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
2009
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. PLOS Computational Biology 2009, 5: e1000432. PMID: 19593373, PMCID: PMC2700963, DOI: 10.1371/journal.pcbi.1000432.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingComputer SimulationDatabases, GeneticGenomicsModels, GeneticModels, StatisticalOligonucleotide Array Sequence AnalysisSequence Analysis, DNASoftwareConceptsDifferent read lengthsDifferent technologiesSemi-realistic simulationComputational complexityMaximum accuracyAssembly algorithmReconstruction efficiencySimulation toolboxPersonal genomicsAccurate detectionLow costChallenging stepTechnologyCostAlgorithmAccurate assemblyComplexitySmall enough scalesReconstructionGoalIndividual genomesCanonical problemImportant goalToolboxSimulationsPeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology 2009, 27: 66-75. PMID: 19122651, PMCID: PMC2924752, DOI: 10.1038/nbt.1518.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesBiotechnologyChromatinChromatin ImmunoprecipitationDNAFalse Positive ReactionsGenetic VariationGenomeGenomicsHumansModels, GeneticOligonucleotide Array Sequence AnalysisRNA Polymerase IISequence Analysis, DNASoftware