2016
A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals
Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M. A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals. Nature Communications 2016, 7: 11101. PMID: 27089393, PMCID: PMC4837449, DOI: 10.1038/ncomms11101.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsBinding SitesChromosome MappingComputational BiologyDatabases, GeneticGene ExpressionGene FrequencyGenome, HumanGenomicsGenotypeHigh-Throughput Nucleotide SequencingHuman Genome ProjectHumansInternetMolecular Sequence AnnotationPolymorphism, Single NucleotidePrecision MedicineConceptsSingle nucleotide variantsAllele-specific bindingFunctional genomics data setsAllele-specific behaviorLarge-scale sequencingGenomic data setsAllelic imbalanceNumber of readsChIP-seqRNA-seqGenome ProjectMaternal chromosomesNucleotide variantsPersonal genomesMapping biasAllelic variantsVariant catalogMultiple individualsFunctional effectsProject individualsBindingExpressionVariantsGenomeChromosomes
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
2008
MSB: A mean-shift-based approach for the analysis of structural variation in the genome
Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. MSB: A mean-shift-based approach for the analysis of structural variation in the genome. Genome Research 2008, 19: 106-117. PMID: 19037015, PMCID: PMC2612956, DOI: 10.1101/gr.080069.108.Peer-Reviewed Original ResearchConceptsProbability density functionNumber of segmentsGood parameter initializationLikelihood functionArray CGH experimentsKernel-based approachUnderlying distributionModel parametersParameter initializationParticular assumptionsNonparametric methodsExpectation maximizationComputational methodsConvergenceGlobal criterionLocal gradients
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 applicationsMotif