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
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
2006
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
Leslin C, Abyzov A, Ilyin V. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research 2006, 35: d317-d321. PMID: 17065464, PMCID: PMC1635338, DOI: 10.1093/nar/gkl809.Peer-Reviewed Original Research
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