2011
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
Kong Y. Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 2011, 98: 152-153. PMID: 21651976, DOI: 10.1016/j.ygeno.2011.05.009.Peer-Reviewed Original Research
2010
MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions
Garla V, Kong Y, Szpakowski S, Krauthammer M. MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinformatics 2010, 27: 416-418. PMID: 21149339, PMCID: PMC3031033, DOI: 10.1093/bioinformatics/btq658.Peer-Reviewed Original ResearchConceptsProtein productsSequence variantsNext-generation sequencing technologiesGenomic sequence variantsTranscript librariesGenomic coordinatesGenomic positionsReference genomeSequencing technologiesSequence variationGenomeGenomic variantsBase substitutionsVariant annotationTranscriptomeTranscriptsVariantsAnnotationMapping
2009
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. PLOS Computational Biology 2009, 5: e1000432. PMID: 19593373, PMCID: PMC2700963, DOI: 10.1371/journal.pcbi.1000432.Peer-Reviewed Original ResearchConceptsDifferent read lengthsDifferent technologiesSemi-realistic simulationComputational complexityMaximum accuracyAssembly algorithmReconstruction efficiencySimulation toolboxPersonal genomicsAccurate detectionLow costChallenging stepTechnologyCostAlgorithmAccurate assemblyComplexitySmall enough scalesReconstructionGoalIndividual genomesCanonical problemImportant goalToolboxSimulationsStatistical Distributions of Pyrosequencing
Kong Y. Statistical Distributions of Pyrosequencing. Journal Of Computational Biology 2009, 16: 31-42. PMID: 19072582, DOI: 10.1089/cmb.2008.0106.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