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
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