2025
Host-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, e0024225. PMID: 40492732, DOI: 10.1128/msphere.00242-25.Peer-Reviewed Original ResearchRegulation 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 PMID: 40409678, DOI: 10.1016/j.jid.2025.04.033.Peer-Reviewed Original ResearchRetroelement 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 ResearchConceptsFarm 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 ResearchTwo-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 ResearchT cell receptorImmune responseNaive CD4<sup>+</sup> T cellsCD4<sup>+</sup> 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 ResearchBat 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 restrictionNearest Neighbors of Multivariate Runs
Kong Y. Nearest Neighbors of Multivariate Runs. 2024, 275-299. DOI: 10.1007/978-1-4614-8033-4_63.Peer-Reviewed Original ResearchGenerating Function Methods for Run and Scan Statistics
Kong Y. Generating Function Methods for Run and Scan Statistics. 2024, 205-223. DOI: 10.1007/978-1-4614-8033-4_56.Peer-Reviewed Original ResearchFinite Markov chain imbedding approachMarkov chain imbedding approachNearest-neighbor interactionsImbedding approachGenerating functionCombinatorial difficultiesMulti-objective systemCombinatorial methodsCombinatorial complexityStatistical physicsMultiple objectivesNeighbor interactionsPattern statisticsFunction methodResults of distributionIndependent stepsInteraction of elementsFormulaObjectiveFunction
2023
Nearest Neighbors of Multivariate Runs
Kong Y. Nearest Neighbors of Multivariate Runs. 2023, 1-25. DOI: 10.1007/978-1-4614-8414-1_63-1.Peer-Reviewed Original ResearchGenomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda
Saarman N, Son J, Zhao H, Cosme L, Kong Y, Li M, Wang S, Weiss B, Echodu R, Opiro R, Aksoy S, Caccone A. Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda. Infection Genetics And Evolution 2023, 114: 105501. PMID: 37709241, PMCID: PMC10593118, DOI: 10.1016/j.meegid.2023.105501.Peer-Reviewed Original ResearchConceptsGenome-wide association analysisNovel vector control strategiesAnimal African trypanosomiasisSex chromosome aneuploidyNatural populationsGenome assemblySex chromosomesGenomic regionsGenomic evidenceGenetic variationBp upstreamAutosomal SNPsSeq dataTrypanosome infectionTrypanosome parasitesAssociation analysisMolecular pathwaysAssembly metricsLinkage disequilibriumLecithin-cholesterol acyltransferaseAfrican trypanosomiasisMajor vectorGenomeSNPsPrimary vectorQuantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal Cancer
Cecchini M, Zhang J, Wei W, Sklar J, Lacy J, Zhong M, Kong Y, Zhao H, DiPalermo J, Devine L, Stein S, Kortmansky J, Johung K, Bindra R, LoRusso P, Schalper K. Quantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal Cancer. Cancer Research Communications 2023, 3: 1132-1139. PMID: 37387791, PMCID: PMC10305782, DOI: 10.1158/2767-9764.crc-23-0045.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingMGMT protein expressionColorectal cancerStable diseaseQuantitative immunofluorescenceT cellsProtein expressionPromoter hypermethylationLow MGMT protein expressionPARP inhibitorsRadiographic tumor regressionMetastatic colorectal cancerAdvanced colorectal cancerPretreatment tumor biopsiesEffector T cellsTumor-infiltrating lymphocytesMGMT proteinDNA repair biomarkersBaseline CD8Eligible patientsIncreased CD8Methylguanine-DNA methyltransferaseObjective responseProgressive diseaseImmune markersResponse to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect
Takahashi T, Stoiljkovic M, Song E, Gao X, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu Z, Kristant A, Zhang Y, Sulkowski P, Glazer P, Kaczmarek L, Horvath T, Iwasaki A. Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. Neuron 2023, 111: 612-613. PMID: 36863323, DOI: 10.1016/j.neuron.2023.02.006.Peer-Reviewed Original ResearchInflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosa
Mercau M, Akalu Y, Mazzoni F, Gyimesi G, Alberto E, Kong Y, Hafler B, Finnemann S, Rothlin C, Ghosh S. Inflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosa. Science Advances 2023, 9: eade9459. PMID: 36662852, PMCID: PMC9858494, DOI: 10.1126/sciadv.ade9459.Peer-Reviewed Original ResearchConceptsRetinal pigment epitheliumEarly-onset photoreceptor degenerationPR degenerationPigment epitheliumPhotoreceptor degenerationMERTK-associated retinitis pigmentosaJAK1/2 inhibitor ruxolitinibMicroglia activationMonocyte infiltrationInhibitor ruxolitinibMouse modelInflammationLoss of functionDefective phagocytosisInflammation drivesRetinitis pigmentosaDegenerationHypomorphic expressionMiceEpitheliumPhagocytosisRuxolitinibPigmentosaSeverity
2022
Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia
Kwon J, Kong Y, Wade M, Williams DJ, Creech CB, Evans S, Walter EB, Martin JM, Gerber JS, Newland JG, Hofto ME, Staat MA, Chambers HF, Fowler VG, Huskins WC, Pettigrew M. Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia. The Journal Of Infectious Diseases 2022, 226: 1109-1119. PMID: 35249113, PMCID: PMC9492313, DOI: 10.1093/infdis/jiac082.Peer-Reviewed Original ResearchConceptsAAD groupAntibiotic-associated diarrheaCommunity-acquired pneumoniaCommon side effectsStudy days 1Days of diarrheaPatient characteristicsAntibiotic therapyNineteen childrenStool samplesSide effectsDay 1Microbiome disruptionMicrobiota profilesGastrointestinal microbiotaMicrobiota characteristicsDiarrheaBacteroides speciesPneumoniaChildrenAntibioticsΒ-lactamsAADBaseline abundanceDysbiosisMultiple consecutive runs of multi-state trials: Distributions of ( k 1 , k 2 , … , k ℓ ) patterns
Kong Y. Multiple consecutive runs of multi-state trials: Distributions of ( k 1 , k 2 , … , k ℓ ) patterns. Journal Of Computational And Applied Mathematics 2022, 403: 113846. DOI: 10.1016/j.cam.2021.113846.Peer-Reviewed Original Research
2021
A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793).
