2020
Complex mosaic structural variations in human fetal brains
Sekar S, Tomasini L, Proukakis C, Bae T, Manlove L, Jang Y, Scuderi S, Zhou B, Kalyva M, Amiri A, Mariani J, Sedlazeck F, Urban AE, Vaccarino F, Abyzov A. Complex mosaic structural variations in human fetal brains. Genome Research 2020, 30: gr.262667.120. PMID: 33122304, PMCID: PMC7706730, DOI: 10.1101/gr.262667.120.Peer-Reviewed Original ResearchMeSH KeywordsBrainClonal EvolutionDNA, CircularFemaleGenomic Structural VariationGenotyping TechniquesGestational AgeHumansMosaicismNeurogenesisPregnancySequence Analysis, DNAConceptsSingle nucleotide variantsCopy number variantsStructural variantsMegabase-scale copy number variantsHuman fetal brainFunctional consequencesMobile element insertionsSimilar functional consequencesFetal brainMosaic single-nucleotide variantsAdult brain neuronsStructural variationsPotential functional consequencesKilobase scaleDNA eventsGenomic fragmentDifferent chromosomesElement insertionsClonal approachHuman brain cellsFetal human brainNucleotide variantsReplication errorsHuman brainNumber variantsLongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads
Tran Q, Abyzov A. LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. Bioinformatics 2020, 37: 1015-1017. PMID: 32777815, PMCID: PMC8128450, DOI: 10.1093/bioinformatics/btaa703.Peer-Reviewed Original Research
2019
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Zhou B, Ho S, Greer S, Spies N, Bell J, Zhang X, Zhu X, Arthur J, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong W, Ji H, Abyzov A, Urban A. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research 2019, 47: 3846-3861. PMID: 30864654, PMCID: PMC6486628, DOI: 10.1093/nar/gkz169.Peer-Reviewed Original ResearchConceptsGenome sequenceStructural variantsGenomic structural featuresSomatic genomic rearrangementsFunctional genomics dataAllele-specific expressionEntire chromosome armsIntegrated genome analysisCRISPR/Cas9Cell linesMain cell linesGenome structureEpigenomic characteristicsChromosome armsGenome analysisDNA methylationGenome characteristicsRetrotransposon insertionChromosomal segmentsGenomic rearrangementsGenomic dataRegulatory complexityCell line HepG2Copy numberLoss of heterozygosityChromatin organization modulates the origin of heritable structural variations in human genome
Roychowdhury T, Abyzov A. Chromatin organization modulates the origin of heritable structural variations in human genome. Nucleic Acids Research 2019, 47: 2766-2777. PMID: 30773596, PMCID: PMC6451188, DOI: 10.1093/nar/gkz103.Peer-Reviewed Original Research
2013
Child Development and Structural Variation in the Human Genome
Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child Development and Structural Variation in the Human Genome. Child Development 2013, 84: 34-48. PMID: 23311762, DOI: 10.1111/cdev.12051.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsAlgorithmsContig MappingGenome, HumanGenomic Structural VariationHumansSequence AlignmentSoftwareConceptsLocal alignmentDownloadable software packageMemory-efficient implementationDynamic programming algorithmPersonal genome sequencesClassical algorithmsOptimal alignmentAlignment scoresOptimal solutionSoftware packageCorrect sequence alignmentAlgorithmComplex eventsImportant problemBreakpoint resolutionSequence alignmentImplementationCorrect alignmentAlignmentComputation
2009
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biology 2009, 10: r23. PMID: 19236709, PMCID: PMC2688268, DOI: 10.1186/gb-2009-10-2-r23.Peer-Reviewed Original ResearchBase SequenceComputational BiologyComputer SimulationGenomeGenomic Structural VariationGenomicsInternetModels, GeneticSoftware