2024
A supervised Bayesian factor model for the identification of multi-omics signatures
Gygi J, Konstorum A, Pawar S, Aron E, Kleinstein S, Guan L. A supervised Bayesian factor model for the identification of multi-omics signatures. Bioinformatics 2024, 40: btae202. PMID: 38603606, PMCID: PMC11078774, DOI: 10.1093/bioinformatics/btae202.Peer-Reviewed Original ResearchConceptsMulti-omics signaturesBayesian factor modelMulti-omics dataMulti-omics integrationSupplementary dataOmics datasetsMulti-OmicsProfiling datasetsR packageDiverse assaysImproved biological understandingProfiling assaysSignature discoveryBioinformaticsProfiling studiesBiological understandingDimensionality reductionBiological responsesBiological signaturesCombination of dimensionality reduction
2020
Analyzing Metabolomics Data for Environmental Health and Exposome Research
Cai Y, Rosen Vollmar AK, Johnson CH. Analyzing Metabolomics Data for Environmental Health and Exposome Research. Methods In Molecular Biology 2020, 2104: 447-467. PMID: 31953830, DOI: 10.1007/978-1-0716-0239-3_22.Peer-Reviewed Original ResearchConceptsLiquid chromatography-mass spectrometryChromatography-mass spectrometryBiological samplesExposure chemicalsExternal exposureSimultaneous analysisExposome researchHealth outcomesDisease preventionUnique advantagesBiological responsesUntargeted metabolomicsExposure risk assessmentHost susceptibilityMetabolomics technologyExposomeMetabolomic analysisRecent advancesSpectrometryExposureUntargeted metabolomics dataMetabolomicsHuman healthMetabolomics dataCumulative measure
2015
Receptors and Transduction Mechanisms II: Indirectly Coupled Receptor/Ion Channel Systems
Levitan I, Kaczmarek L. Receptors and Transduction Mechanisms II: Indirectly Coupled Receptor/Ion Channel Systems. 2015, 263-294. DOI: 10.1093/med/9780199773893.003.0012.ChaptersProtein phosphorylationSecond messenger-dependent protein kinasesReceptor-channel couplingIon channel proteinsAppropriate biological responseExtracellular signalsDirect phosphorylationSpecific membrane receptorsProtein kinaseRegulatory componentsChannel proteinsSecond messenger systemsMembrane receptorsTransduction mechanismsIon channelsPhosphorylationBiological responsesMessenger systemsIon channel systemsDiversityTarget cellsSignal recognitionNeuronal excitabilityCellsKinase
2012
Genome-wide analysis of transcriptional changes in the thoracic muscle of the migratory locust, Locusta migratoria, exposed to hypobaric hypoxia
Zhao D, Zhang Z, Harrison J, Kang L. Genome-wide analysis of transcriptional changes in the thoracic muscle of the migratory locust, Locusta migratoria, exposed to hypobaric hypoxia. Journal Of Insect Physiology 2012, 58: 1424-1431. PMID: 22985864, DOI: 10.1016/j.jinsphys.2012.08.006.Peer-Reviewed Original ResearchConceptsAnalysis of transcriptional changesHypoxia-inducible factorGenome-wide analysisPentose phosphate pathwayThoracic musclesPhosphate pathwayEndoplasmic reticulumMitochondrial biogenesisTranscriptional changesTranscriptional profilesDysfunctional proteinsTarget genesMitochondrial activityBiological response to hypoxiaMigratory locustLiving organismsResponse to hypoxiaLocusta migratoriaHigh-altitude regionsBiological responsesOxidative stressBiogenesisImpact of hypobaric hypoxiaPentoseInvertebrates
2011
Vapor conjugation of toluene diisocyanate to specific lysines of human albumin
Hettick JM, Siegel PD, Green BJ, Liu J, Wisnewski AV. Vapor conjugation of toluene diisocyanate to specific lysines of human albumin. Analytical Biochemistry 2011, 421: 706-711. PMID: 22206939, PMCID: PMC3324820, DOI: 10.1016/j.ab.2011.12.013.Peer-Reviewed Original ResearchThe Fiber Diameter of Synthetic Bioresorbable Extracellular Matrix Influences Human Fibroblast Morphology and Fibronectin Matrix Assembly
