Yong Kong, PhD
Senior Research ScientistDownloadHi-Res Photo
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Biostatistics
Primary
Additional Titles
Associate Director, Bioinformatics Resource at W.M. Keck Foundation Biotechnology Laboratory
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Appointments
Biostatistics
Primary
Additional Titles
Associate Director, Bioinformatics Resource at W.M. Keck Foundation Biotechnology Laboratory
Contact Info
Appointments
Biostatistics
Primary
Additional Titles
Associate Director, Bioinformatics Resource at W.M. Keck Foundation Biotechnology Laboratory
Contact Info
About
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Senior Research Scientist
Associate Director, Bioinformatics Resource at W.M. Keck Foundation Biotechnology Laboratory
Appointments
Biostatistics
Senior Research ScientistPrimary
Other Departments & Organizations
Education & Training
- PhD
- Washington University School of Medicine (1997)
- BA
- Tsinghua University, Biomedical Engineering / Computer Science
- MS
- Shanghai Institute of Physiology, Chinese Academy of Sciences (CAS), Neurobiology
Research
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Overview
Medical Research Interests
Information Science; Mathematical Computing
Public Health Interests
Infectious Diseases
ORCID
0000-0002-2881-5274
Research at a Glance
Yale Co-Authors
Frequent collaborators of Yong Kong's published research.
Publications Timeline
A big-picture view of Yong Kong's research output by year.
Melinda Pettigrew, PhD
Akiko Iwasaki, PhD
Hongyu Zhao, PhD
Jiye Kwon, MPH
Martina Wade
Alexej Abyzov, PhD
90Publications
6,213Citations
Publications
2025
Promotion of a new gap junction gene Cx46 (GJA3) expression in the cochlea after Cx26 (GJB2) deficiency
Zhai T, Chen J, Kong Y, Liang C, Zhao H. Promotion of a new gap junction gene Cx46 (GJA3) expression in the cochlea after Cx26 (GJB2) deficiency. Hearing Research 2025, 468: 109454. PMID: 41115329, PMCID: PMC12645451, DOI: 10.1016/j.heares.2025.109454.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsCx26 deficiencyCx46 expressionGene Set Enrichment AnalysisNonsyndromic hearing lossDigital droplet PCRCx26 expressionCx26 functionHearing lossCx46Cx26Gene mutationsHereditary deafnessImmunofluorescence stainingDroplet PCRCochleaPathological changesCx30GJA3Genetic changesQuantitative PCRDeficiencyChannel propertiesKnockoutGenes up-ExpressionMicrobiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach
Kwon J, Correa M, Kong Y, Pelletiers W, Wade M, Olson D, Pettigrew M. Microbiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach. MSphere 2025, 10: e00435-25. PMID: 40996044, PMCID: PMC12570482, DOI: 10.1128/msphere.00435-25.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsToxin-encoding genesGut microbiomeMicrobiome signaturesDiarrhea to pseudomembranous colitisShotgun metagenomic approachBifidobacterium adolescentisMicrobiome community structureGut microbiome profilesStool samplesAntibiotic exposureAntibiotic resistance genesProduction of toxinsToxin-mediated diseaseMetagenomic approachBeta diversityGene presenceGut bacteriaAkkermansia muciniphilaResistance genesToxin productionMicrobiome profilesCommunity structureGastrointestinal pathogensGlutamate dehydrogenaseMicrobiomeHigh MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties
Zhang J, Rajendran B, Desai S, Gibson J, DiPalermo J, LoRusso P, Kong Y, Zhao H, Cecchini M, Schalper K. High MGMT expression identifies aggressive colorectal cancer with distinct genomic features and immune evasion properties. Journal For ImmunoTherapy Of Cancer 2025, 13: e011653. PMID: 40935566, PMCID: PMC12506448, DOI: 10.1136/jitc-2025-011653.Peer-Reviewed Original ResearchThis study shows that high MGMT expression in colorectal cancer is linked to aggressive behavior, distinct genomic features, immune evasion, and shorter survival, highlighting its potential as a biomarker for prognosis and therapeutic targeting.On the Joint Distributions of Increasing and Decreasing Successions of Arbitrary Multisets
Kong Y. On the Joint Distributions of Increasing and Decreasing Successions of Arbitrary Multisets. Methodology And Computing In Applied Probability 2025, 27: 57. DOI: 10.1007/s11009-025-10186-2.Peer-Reviewed Original ResearchHost-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells
D’Mello A, Murphy T, Wade M, Kirkham C, Kong Y, Tettelin H, Pettigrew M. Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells. MSphere 2025, 10: e00242-25. PMID: 40492732, PMCID: PMC12306180, DOI: 10.1128/msphere.00242-25.Peer-Reviewed Original ResearchCitationsConceptsRegulation of quorum sensingTranscriptome profilingBioinformatics analysisCell culture modelBiological pathwaysIron-sulfur metabolismHost-pathogen interactionsHost biological pathwaysHost cell pathwaysIscR regulonChronic obstructive pulmonary diseaseEpithelial cellsQuorum sensingEpithelial cell infectionRNA-seqH292 cell lineHost pathwaysExacerbation of chronic obstructive pulmonary diseaseNontypeable Haemophilus influenzaeRNA sequencingHost cellsDifferential regulationCulture modelBronchial epithelial cellsMono-infectionCutaneous Lupus Features Specialized Stromal Niches and Altered Retroelement Expression
