2023
Inflammation 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
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 adaptation
2013
Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length
Mis EK, Liem KF, Kong Y, Schwartz NB, Domowicz M, Weatherbee SD. Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length. Developmental Biology 2013, 385: 67-82. PMID: 24161523, PMCID: PMC3895954, DOI: 10.1016/j.ydbio.2013.10.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBone and BonesCell DifferentiationCell ProliferationChondrocytesDwarfismFibroblast Growth FactorsHedgehog ProteinsMiceMice, Inbred C57BLMice, TransgenicMutation, MissenseOsteogenesisParathyroid Hormone-Related ProteinPentosyltransferasesSequence Analysis, DNASignal TransductionConceptsChondrocyte maturationCartilage templateN-ethyl-N-nitrosourea (ENU) mutagenesis screenSkeletal precursor cellsWild-type embryosHigh-throughput sequencingHuman birth defectsProteoglycan core proteinMutagenesis screenSequence captureVertebrate bodySubcellular localizationProteoglycan functionCoordinated processMouse mutantsMutantsAbnormal bone developmentMissense mutationsCore proteinBone developmentSkeletal elementsPrecursor cellsDwarfismMaturationGAG chainsForward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation–differentiation decision in epidermal progenitor cells
Lee S, Kong Y, Weatherbee SD. Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation–differentiation decision in epidermal progenitor cells. Developmental Biology 2013, 383: 201-213. PMID: 24075906, PMCID: PMC3841015, DOI: 10.1016/j.ydbio.2013.09.022.Peer-Reviewed Original ResearchMeSH Keywords14-3-3 ProteinsAllelesAnimalsBase SequenceCell DifferentiationCell ProliferationCleft PalateEmbryo LossEpidermisFemaleGene Expression Regulation, DevelopmentalGenes, RecessiveGenetic Complementation TestHeterozygoteKeratinocytesMaleMiceMice, Inbred C57BLMolecular Sequence DataPhenotypePhosphoproteinsPoint MutationProtein BindingProteinsRNA SplicingStem CellsTrans-ActivatorsConceptsEpidermal progenitor cellsEssential regulatorProgenitor cellsProliferation-differentiation balanceUnbiased genetic screenCell fate decisionsProliferation-differentiation decisionsCell proliferationUncontrolled cell proliferationFactor 1 geneProgenitor cell proliferationGenetic screenFate decisionsRepressive signalsTerminal fateInductive signalsPremature differentiationGenetic mechanismsInhibition of p63Terminal differentiationCell differentiationEpidermal cellsKDF1Rapid turnoverRate of proliferation
2012
Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing
del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012, 13: 649. PMID: 23171430, PMCID: PMC3526394, DOI: 10.1186/1471-2164-13-649.Peer-Reviewed Original ResearchConceptsBulk segregant analysisForward genetic screenSegregant analysisGenetic screenGenome assemblyExon captureCausative mutationsVertebrate model systemHigh-throughput sequencingHuman genetic analysisThousands of SNPsAssembly of scaffoldsModel systemGenomic resourcesVertebrate modelXenopus tropicalisFine mappingGenetic analysisCapture sequencingSequence variantsSequencingMutationsRapid discoveryMutantsExome sequencingForward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling
Christopher KJ, Wang B, Kong Y, Weatherbee SD. Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling. Developmental Biology 2012, 368: 382-392. PMID: 22698544, PMCID: PMC3402655, DOI: 10.1016/j.ydbio.2012.06.008.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBody PatterningCells, CulturedCiliaEmbryo, MammalianExtremitiesFemaleGene Expression Regulation, DevelopmentalHedgehog ProteinsIn Situ HybridizationKruppel-Like Transcription FactorsMaleMembrane ProteinsMiceMice, Inbred C3HMice, Inbred C57BLMice, Mutant StrainsMicroscopy, Electron, ScanningMolecular Sequence DataMutationNerve Tissue ProteinsNeural TubeSequence Homology, Amino AcidSignal TransductionZinc Finger Protein Gli2Zinc Finger Protein Gli3ConceptsCilia formationDistinct tissuesLeft-right patterning defectsForward genetic approachDevelopmental patterning eventsLeft-right specificationShh target genesNovel mutant allelesSonic hedgehog (Shh) signalingNeuronal cell typesEmbryonic patterningMutant phenotypeCilia mutantsDynamic organellesGli activatorPatterning defectsPatterning eventsRepressor formCilia biogenesisUnknown regulatorCilia formGenetic approachesSkeletal formationTarget genesTmem107
2011
Streptococcus pneumoniae Clonal Complex 199: Genetic Diversity and Tissue-Specific Virulence
