2014
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinformatics 2014, 31: 1469-1471. PMID: 25524895, PMCID: PMC4410653, DOI: 10.1093/bioinformatics/btu828.Peer-Reviewed Original ResearchConceptsMap data structureCompute frameworkGraphical reportsData structureParallel computationValidation frameworkRead alignmentSupplementary dataValidation toolReal dataHigh-fidelity simulationHigh-throughput genome sequencingDetailed statisticsFrameworkValidation resultsPythonInformationJavaSimulatorSupplementary informationComputationBioinformaticsRealistic modelCodeImplementation
2011
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
Abyzov A, Gerstein M. AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics 2011, 27: 595-603. PMID: 21233167, PMCID: PMC3042181, DOI: 10.1093/bioinformatics/btq713.Peer-Reviewed Original ResearchConceptsLocal alignmentDownloadable software packageMemory-efficient implementationDynamic programming algorithmPersonal genome sequencesClassical algorithmsOptimal alignmentAlignment scoresOptimal solutionSoftware packageCorrect sequence alignmentAlgorithmComplex eventsImportant problemBreakpoint resolutionSequence alignmentImplementationCorrect alignmentAlignmentComputation