2017
Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant
Williams KR, Colangelo CM, Hou L, Chung L, Belcher JM, Abbott T, Hall IE, Zhao H, Cantley LG, Parikh CR. Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant. Proteomics Clinical Applications 2017, 11 PMID: 28261998, PMCID: PMC5549272, DOI: 10.1002/prca.201600132.Peer-Reviewed Original ResearchConceptsImmediate graft functionKidney transplantGraft functionLong-term graft outcomeMore effective treatmentsProtein biomarkersIGF patientsGraft outcomeIGF levelsPoor outcomeEffective treatmentKidney implantationClinical relevanceBiomarker panelPotential biomarkersUrine proteomeDGFTransplantBiomarkersPatientsOutcomesTreatmentEarly stagesAssaysPrognosis
2015
Development of a Targeted Urine Proteome Assay for kidney diseases
Cantley LG, Colangelo CM, Stone KL, Chung L, Belcher J, Abbott T, Cantley JL, Williams KR, Parikh CR. Development of a Targeted Urine Proteome Assay for kidney diseases. Proteomics Clinical Applications 2015, 10: 58-74. PMID: 26220717, PMCID: PMC5003777, DOI: 10.1002/prca.201500020.Peer-Reviewed Original ResearchConceptsKidney diseaseUrinary proteinGraft functionImmediate graft functionDelayed graft functionKidney transplant patientsMultiple kidney diseasesTransplant patientsKidney transplantClinical relevancePotential biomarkersUrine proteomeDiseaseAvailable biofluidBiomarkersPatientsProtein biomarkersAssaysSingle assayProteome changesHuman urineQuantifiable proteinsTransplantProteinPeptidesYPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research. Genomics Proteomics & Bioinformatics 2015, 13: 25-35. PMID: 25712262, PMCID: PMC4411476, DOI: 10.1016/j.gpb.2014.11.002.Peer-Reviewed Original ResearchConceptsMultiple reaction monitoringPeptides/proteinsYale Protein Expression DatabaseReaction monitoringProteomics researchMass spectrometry-based proteomics researchMS/MSMass spectrometryDatabase search resultsPeptide identificationSpectral librarySite localizationProteomics communityGroup of laboratoriesSpectrometryProtein Expression DatabaseMS
2012
Yale Center for Clinical Investigation: Leveraging Industry Partnerships and Research Cores
Sherwin R, Slayman C, Rockwell S, Herold K, Williams K, Carson R, Mane S, Seow H, Max J, Johnson T. Yale Center for Clinical Investigation: Leveraging Industry Partnerships and Research Cores. Clinical And Translational Science 2012, 5: 435-436. PMID: 23253663, PMCID: PMC5350809, DOI: 10.1111/cts.12016.Peer-Reviewed Original Research
2008
The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis
SIERAKOWSKA H, WILLIAMS K, SZER I, SZER W. The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis. Clinical & Experimental Immunology 2008, 94: 435-439. PMID: 8252804, PMCID: PMC1534440, DOI: 10.1111/j.1365-2249.1993.tb08214.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsArthritis, JuvenileAutoantigensCells, CulturedChild, PreschoolChromatography, High Pressure LiquidChromatography, Ion ExchangeChromosomal Proteins, Non-HistoneElectrophoresis, Polyacrylamide GelHeLa CellsHumansLeukemia, MyeloidMolecular Sequence DataMolecular WeightOncogene ProteinsPeptide MappingPoly-ADP-Ribose Binding ProteinsRatsConceptsJuvenile rheumatoid arthritisAcute myeloid leukemiaRheumatoid arthritisMyeloid leukemiaRare subtypeLeukaemic cellsBone marrowImmunoblot assayRat tissuesDEK proteinArthritisFive-step chromatographic procedureAutoantigensLeukemiaOncogene DEKAntigenSerumPartial amino acid sequencingDEKAmino acid sequencingOncoprotein DEKPatientsSpleenProteinMarrow
2003
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 2003, 19: 1636-1643. PMID: 12967959, DOI: 10.1093/bioinformatics/btg210.Peer-Reviewed Original Research
1997
Identification of N G-Methylarginine Residues in Human Heterogeneous RNP Protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe Is a Preferred Recognition Motif †
Kim S, Merrill B, Rajpurohit R, Kumar A, Stone K, Papov V, Schneiders J, Szer W, Wilson S, Paik W, Williams K. Identification of N G-Methylarginine Residues in Human Heterogeneous RNP Protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe Is a Preferred Recognition Motif †. Biochemistry 1997, 36: 5185-5192. PMID: 9136880, DOI: 10.1021/bi9625509.Peer-Reviewed Original ResearchAmino Acid SequenceArginineChromatography, High Pressure LiquidEnzyme InhibitorsHeLa CellsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHumansMethylationMolecular Sequence DataPeptide MappingRibonucleoproteinsRNA, Heterogeneous NuclearRNA-Binding ProteinsSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationCrystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution
Shamoo Y, Krueger U, Rice L, Williams K, Steitz T. Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 Å resolution. Nature Structural & Molecular Biology 1997, 4: 215-222. PMID: 9164463, DOI: 10.1038/nsb0397-215.Peer-Reviewed Original ResearchBinding SitesComputer SimulationCrystallography, X-RayHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHumansModels, MolecularModels, StructuralProtein FoldingProtein Structure, SecondaryRibonucleoproteinsRNA SplicingRNA, Small NuclearRNA-Binding ProteinsSoftware
1991
[25] Identification of amino acid residues at interface of protein—Nucleic acid complexes by photochemical cross-linking
Williams K, Konigsberg W. [25] Identification of amino acid residues at interface of protein—Nucleic acid complexes by photochemical cross-linking. Methods In Enzymology 1991, 208: 516-539. PMID: 1779846, DOI: 10.1016/0076-6879(91)08027-f.Peer-Reviewed Original ResearchAdenosine TriphosphateAnimalsBinding SitesChromatography, High Pressure LiquidChromatography, Ion ExchangeColiphagesCross-Linking ReagentsDNADNA-Binding ProteinsElectrophoresis, Polyacrylamide GelEscherichia coliHumansKineticsOligodeoxyribonucleotidesPeptide FragmentsPhosphorus RadioisotopesPhotochemistryPolydeoxyribonucleotidesProtein BindingRadioisotope Dilution Technique
1990
Purification and functional characterization of adenovirus ts111A DNA-binding protein. Fluorescence studies of protein-nucleic acid binding.
Meyers M, Keating K, Roberts W, Williams K, Chase J, Horwitz M. Purification and functional characterization of adenovirus ts111A DNA-binding protein. Fluorescence studies of protein-nucleic acid binding. Journal Of Biological Chemistry 1990, 265: 5875-5882. PMID: 2318838, DOI: 10.1016/s0021-9258(19)39444-x.Peer-Reviewed Original Research
1989
Primary structure differences between proteins C1 and C2 of HeLa 40S nuclear ribonucleoprotein particles
Merrill B, Barnett S, LeStourgeon W, Williams K. Primary structure differences between proteins C1 and C2 of HeLa 40S nuclear ribonucleoprotein particles. Nucleic Acids Research 1989, 17: 8441-8449. PMID: 2587210, PMCID: PMC335017, DOI: 10.1093/nar/17.21.8441.Peer-Reviewed Original ResearchConceptsInsert sequenceHeterogeneous nuclear ribonucleoprotein particleSingle transcription unitAlternative splicing mechanismNuclear ribonucleoprotein particleAmino acid sequencingResidue insertHnRNP proteinsTranscription unitTryptic peptide mappingSplicing mechanismPrimary structure differencesC2 proteinSDS-polyacrylamide gel electrophoresisNuclear ribonucleoproteinProtein C1Ribonucleoprotein particleUntranslated regionPrimary structurePolyacrylamide gel electrophoresisAmino acidsPeptide mappingGel electrophoresisMolecular weight differencesProtein
1987
Isolation of cDNA clones coding for human tissue factor: primary structure of the protein and cDNA.
Spicer E, Horton R, Bloem L, Bach R, Williams K, Guha A, Kraus J, Lin T, Nemerson Y, Konigsberg W. Isolation of cDNA clones coding for human tissue factor: primary structure of the protein and cDNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1987, 84: 5148-5152. PMID: 3037536, PMCID: PMC298811, DOI: 10.1073/pnas.84.15.5148.Peer-Reviewed Original ResearchConceptsMature proteinPrimary structureHuman placental cDNA libraryAmino acid sequenceHigh molecular weight precursorTissue factor genePlacental cDNA librarySequence data banksCarbohydrate attachment sitesSingle polypeptide chainMolecular weight precursorDependent serine proteaseSignificant homologyCDNA clonesCDNA librarySequence dataLeader sequenceNucleotide sequenceFactor genesAcid sequenceTissue factorExtracellular domainLambda phageDistinct domainsPolypeptide chain
1986
Coding sequence of the precursor of the beta subunit of rat propionyl-CoA carboxylase.
