2012
Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing
del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012, 13: 649. PMID: 23171430, PMCID: PMC3526394, DOI: 10.1186/1471-2164-13-649.Peer-Reviewed Original ResearchConceptsBulk segregant analysisForward genetic screenSegregant analysisGenetic screenGenome assemblyExon captureCausative mutationsVertebrate model systemHigh-throughput sequencingHuman genetic analysisThousands of SNPsAssembly of scaffoldsModel systemGenomic resourcesVertebrate modelXenopus tropicalisFine mappingGenetic analysisCapture sequencingSequence variantsSequencingMutationsRapid discoveryMutantsExome sequencing
2011
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele‐specific expression and binding in a network framework. Molecular Systems Biology 2011, 7: msb201154. PMID: 21811232, PMCID: PMC3208341, DOI: 10.1038/msb.2011.54.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineChromosome MappingChromosomes, Human, XChromosomes, Human, YDatabases, GeneticDNA-Binding ProteinsGene Expression RegulationGene Regulatory NetworksGenome, HumanHumansMolecular Sequence AnnotationOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSequence Analysis, RNATranscription FactorsConceptsAllele-specific expressionGenome sequenceFunctional genomics data setsAllele-specific behaviorAllele-specific eventsDiploid genome sequenceChIP-seq data setsGenomic data setsGenomic sequence variantsPersonal genome sequencesAlignment of readsRNA-seqGenome ProjectPaternal alleleComputational pipelineReads mappingSequence variantsNetwork motifsVariation dataReference alleleAllelesReadsSequenceExpressionMaternally
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