Gehlhausen J, Kong Y, Baker E, Ramachandran S, Koumpouras F, Ko C, Vesely M, Little A, Damsky W, King B, Iwasaki A. Cutaneous Lupus Features Specialized Stromal Niches and Altered Retroelement Expression. Journal Of Investigative Dermatology 2025, 145: 3011-3024.e11. PMID: 40409678, PMCID: PMC12354343, DOI: 10.1016/j.jid.2025.04.033.Peer-Reviewed Original ResearchCitationsAltmetricConceptsRetroelement expressionCGAS-STING pathwayRIG-IType I interferonCutaneous lupusCGAS-STINGElevated expression of genesPathway enrichment analysisI interferonExpression of genesResponse to type I interferonsLupus skinRetroelement familiesInterferon-stimulated genesNucleic acid signalsApoptotic signalingSingle-cell RNAMultiple cell typesAcid signalingEnrichment analysisInflammatory cell recruitmentType II interferonInflammatory skin diseaseTumor necrosis factorCell typesProspective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems
Kwon J, Tanner W, Kong Y, Wade M, Bitler C, Chiavegato M, Pettigrew M. Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems. MSphere 2025, 10: e00738-24. PMID: 39950811, PMCID: PMC11934311, DOI: 10.1128/msphere.00738-24.Peer-Reviewed Original ResearchMeSH Keywords and ConceptsConceptsFarm management strategiesPost-weaningGrain dietGrass-fedFeed additivesPre-harvestProduction systemsResistance genesCattle production systemsPre-weaning periodFarm management practicesAbundance of antibiotic resistance genesBacterial communitiesFecal swab samplesPasture-raisedDiversity of ARGsGrain-fedBeef cattlePre-weaningMonths of ageGrowth promotionCattleBacterial community changesFood animalsFecal swabs
2024
Recurrence solution of monomer-polymer models on two-dimensional rectangular lattices
Kong Y. Recurrence solution of monomer-polymer models on two-dimensional rectangular lattices. Physical Review E 2024, 110: 054135. PMID: 39690661, DOI: 10.1103/physreve.110.054135.Peer-Reviewed Original ResearchAltmetricConceptsTwo-dimensional rectangular latticeRecurrence relationsRectangular latticeMonomer-dimer problemPlanar latticesRecurrent solutionsLong standing problemLattice sitesAdjacent lattice sitesLatticeProblemComputational complexitySolutionRelationsEnumerationPolymer coverUnoccupied lattice sitesRigid polymersMonomer-polymerSolution of long-standing problemsPolymerPolymer lengthThe amalgam of naive CD4+ T cell transcriptional states is reconfigured by helminth infection to dampen the amplitude of the immune response
Even Z, Meli A, Tyagi A, Vidyarthi A, Briggs N, de Kouchkovsky D, Kong Y, Wang Y, Waizman D, Rice T, De Kumar B, Wang X, Palm N, Craft J, Basu M, Ghosh S, Rothlin C. The amalgam of naive CD4+ T cell transcriptional states is reconfigured by helminth infection to dampen the amplitude of the immune response. Immunity 2024, 57: 1893-1907.e6. PMID: 39096910, PMCID: PMC11421571, DOI: 10.1016/j.immuni.2024.07.006.Peer-Reviewed Original ResearchCitationsAltmetricConceptsT cell receptorImmune responseNaive CD4+ T cellsCD4+ T cellsIFN-IHelminth infectionsNippostrongylus brasiliensis infectionDecreased immune responseType I interferonNaive TT cellsMemory-likeUnrelated antigensTranscriptional changesExtracellular matrixSPF miceCell receptorsI interferonGerm-freeResponse to certain environmental cuesInfectionMiceFunctional changesCell transcriptional statesTranscriptional heterogeneitySARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity
Peña-Hernández M, Alfajaro M, Filler R, Moriyama M, Keeler E, Ranglin Z, Kong Y, Mao T, Menasche B, Mankowski M, Zhao Z, Vogels C, Hahn A, Kalinich C, Zhang S, Huston N, Wan H, Araujo-Tavares R, Lindenbach B, Homer R, Pyle A, Martinez D, Grubaugh N, Israelow B, Iwasaki A, Wilen C. SARS-CoV-2-related bat viruses evade human intrinsic immunity but lack efficient transmission capacity. Nature Microbiology 2024, 9: 2038-2050. PMID: 39075235, DOI: 10.1038/s41564-024-01765-z.Peer-Reviewed Original ResearchCitationsAltmetricConceptsBat coronavirusesRelatives of SARS-CoV-2Upper airwayUpper airways of miceEpithelial cellsHuman nasal epithelial cellsAirways of miceMajor histocompatibility complex class I.SARS-CoV-2Nasal epithelial cellsHistocompatibility complex class I.Human bronchial epithelial cellsGenetic similarityBronchial epithelial cellsInnate immune restrictionCoronavirus replicationFunctional characterizationMolecular cloningReduced pathogenesisImpaired replicationBat virusCoronavirus pathogenesisPandemic potentialHigh-risk familiesImmune restriction
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