Hsia HC, Nair MR, Mintz RC, Corbett SA. The Fiber Diameter of Synthetic Bioresorbable Extracellular Matrix Influences Human Fibroblast Morphology and Fibronectin Matrix Assembly. Plastic & Reconstructive Surgery 2011, 127: 2312-2320. PMID: 21617465, PMCID: PMC3103705, DOI: 10.1097/prs.0b013e3182139fa4.Peer-Reviewed Original ResearchConceptsFibronectin matrix assemblyMatrix assemblyActin cytoskeletal morphologyFocal adhesion complexesFocal adhesion sizeActin stress fibersCell proliferationAdhesion complexesAdhesion sizeEnvironmental cuesStress fibersCellular responsesAbility of scaffoldsCytoskeletal morphologyScaffold fiber diameterHuman dermal fibroblastsFibril formationCell functionImmunofluorescent microscopyBiological responsesMicrofiber scaffoldsFibroblast morphologyDermal fibroblastsHigher cell proliferationCellsRegulated Intramembrane Proteolysis: Signaling Pathways and Biological Functions
Lal M, Caplan M. Regulated Intramembrane Proteolysis: Signaling Pathways and Biological Functions. Physiology 2011, 26: 34-44. PMID: 21357901, DOI: 10.1152/physiol.00028.2010.Peer-Reviewed Original ResearchConceptsFundamental cellular processesIntegral membrane proteinsFunctional protein domainsCellular processesProtein domainsElicit biological responsesMembrane proteinsTransmembrane proteinIntramembrane cleavageBiological functionsPhysiological processesProteolytic cleavageBiological responsesProteinCleavageDomainMessengerEnzymePathwayMembrane
2008
Functional selectivity of EGF family peptide growth factors: Implications for cancer
Wilson KJ, Gilmore JL, Foley J, Lemmon MA, Riese DJ. Functional selectivity of EGF family peptide growth factors: Implications for cancer. Pharmacology & Therapeutics 2008, 122: 1-8. PMID: 19135477, PMCID: PMC2665203, DOI: 10.1016/j.pharmthera.2008.11.008.Peer-Reviewed Original ResearchConceptsEGF family membersPeptide growth factorsFunctional selectivityGrowth factorErbB family receptorsFamily membersNeck cancerReceptor couplingReceptor tyrosine phosphorylationMalignant phenotypeDivergent biological responsesSame receptorFamily receptorsEGF familyReceptorsErbB receptorsG proteinsCancerCancer chemotherapeuticsCell culturesLigand activityTyrosine phosphorylationColorectalSubsequent differencesBiological responses
2007
Clinical Impact of 4D-CT Imaging on Lung Cancer Radiotherapy Treatment Planning and Biological Response
Antony J, Carlson D, Keall P, Xing L. Clinical Impact of 4D-CT Imaging on Lung Cancer Radiotherapy Treatment Planning and Biological Response. International Journal Of Radiation Oncology • Biology • Physics 2007, 69: s526. DOI: 10.1016/j.ijrobp.2007.07.1759.Peer-Reviewed Original ResearchThe length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation
McCarthy C, Shepherd D, Fleire S, Stronge V, Koch M, Illarionov P, Bossi G, Salio M, Denkberg G, Reddington F, Tarlton A, Reddy B, Schmidt R, Reiter Y, Griffiths G, van der Merwe P, Besra G, Jones E, Batista F, Cerundolo V. The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation. Journal Of Experimental Medicine 2007, 204: 1131-1144. PMID: 17485514, PMCID: PMC2118584, DOI: 10.1084/jem.20062342.Peer-Reviewed Original ResearchConceptsAlpha-GalCer analoguesInvariant NKTT cell receptorAlpha-GalCerINKT cell activationHuman CD1d moleculesCell activationRecognition of lipidCell T cell receptorNKT cell activationStable immunological synapseF-channelsCD1d moleculesLipid antigensRecognition surfaceImmunological synapseSpecificity of antigen recognitionAlpha-GalactosylceramideSynapse formationConformational changesConformational differencesAntigen recognitionEngineered antibodiesLymphocytesBiological responses
