2023
Efficient reconstruction of cell lineage trees for cell ancestry and cancer
Jang Y, Fasching L, Bae T, Tomasini L, Schreiner J, Szekely A, Fernandez T, Leckman J, Vaccarino F, Abyzov A. Efficient reconstruction of cell lineage trees for cell ancestry and cancer. Nucleic Acids Research 2023, 51: e57-e57. PMID: 37026484, PMCID: PMC10250207, DOI: 10.1093/nar/gkad254.Peer-Reviewed Original ResearchConceptsLineage treesCell ancestryCell lineage treesFirst cell divisionStem cell linesPluripotent stem cell lineLineage reconstructionInduced pluripotent stem cell lineCell divisionCancer progressionLineage representationCell linesMosaic mutationsHuman skin fibroblastsTreesMutationsAncestrySkin fibroblastsMultiple cellsGenomeLineagesZygotesLinesFibroblastsCellsControl-independent mosaic single nucleotide variant detection with DeepMosaic
Yang X, Xu X, Breuss M, Antaki D, Ball L, Chung C, Shen J, Li C, George R, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov L, Sebat J, Gleeson J. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nature Biotechnology 2023, 41: 870-877. PMID: 36593400, PMCID: PMC10314968, DOI: 10.1038/s41587-022-01559-w.Peer-Reviewed Original Research
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 Research
2020
LongAGE: 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
2015
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing
Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY. MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinformatics 2015, 31: 2741-2744. PMID: 25861968, PMCID: PMC4528635, DOI: 10.1093/bioinformatics/btv204.Peer-Reviewed Original ResearchConceptsCoverage information
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
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions
Bhardwaj N, Abyzov A, Clarke D, Shou C, Gerstein MB. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions. Protein Science 2011, 20: 1745-1754. PMID: 21826754, PMCID: PMC3218368, DOI: 10.1002/pro.710.Peer-Reviewed Original ResearchConceptsMulti-interface hubsMolecular networksConformational changesInteraction networksTransient interactionsStructural interaction networksProtein interaction networksClassification of proteinsDynamic conformational changesProtein structural featuresSmall conformational changesTransient associationGene expressionMore plasticityProtein motionsStructural databankProteinAlternate conformationDifferent mechanismsDrastic structural changesDomainInteractionCNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research 2011, 21: 974-984. PMID: 21324876, PMCID: PMC3106330, DOI: 10.1101/gr.114876.110.Peer-Reviewed Original ResearchAGE: 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
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 Research
2007
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
Uzun A, Leslin C, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Research 2007, 35: w384-w392. PMID: 17537826, PMCID: PMC1933130, DOI: 10.1093/nar/gkm232.Peer-Reviewed Original ResearchConceptsMetabolic pathwaysSNP databasePathway informationProtein structureMulti-protein complexesOpen reading frameAmino acid sequenceMetabolic pathway informationDisease-related pathwaysNCBI SNP databaseProtein databaseReading frameMolecular basisAcid sequencePathway relationsNsSNPsFunctional consequencesComparative modelingProteinEdu/PathwayGenesWeb serverSNPsStructure data
2005
Friend, an integrated analytical front-end application for bioinformatics
Abyzov A, Errami M, Leslin C, Ilyin V. Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics 2005, 21: 3677-3678. PMID: 16076889, DOI: 10.1093/bioinformatics/bti602.Peer-Reviewed Original ResearchConceptsSpecific interaction motifsProtein-DNA interactionsSequences of proteinsProtein folding studiesSequence-structure relationshipFunctional annotationInteraction motifsPhylogeny analysisDNA/RNAProtein modelingSequence alignmentFolding studiesRemote sequencesProteinStructural alignmentStructure databaseProgramming experienceBioinformatics applicationsSequenceCommand line interfaceExtensive GUIRNABioinformaticsFront-end applicationsMotifACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS
SHEHADI I, ABYZOV A, UZUN A, WEI Y, MURGA L, ILYIN V, ONDRECHEN M. ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS. Journal Of Bioinformatics And Computational Biology 2005, 3: 127-143. PMID: 15751116, DOI: 10.1142/s0219720005000916.Peer-Reviewed Original Research
2004
Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point
Ilyin V, Abyzov A, Leslin C. Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science 2004, 13: 1865-1874. PMID: 15215530, PMCID: PMC2279929, DOI: 10.1110/ps.04672604.Peer-Reviewed Original Research