Roque D, Bellone S, Siegel E, Buza N, Bonazzoli E, Guglielmi A, Zammataro L, Nagarkatti N, Zaidi S, Lee J, Schwartz P, Ratner E, Alexandrov L, Iwasaki A, Kong Y, Song E, Dong W, Elvin J, Choi J, Santin A. A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793). Journal Of Clinical Oncology 2021, 39: 5523-5523. DOI: 10.1200/jco.2021.39.15_suppl.5523.Peer-Reviewed Original ResearchObjective response rateImmune checkpoint inhibitorsEndometrial cancer patientsTumor mutational burdenCancer patientsGrade 3/4 treatment-related adverse eventsSolid Tumors version 1.1Treatment-related adverse eventsSporadic tumorsPhase II pilot studyOverall survival proportionPrimary end pointResponse Evaluation CriteriaPhase II evaluationAntigen processing/presentationProcessing/presentationAdverse eventsICI resistancePrognostic significanceMechanisms of resistancePolymerase chain reactionII evaluationClinical studiesMutational burdenPatientsEndogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection
Tokuyama M, Jayewickreme R, Mao T, Philbrick W, Kong Y, Dong H, Treger R, Rakib T, Iwasaki A. Endogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection. The Journal Of Immunology 2021, 206: 20.39-20.39. DOI: 10.4049/jimmunol.206.supp.20.39.Peer-Reviewed Original ResearchHSV-2 infectionVaginal HSV-2 infectionTight junction proteinsB6 miceVaginal epitheliumHerpes simplex virus type 2 infectionSimplex virus type 2 infectionEnhanced type I interferonIntravaginal HSV-2 infectionVirus type 2 infectionToll-like receptor 7Epithelial tight junction proteinsEndogenous retrovirusesReceptor-deficient miceJunction proteinsType 2 infectionHigh systemic levelsWildtype C57BL/6 miceType I interferonDisease courseC57BL/6 miceInfectious endogenous retrovirusReceptor 7Disease burdenHSV-2
2020
Distributions of successions of arbitrary multisets
Kong Y. Distributions of successions of arbitrary multisets. Communication In Statistics- Theory And Methods 2020, 51: 1693-1705. DOI: 10.1080/03610926.2020.1767137.Peer-Reviewed Original Research
2019
Ketogenic diet activates protective γδ T cell responses against influenza virus infection
Goldberg EL, Molony RD, Kudo E, Sidorov S, Kong Y, Dixit VD, Iwasaki A. Ketogenic diet activates protective γδ T cell responses against influenza virus infection. Science Immunology 2019, 4 PMID: 31732517, PMCID: PMC7189564, DOI: 10.1126/sciimmunol.aav2026.Peer-Reviewed Original ResearchConceptsΓδ T cellsKetogenic dietIAV infectionT cellsGlobal health care concernHigh-fat ketogenic dietΓδ T cell responsesInfection-associated morbidityLethal IAV infectionT cell responsesInfluenza virus infectionHealth care concernHigh-carbohydrate dietInfluenza diseaseKD feedingVirus infectionNew therapiesAntiviral resistanceHepatic ketogenesisCare concernsCell responsesInfectionBarrier functionDietMetabolic adaptationDiscovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion
Ahearn C, Kirkham C, Chaves L, Kong Y, Pettigrew M, Murphy T. Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion. Infection And Immunity 2019, 87: 10.1128/iai.00462-19. PMID: 31427451, PMCID: PMC6803334, DOI: 10.1128/iai.00462-19.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseRespiratory epithelial cellsEnzyme-linked immunosorbent assayEpithelial cellsAirways of adultsObstructive pulmonary diseaseCell invasionHuman respiratory epithelial cellsNontypeable Haemophilus influenzaeCell enzyme-linked immunosorbent assayAlveolar epithelial cellsAcute exacerbationLower airwaysPulmonary diseaseSerum IgGNTHi strainsTherapeutic interventionsHaemophilus influenzaeHuman bronchialSurface-exposed epitopesEpithelial cell invasionIsogenic knockout mutantsNTHiImmunosorbent assayIntracellular survival
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply