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 proteinsTransplantProteinPeptides
2013
Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies
Bruce C, Stone K, Gulcicek E, Williams K. Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies. Current Protocols In Bioinformatics 2013, 41: 13.21.1-13.21.17. PMID: 23504934, PMCID: PMC3688054, DOI: 10.1002/0471250953.bi1321s41.Peer-Reviewed Original ResearchConceptsMore post-translational modificationsStudy of proteomesPost-translational modificationsFragment ionsChemical structureProtein profiling technologiesMass spectrometryProteolytic peptidesCharge ratioProteomic dataProtein sequencesSpectral dataPrecursor proteinProteomeProteomicsProteinQuantitationSpectrometryIons
2012
A molecular characterization of the choroid plexus and stress-induced gene regulation
Sathyanesan M, Girgenti MJ, Banasr M, Stone K, Bruce C, Guilchicek E, Wilczak-Havill K, Nairn A, Williams K, Sass S, Duman JG, Newton SS. A molecular characterization of the choroid plexus and stress-induced gene regulation. Translational Psychiatry 2012, 2: e139-e139. PMID: 22781172, PMCID: PMC3410626, DOI: 10.1038/tp.2012.64.Peer-Reviewed Original ResearchConceptsStress-induced gene regulationGene expression changesGene expression analysisCP gene expressionGlial fibrillary acidic proteinChoroid plexusMolecular functionsGene regulationSitu hybridization analysisTranscriptomic characterizationHigh-resolution tandem mass spectrometryTarget genesExpression analysisGene expressionExpression changesTarget proteinsCP proteinsMolecular characterizationAdult choroid plexusHybridization analysisCP functionGene profilesProteinBlood-cerebrospinal fluid barrierResolution tandem mass spectrometry
2004
A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies
Carriero N, Osier MV, Cheung KH, Miller PL, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M. A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. Journal Of The American Medical Informatics Association 2004, 12: 90-98. PMID: 15492032, PMCID: PMC543832, DOI: 10.1197/jamia.m1571.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceComputational BiologyComputing MethodologiesMass SpectrometryMicroarray AnalysisPhenotypeSequence AnalysisConceptsHigh performance computationLow-maintenance approachBioinformatics applicationsRepresentative bioinformatics applicationsIntensive bioinformatics applicationsBioinformatics case studyGenome-wide sequence comparisonHPC expertsHPC platformsComplex genetic analysisBioinformatics researchersSignificant speedupMass spectrometry data setsHigh-throughput biotechnologiesSequence comparisonVast amountProteomic dataOrdinal phenotypesSpectrum of techniquesDNA microarraysGenetic analysisGene expressionCase studyIterative refinementMaintenance approach
1996
Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry
McAtee C, Zhang Y, Yarbough P, Fuerst T, Stone K, Samander S, Williams K. Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry. Journal Of Chromatography B 1996, 685: 91-104. PMID: 8930757, DOI: 10.1016/0378-4347(96)00143-0.Peer-Reviewed Original ResearchConceptsMass spectrometryCarboxyl terminusReversed phase liquid chromatographyAmino terminusLaser desorption mass spectrometryDesorption mass spectrometryMolecular massLiquid chromatography-mass spectrometryCarboxyl-terminal sequencingChromatography-mass spectrometryBaculovirus expression vectorSodium dodecyl sulfate-polyacrylamide gel electrophoresisDodecyl sulfate-polyacrylamide gel electrophoresisSulfate-polyacrylamide gel electrophoresisLC-MSLiquid chromatographyExpression vectorTerminal sequencingSequence analysisPolyacrylamide gel electrophoresisSpectrometryIntact proteinInternal sequencesDoublet proteinsTerminus
1988
Synthesis of the p10 single-stranded nucleic acid binding protein from murine leukemia virus.
Roberts W, Elliott J, McMurray W, Williams K. Synthesis of the p10 single-stranded nucleic acid binding protein from murine leukemia virus. Chemical Biology & Drug Design 1988, 1: 74-80. PMID: 2856555.Peer-Reviewed Original ResearchConceptsBeta strandsAlpha-helixDirect amino acid sequencingSynthetic peptide bindsMurine leukemia virus proteinsAmino acid sequencingLys-C peptidesRetroviral Gag polyproteinFasman analysisGene 32Nucleic acidsP10 proteinCircular dichroism experimentsCys-X2Cysteine positionsBacteriophage T4Endoproteinase Lys-C peptidesPrimary sequenceMurine leukemia virusNative proteinPrimary structureCys-X4Amino acid analysisProteinSimilar sequences