2006
Pathophysiology of leukocyte–tissue interactions
Molteni R, Fabbri M, Bender JR, Pardi R. Pathophysiology of leukocyte–tissue interactions. Current Opinion In Cell Biology 2006, 18: 491-498. PMID: 16904306, DOI: 10.1016/j.ceb.2006.08.001.Peer-Reviewed Original ResearchPECAM-1 Affects GSK-3β-Mediated β-Catenin Phosphorylation and Degradation
Biswas P, Canosa S, Schoenfeld D, Schoenfeld J, Li P, Cheas LC, Zhang J, Cordova A, Sumpio B, Madri JA. PECAM-1 Affects GSK-3β-Mediated β-Catenin Phosphorylation and Degradation. American Journal Of Pathology 2006, 169: 314-324. PMID: 16816383, PMCID: PMC1698776, DOI: 10.2353/ajpath.2006.051112.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsbeta CateninBlotting, WesternCapillary PermeabilityCells, CulturedEndothelial CellsFluorescent Antibody TechniqueGlycogen Synthase Kinase 3Glycogen Synthase Kinase 3 betaHistamineHistamine AgentsHumansMiceModels, BiologicalPhosphatidylinositol 3-KinasesPhosphorylationPlatelet Endothelial Cell Adhesion Molecule-1Proto-Oncogene Proteins c-aktReceptors, HistamineSignal TransductionConceptsAdherens junctionsSerine phosphorylationSrc homology 2 domainBeta-catenin expression levelsAdherens junction componentsSerine phosphorylation levelEndothelial cellsΒ-catenin phosphorylationPECAM-1Cell biological responsesCytoplasmic domainSHP-2Proteosomal degradationGSK-3betaDynamic regulatorJunction componentsPhosphorylation levelsPhosphorylationEndothelial cell adhesion molecule-1Expression levelsGSK-3βBiological responsesEndothelial barrier permeabilityMice exhibitCell adhesion molecule-1
2005
Relative Biological Effectiveness of 103Pd and 125I Photons for Continuous Low-Dose-Rate Irradiation of Chinese Hamster Cells
Nath R, Bongiorni P, Chen Z, Gragnano J, Rockwell S. Relative Biological Effectiveness of 103Pd and 125I Photons for Continuous Low-Dose-Rate Irradiation of Chinese Hamster Cells. Radiation Research 2005, 163: 501-509. PMID: 15850411, DOI: 10.1667/rr3363.Peer-Reviewed Original ResearchConceptsContinuous low doseRate irradiationDose-rate effectInverse dose-rate effectCGy/hInitial dose rateChinese hamster lung cellsHigher initial dose rateLow doseHamster lung cellsLung cellsDose rateCell survivalX-ray beamRelative biological effectivenessChinese hamster cellsCellsImplantsAverage RBEHamster cellsBiological responsesBiological effectivenessMonoenergetic X-ray beam
2003
Structures of neuropeptide γ from goldfish and mammalian neuropeptide γ, as determined by 1H NMR spectroscopy
Lee K, Lee S, Kim Y, Park NG. Structures of neuropeptide γ from goldfish and mammalian neuropeptide γ, as determined by 1H NMR spectroscopy. Chemical Biology & Drug Design 2003, 61: 274-285. PMID: 12662361, DOI: 10.1034/j.1399-3011.2003.00058.x.Peer-Reviewed Original ResearchConceptsAmino acid sequenceN-terminal regionAlpha-helical conformationAqueous TFE solutionAcid sequenceShort helixAlpha-helical structureC-terminal regionTerminal amino acid sequencePost-translational processingBeta-turn regionMammalian systemsTFE solutionC-terminusMet21Solution structureNeuropeptide γHelixBiological responsesGold fishBiological actionsSodium dodecyl sulfate micellesHis12Nuclear magnetic resonance spectroscopyNeuropeptide gamma
2001
Receptors and Transduction Mechanisms I: Receptors Coupled Directly to Ion Channels
B.Levitan I, Kaczmarek L. Receptors and Transduction Mechanisms I: Receptors Coupled Directly to Ion Channels. 2001, 253-284. DOI: 10.1093/oso/9780195145236.003.0011.Peer-Reviewed Original ResearchTarget neuronsIon channelsParticular neurotransmitterNeuroactive substancesTransmitter releaseNervous systemNeurotransmitter receptorsNerve cellsHormone receptorsNeuronsTarget cellsReceptorsBiological responsesNeurotransmittersIntercellular communicationCell typesExtracellular signalsChemical signalsTransduction mechanismsResponseCellsNeurohormonesReceptors and Transduction Mechanisms II: Indirectly Coupled Receptor/Ion Channel Systems
B.Levitan I, Kaczmarek L. Receptors and Transduction Mechanisms II: Indirectly Coupled Receptor/Ion Channel Systems. 2001, 285-314. DOI: 10.1093/oso/9780195145236.003.0012.Peer-Reviewed Original ResearchExtracellular signalsSingle protein complexIon channel familyMembrane ion channelsBiological responsesFamily of receptorsProtein complexesIntercellular communicationTarget cellsChannel familyIon channelsIon channel systemsCellsSpecific receptorsNeuronal excitabilityParticular target cellsFinal stepReceptorsFamilyTransductionBiochemistryComplexesResponseExcitabilityNeurons
2000
Integrin cytoplasmic domain-binding proteins
Liu S, Calderwood D, Ginsberg M. Integrin cytoplasmic domain-binding proteins. Journal Of Cell Science 2000, 113: 3563-3571. PMID: 11017872, DOI: 10.1242/jcs.113.20.3563.Peer-Reviewed Original ResearchConceptsDomain-binding proteinCytoplasmic domainCellular proteinsIntegrin cytoplasmic domainActin-binding proteinsMore cellular proteinsCell surface receptorsGene regulationCellular functionsTransduce signalsSignal transductionBiological functionsGene expressionFunctional analysisCell adhesionLarge familySurface receptorsProteinCytoskeletonIntegrin chainsIntegrinsBiological responsesPivotal roleMechanical linkImportant role
1998
The IRS-signalling system: A network of docking proteins that mediate insulin action
White M. The IRS-signalling system: A network of docking proteins that mediate insulin action. Molecular And Cellular Biochemistry 1998, 182: 3-11. PMID: 9609109, DOI: 10.1023/a:1006806722619.Peer-Reviewed Original ResearchConceptsIRS proteinsTyrosine phosphorylationIntrinsic protein tyrosine kinase activityProtein tyrosine kinase activityInsulin-stimulated tyrosine phosphorylationTyrosine kinase activityDocking proteinKinase activityInsulin actionCellular substratesTyrosine kinaseTransmembrane glycoproteinInsulin receptorBiological responsesPhosphorylationGrowth factorComplete understandingNew moleculesTransductionKinaseType II diabetesProteinEnzymeMoleculesII diabetesSpecificity within the EGF family/ErbB receptor family signaling network
Riese D, Stern D. Specificity within the EGF family/ErbB receptor family signaling network. BioEssays 1998, 20: 41-48. PMID: 9504046, DOI: 10.1002/(sici)1521-1878(199801)20:1<41::aid-bies7>3.0.co;2-v.Peer-Reviewed Original ResearchConceptsErbB family receptorsFamily receptorsEpidermal growth factor (EGF) familyErbB receptor familyGrowth factor familyPeptide growth factorsReceptor couplingHormone-receptor interactionBiological responsesGrowth factorHormoneMultiple receptorsReceptorsReceptor familyCell proliferationErbB familyMultiple hormonesReceptor partnersTyrosine kinaseDiverse biological responsesThe IRS-signalling system: A network of docking proteins that mediate insulin action
White M. The IRS-signalling system: A network of docking proteins that mediate insulin action. Developments In Molecular And Cellular Biochemistry 1998, 3-11. DOI: 10.1007/978-1-4615-5647-3_1.Peer-Reviewed Original ResearchIRS proteinsTyrosine phosphorylationIntrinsic protein tyrosine kinase activityProtein tyrosine kinase activityInsulin-stimulated tyrosine phosphorylationTyrosine kinase activityDocking proteinKinase activityInsulin actionCellular substratesTyrosine kinaseTransmembrane glycoproteinInsulin receptorBiological responsesPhosphorylationGrowth factorComplete understandingNew moleculesTransductionKinaseType II diabetesProteinEnzymeMoleculesII diabetes
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