, Xu M. Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series. Journal Of Computational Biology 2022, 29: 932-941. PMID: 35862434, PMCID: PMC9419945, DOI: 10.1089/cmb.2021.0606.Peer-Reviewed Original ResearchConceptsObject localizationPrediction taskEdge detectionState-of-the-art object detection methodsObject detection methodsState-of-the-artTask of segmentationStructural information lossSemantic segmentationCryo-ETTwo-dimensional (2D) projectionInformation lossDetection processCryo-ET dataIndividual tasksStructure detectionDetection methodCalcium phosphate granulesNear-native environmentAlgorithmConventional processTilt seriesExperimental validationQualitative resultsSpherical edgeThe steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract
Zhou Y, Gu B, Brichant G, Singh JP, Yang H, Chang H, Zhao Y, Cheng C, Liu ZW, Alderman MH, Lu L, Yang X, Gao XB, Taylor HS. The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract. BMC Biology 2022, 20: 93. PMID: 35491423, PMCID: PMC9059368, DOI: 10.1186/s12915-022-01293-4.Peer-Reviewed Original ResearchConceptsEstrogen receptorMaintenance of pregnancyFetal mouse brainReproductive systemE3 micePregnancy outcomesEstrogen actionEstrogen potencyPregnant miceEstrogen exposureEstrogen signalingFetal developmentMouse brainSteroid hormonesUnexpected functional rolesPregnancyReproductive tractHormone estriolBrainReceptorsExpression levelsFetusesExploratory behaviorMiceNovel mechanismAddressing Extreme Propensity Scores in Estimating Counterfactual Survival Functions via the Overlap Weights
Cheng C, Li F, Thomas L, Li F. Addressing Extreme Propensity Scores in Estimating Counterfactual Survival Functions via the Overlap Weights. American Journal Of Epidemiology 2022, 191: 1140-1151. PMID: 35238335, DOI: 10.1093/aje/kwac043.Peer-Reviewed Original ResearchConceptsDegrees of covariate overlapCovariate overlapGeneral class of balancing weightsSurvival functionInverse probability of censoring weightingProbability of censoring weightingTime-to-event outcomesConfidence interval coverageOverlap weightingCensoring ratesTime-to-eventGeneral classEvaluate causal effectsInterval coverageEmpirical performanceInverse probabilityBinary outcomesCausal effectsEstimationInverse probability of treatment weightingWeighting schemeWeighting approachPropensity scoreVarianceExcess variance
2021
Estimating the natural indirect effect and the mediation proportion via the product method
Cheng C, Spiegelman D, Li F. Estimating the natural indirect effect and the mediation proportion via the product method. BMC Medical Research Methodology 2021, 21: 253. PMID: 34800985, PMCID: PMC8606099, DOI: 10.1186/s12874-021-01425-4.Peer-Reviewed Original ResearchConceptsInterval estimatorsApproximate estimatorExact estimatorMultivariate delta methodFinite sample performanceProduct methodNon-negligible biasBinary outcomesRare outcome assumptionExact expressionDelta methodVariance estimationEmpirical performanceEstimatorCommon data typesBootstrap approachBinary mediatorNatural indirect effectSample sizeTesting gene–environment interactions in the presence of confounders and mismeasured environmental exposures
Cheng C, Spiegelman D, Wang Z, Wang M. Testing gene–environment interactions in the presence of confounders and mismeasured environmental exposures. G3: Genes, Genomes, Genetics 2021, 11: jkab236. PMID: 34568916, PMCID: PMC8473983, DOI: 10.1093/g3journal/jkab236.Peer-Reviewed Original ResearchConceptsStandard logistic regression approachGreater statistical powerStatistical powerBinary disease outcomeComputational efficiencyIllustrative exampleComputation timeExtensive simulation experimentsMost simulation scenariosMeasurement errorRegression approachConsideration adjustmentsSimulation experimentsExposure measurement errorReverse testLogistic regression approachSimulation scenariosLinear discriminant analysisApproachReverse approachPowerErrorDiscriminant analysisResident and circulating memory T cells persist for years in melanoma patients with durable responses to immunotherapy
Han J, Zhao Y, Shirai K, Molodtsov A, Kolling FW, Fisher JL, Zhang P, Yan S, Searles TG, Bader JM, Gui J, Cheng C, Ernstoff MS, Turk MJ, Angeles CV. Resident and circulating memory T cells persist for years in melanoma patients with durable responses to immunotherapy. Nature Cancer 2021, 2: 300-311. PMID: 34179824, PMCID: PMC8223731, DOI: 10.1038/s43018-021-00180-1.Peer-Reviewed Original ResearchConceptsT cell responsesMemory T cellsT cellsEffector memory T cellsResident memory T cellsMetastatic melanoma survivorsT cells persistStrong prognostic valueT cell receptorDurable responsesMemory CD8Melanoma patientsCancer survivorsPrognostic valueCancer immunotherapyMelanoma survivorsCells persistClonal repertoireSingle-cell RNA sequencingImmunotherapyTumorsExceptional responsePatient's skinClonotypesBlood
2020
An integrative ENCODE resource for cancer genomics
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. An integrative ENCODE resource for cancer genomics. Nature Communications 2020, 11: 3696. PMID: 32728046, PMCID: PMC7391744, DOI: 10.1038/s41467-020-14743-w.Peer-Reviewed Original ResearchConceptsCell typesFunctional genomics datasetsEffect of MycStem-like stateNetwork-based annotationUncharacterized RBPsOncogenic TFSTARR-seqOncogene knockdownTranscription factorsGenomic datasetsOncogenic transformationGenome interpretationUniversal annotationCancer genomicsDifferential expressionSiRNA knockdownLuciferase assayTargeted validationRegulatorTumor transitionCustom annotationsAnnotationKnockdownCoherent workflow
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