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
2007
Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search
Kong Y. Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search. Journal Of Computational Biology 2007, 14: 238-254. PMID: 17456017, DOI: 10.1089/cmb.2006.0008.Peer-Reviewed Original ResearchConceptsGeneralized correlation functionCorrelation functionsHigher order approximationsGoulden–Jackson cluster methodHeuristic search methodsOrder approximationProbability qAverage propertiesSearch methodCluster methodLarge genomic dataProbability of occurrenceTheoretical backgroundMultiple seedsSpaced seedsPowerful methodOptimal seedApproximationEmpirical observationsNumber of wildcardsSet of patternsProbabilityProblemFunctionMatrix
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