Kraus J, Firgaira F, Novotný J, Kalousek F, Williams K, Williamson C, Ohura T, Rosenberg L. Coding sequence of the precursor of the beta subunit of rat propionyl-CoA carboxylase. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 8049-8053. PMID: 3464942, PMCID: PMC386864, DOI: 10.1073/pnas.83.21.8049.Peer-Reviewed Original ResearchConceptsPropionyl-CoA carboxylaseNH2-terminal leader peptideAmino acid sequenceBeta subunitBeta-subunit precursorMature subunitAcid sequenceLeader peptideMitochondrial enzyme propionyl-CoA carboxylaseAmino acidsSubunit precursorOpen reading frameAlpha-helical segmentsEnzyme propionyl-CoA carboxylaseCarboxylaseNH2-terminal residuesFirst helixReading frameDNA sequencesPrecursorsCytoplasmic precursorMRNA sequencesArginine residuesHydrophobic momentMRNA transcriptsMammalian single‐stranded DNA binding protein UP I is derived from the hnRNP core protein A1.
Riva S, Morandi C, Tsoulfas P, Pandolfo M, Biamonti G, Merrill B, Williams K, Multhaup G, Beyreuther K, Werr H. Mammalian single‐stranded DNA binding protein UP I is derived from the hnRNP core protein A1. The EMBO Journal 1986, 5: 2267-2273. PMID: 3023065, PMCID: PMC1167110, DOI: 10.1002/j.1460-2075.1986.tb04494.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAntibodiesBase SequenceCattleCell NucleusCross ReactionsDNA HelicasesGenetic VectorsHeLa CellsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHumansMolecular WeightPeptide MappingPlasmidsRibonucleoproteinsStructure-Activity RelationshipThymus GlandThymus HormonesPurification and domain structure of core hnRNP proteins A1 and A2 and their relationship to single-stranded DNA-binding proteins.
Kumar A, Williams K, Szer W. Purification and domain structure of core hnRNP proteins A1 and A2 and their relationship to single-stranded DNA-binding proteins. Journal Of Biological Chemistry 1986, 261: 11266-11273. PMID: 3733753, DOI: 10.1016/s0021-9258(18)67378-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceChromatography, High Pressure LiquidCircular DichroismDNA-Binding ProteinsHeLa CellsHeterogeneous Nuclear Ribonucleoprotein A1Heterogeneous-Nuclear Ribonucleoprotein Group A-BHeterogeneous-Nuclear RibonucleoproteinsHumansMolecular WeightRibonucleoproteinsSpectrophotometry, UltravioletTrypsinConceptsHeterogeneous nuclear ribonucleoproteinsNucleic acid-binding domainProtein A1Glycine-rich proteinSsDNA-binding proteinDNA-binding proteinsHnRNP protein A1Helix-destabilizing activityHnRNP proteinsNuclear ribonucleoproteinTerminal domainHDP-1A1 bindsGlycine residueNative proteinPrimary structureLimited proteolysisHeLa cellsProtein A2Amino acidsProtein
1985
A cDNA clone for the precursor of rat mitochondrial ornithine transcarbamylase: comparison of rat and human leader sequences and conservation of catalytic sites
Kraus J, Hodges P, Williamson C, Horwich A, Kalousek F, Williams K, Rosenberg L. A cDNA clone for the precursor of rat mitochondrial ornithine transcarbamylase: comparison of rat and human leader sequences and conservation of catalytic sites. Nucleic Acids Research 1985, 13: 943-952. PMID: 3839075, PMCID: PMC341044, DOI: 10.1093/nar/13.3.943.Peer-Reviewed Original ResearchConceptsAmino acid sequenceLeader sequenceAcid sequenceBasic residuesAmino-terminal leader sequenceE. coliComplete sequence homologyAmino acid residuesProtein sequence dataOrnithine transcarbamylaseCDNA clonesSequence dataDNA complementaryOrnithine transcarbamylasesSequence homologyEntire proteinHuman enzymeAcid residuesTranscarbamylasesComplementary DNAAmino acidsMessenger RNARat enzymeNucleotidesCatalytic site
1984
Structure and Expression of a Complementary DNA for the Nuclear Coded Precursor of Human Mitochondrial Ornithine Transcarbamylase
Horwich A, Fenton W, Williams K, Kalousek F, Kraus J, Doolittle R, Konigsberg W, Rosenberg L. Structure and Expression of a Complementary DNA for the Nuclear Coded Precursor of Human Mitochondrial Ornithine Transcarbamylase. Science 1984, 224: 1068-1074. PMID: 6372096, DOI: 10.1126/science.6372096.Peer-Reviewed Original ResearchConceptsComplementary DNALeader peptideOrnithine transcarbamylaseAmino-terminal leader peptideMost mitochondrial proteinsComplete primary structureHuman ornithine transcarbamylaseFree cytoplasmic ribosomesMitochondrial matrix enzymeCultured HeLa cellsMitochondrial proteinsCytoplasmic ribosomesRegulatory elementsNucleotide sequenceStable transformantsMatrix enzymeAsparagine residuesAcidic residuesLarger precursorMature formPrimary structureProtein occursHeLa cellsEscherichia coliAmino acids