2021
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing
Suvakov M, Panda A, Diesh C, Holmes I, Abyzov A. CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing. GigaScience 2021, 10: giab074. PMID: 34817058, PMCID: PMC8612020, DOI: 10.1093/gigascience/giab074.Peer-Reviewed Original ResearchComprehensive identification of somatic nucleotide variants in human brain tissue
Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino F, Moran J, Urban A, Kidd J, Mills R, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biology 2021, 22: 92. PMID: 33781308, PMCID: PMC8006362, DOI: 10.1186/s13059-021-02285-3.Peer-Reviewed Original ResearchConceptsSomatic SNVsSomatic single nucleotide variantsWhole-genome sequencing dataSequencing dataBulk DNA samplesCell lineage treesSomatic mosaicismSingle nucleotide variantsLineage treesSomatic nucleotide variantsCellular processesDNA replicationHuman genomeSomatic tissuesDNA repairNucleotide variantsComprehensive identificationDNA samplesMosaic variantsNon-cancerous tissuesDNASingle individualMultiple replicatesHuman brain tissueVariants
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 heterozygosity
2016
Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance)
Boora G, Kanwar R, Kulkarni A, Abyzov A, Sloan J, Ruddy K, Banck M, Loprinzi C, Beutler A. Testing of candidate single nucleotide variants associated with paclitaxel neuropathy in the trial NCCTG N08C1 (Alliance). Cancer Medicine 2016, 5: 631-639. PMID: 26763541, PMCID: PMC4831281, DOI: 10.1002/cam4.625.Peer-Reviewed Original ResearchConceptsPaclitaxel-induced peripheral neuropathyProtective effectAdditional clinical cohortsSingle nucleotide variantsPrevious reportsGene CYP2C8Pharmacogenomic basisPeripheral neuropathyClinical parametersOdds ratioClinical cohortNucleotide variantsCandidate single nucleotide variantsMultiple studiesHigher likelihoodTaqMan PCRCYP2C8AssociationSequencing analysisRisk effectsSubset of findingsReportNeuropathyPrevious studiesPatients
2012
Architecture of the human regulatory network derived from ENCODE data
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O’Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Architecture of the human regulatory network derived from ENCODE data. Nature 2012, 489: 91-100. PMID: 22955619, PMCID: PMC4154057, DOI: 10.1038/nature11245.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineDNAEncyclopedias as TopicGATA1 Transcription FactorGene Expression ProfilingGene Regulatory NetworksGenome, HumanGenomicsHumansK562 CellsMolecular Sequence AnnotationOrgan SpecificityPhosphorylationPolymorphism, Single NucleotideProtein Interaction MapsRegulatory Sequences, Nucleic AcidRNA, UntranslatedSelection, GeneticTranscription FactorsTranscription Initiation SiteConceptsTranscription factorsRegulatory networksHuman transcriptional regulatory networkHuman regulatory networkSpecific genomic locationsTranscription-related factorsState of genesTranscriptional regulatory networksAllele-specific activityPersonal genome sequencesGenomic locationStrong selectionGenome sequenceENCODE dataGenomic informationInformation-flow bottlenecksRegulatory informationConnected network componentsCombinatorial fashionInfluences expressionHuman biologyBinding informationNetwork motifsCo-associationGenes
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