2014
Computational Analysis in Cancer Exome Sequencing
Evans P, Kong Y, Krauthammer M. Computational Analysis in Cancer Exome Sequencing. Methods In Molecular Biology 2014, 1176: 219-227. PMID: 25030931, DOI: 10.1007/978-1-4939-0992-6_18.Peer-Reviewed Original ResearchConceptsSomatic single nucleotide variantsMutational eventsSingle nucleotide variantsHuman genesSequencing readsShort insertionsDriver genesNucleotide variantsNumber alterationsExome sequencingGenesCancer samplesComputational analysisMore mutational eventsPowerful toolComputational methodsExomeSequencingDeletionReads
2006
Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density
Kong Y. Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density. Physical Review E 2006, 74: 061102. PMID: 17280033, DOI: 10.1103/physreve.74.061102.Peer-Reviewed Original ResearchLogarithmic correction termMonomer-dimer modelTwo-dimensional rectangular latticeCorrection termLattice widthLattice stripsFinite-size correctionsExact computational methodsRectangular latticeTwo-dimensional latticeAsymptotic theoryAccurate free energiesInfinite latticeAsymptotic expressionsLarge latticesSeries expansionFinite widthFree energyCorrect digitsLattice sitesFunctional formLatticeComputational methodsDecimal digitsDensity rhoPacking dimers on (2p+1)×(2q+1) lattices
Kong Y. Packing dimers on (2p+1)×(2q+1) lattices. Physical Review E 2006, 73: 016106. PMID: 16486215, DOI: 10.1103/physreve.73.016106.Peer-Reviewed Original ResearchSquare latticeNumber-theoretical propertiesLogarithmic termsMonomer-dimer problemFinite-size correctionsStatistical physics modelsNumber theoryExact solutionLattice stripsN latticePhysics modelsSize correctionsWidth NConfiguration numberLatticeComputational methodsFree energySingle vacancyUnexplored connectionsDistinct behaviorsTheoryTermsProblemSolutionEnergy
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
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