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 ResearchMeSH KeywordsComputational BiologyDNA Copy Number VariationsExomeHigh-Throughput Nucleotide SequencingHumansINDEL MutationLoss of HeterozygosityMutationNeoplasmsPolymorphism, Single NucleotideConceptsSomatic single nucleotide variantsMutational eventsSingle nucleotide variantsHuman genesSequencing readsShort insertionsDriver genesNucleotide variantsNumber alterationsExome sequencingGenesCancer samplesComputational analysisMore mutational eventsPowerful toolComputational methodsExomeSequencingDeletionReads
2013
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.Peer-Reviewed Original Research
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
Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project
Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB. Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Research 2011, 39: 7058-7076. PMID: 21596777, PMCID: PMC3167619, DOI: 10.1093/nar/gkr342.Peer-Reviewed Original ResearchAlleleSeq: 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