Thomas JC, Figueira M, Fennie KP, Laufer AS, Kong Y, Pichichero ME, Pelton SI, Pettigrew MM. Streptococcus pneumoniae Clonal Complex 199: Genetic Diversity and Tissue-Specific Virulence. PLOS ONE 2011, 6: e18649. PMID: 21533186, PMCID: PMC3077395, DOI: 10.1371/journal.pone.0018649.Peer-Reviewed Original ResearchConceptsChinchilla modelHeptavalent pneumococcal conjugate vaccinePneumococcal conjugate vaccineSerotype 19A isolatesMiddle ear isolatesS. pneumoniae isolatesLong-term effectivenessConjugate vaccinePneumococcal diseaseOtitis mediaVaccinated populationReplacement diseaseBlood isolatesInvasive diseaseCarriage isolatesPneumoniae isolatesCerebrospinal fluidEar isolatesFuture vaccinesImportant causeStreptococcus pneumoniaeMiddle earDiseaseVirulence potentialVaccine
2009
Calculating complexity of large randomized libraries
Kong Y. Calculating complexity of large randomized libraries. Journal Of Theoretical Biology 2009, 259: 641-645. PMID: 19376134, DOI: 10.1016/j.jtbi.2009.04.008.Peer-Reviewed Original Research
2008
Substrate Discrimination among Mitogen-activated Protein Kinases through Distinct Docking Sequence Motifs*
Sheridan DL, Kong Y, Parker SA, Dalby KN, Turk BE. Substrate Discrimination among Mitogen-activated Protein Kinases through Distinct Docking Sequence Motifs*. Journal Of Biological Chemistry 2008, 283: 19511-19520. PMID: 18482985, PMCID: PMC2443660, DOI: 10.1074/jbc.m801074200.Peer-Reviewed Original ResearchConceptsDEF sitesProtein kinaseMAPK isoformsSequence requirementsMAPK signal transduction cascadePhosphorylation site motifsMAPK family membersSignal transduction cascadePeptide library screenDocking motifExtracellular stimuliMAPK interactionPhosphorylation sitesSequence motifsTransduction cascadeSite motifSubstrate specificityKey residuesSequence specificityLibrary screenUnique sequencesIndividual MAPKsCellular responsesComputational docking studiesExquisite specificity
2007
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search
Kong Y. Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search. Journal Of Computational Biology 2007, 14: 238-254. PMID: 17456017, DOI: 10.1089/cmb.2006.0008.Peer-Reviewed Original ResearchConceptsGeneralized correlation functionCorrelation functionsHigher order approximationsGoulden–Jackson cluster methodHeuristic search methodsOrder approximationProbability qAverage propertiesSearch methodCluster methodLarge genomic dataProbability of occurrenceTheoretical backgroundMultiple seedsSpaced seedsPowerful methodOptimal seedApproximationEmpirical observationsNumber of wildcardsSet of patternsProbabilityProblemFunctionMatrix
2005
MicroRNA: Biological and Computational Perspective
Kong Y, Han J. MicroRNA: Biological and Computational Perspective. Genomics Proteomics & Bioinformatics 2005, 3: 62-72. PMID: 16393143, PMCID: PMC5172550, DOI: 10.1016/s1672-0229(05)03011-1.Peer-Reviewed Original ResearchConceptsAbundant gene familyNon-coding RNAsDiscovery of miRNAMulticellular speciesGene familyMiRNA researchGene expressionBiological processesRegulatory functionsMiRNAComputational approachMicroarray applicationsComputational methodsMiRNAsDiscoveryMicroRNAsRNANucleotidesSpeciesPlantsIndispensable toolExpressionFamily
2004
Fluorescence Anisotropy Studies on the Ku-DNA Interaction ANION AND CATION EFFECTS*
Arosio D, Costantini S, Kong Y, Vindigni A. Fluorescence Anisotropy Studies on the Ku-DNA Interaction ANION AND CATION EFFECTS*. Journal Of Biological Chemistry 2004, 279: 42826-42835. PMID: 15284231, DOI: 10.1074/jbc.m406529200.Peer-Reviewed Original Research
2003
A Protein Interaction Map of Drosophila melanogaster
Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A Protein Interaction Map of Drosophila melanogaster. Science 2003, 302: 1727-1736. PMID: 14605208, DOI: 10.1126/science.1090289.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalciumCell CycleCell DifferentiationCloning, MolecularComputational BiologyDNA, ComplementaryDrosophila melanogasterDrosophila ProteinsErbB ReceptorsGenes, InsectImmunity, InnateMathematicsModels, StatisticalPhotoreceptor Cells, InvertebrateProtein BindingProtein Interaction MappingProteomeRNA SplicingRNA, MessengerSignal TransductionTranscription, GeneticTwo-Hybrid System TechniquesConceptsProtein interaction mapsDrosophila melanogasterDraft mapComplementary DNA librarySystems biology modelingHigh-confidence mapMulticellular organismsFly proteomeMultiprotein complexesDNA libraryInteraction mapPathway componentsLevels of organizationKnown pathwaysExtended pathwaysHuman biologyMelanogasterModel systemProteinPathwayProteomeComputational methodsTranscriptsOrganismsBiology