2024
Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Maury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.Peer-Reviewed Original ResearchConceptsTranscription factor binding sitesWhole-genome sequencingOpen chromatinMutational processesSomatic mutationsFactor binding sitesSchizophrenia casesSchizophrenia risk genesSomatic mosaicismSomatic variantsRisk genesG mutationGene expressionGermline mutationsBinding sitesGenesMutationsIncreased somatic mutationsChromatinMosaic somatic mutationsPrenatal neurogenesisContext of schizophreniaBrain neuronsSchizophrenia brainVariants
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
2013
Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, Consortium 1, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics. Science 2013, 342: 1235587. PMID: 24092746, PMCID: PMC3947637, DOI: 10.1126/science.1235587.Peer-Reviewed Original Research
2008
An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
Abyzov A, Uzun A, Strauss P, Ilyin V. An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. PLOS Computational Biology 2008, 4: e1000066. PMID: 18437203, PMCID: PMC2289873, DOI: 10.1371/journal.pcbi.1000066.Peer-Reviewed Original Research
2007
UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB
Godoy V, Jarosz D, Simon S, Abyzov A, Ilyin V, Walker G. UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB. Molecular Cell 2007, 28: 1058-1070. PMID: 18158902, PMCID: PMC2265384, DOI: 10.1016/j.molcel.2007.10.025.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBinding SitesBlotting, Far-WesternDNA Polymerase betaDNA-Directed DNA PolymeraseEscherichia coliEscherichia coli ProteinsModels, MolecularMolecular Sequence DataMutagenesisMutationProtein BindingProtein Structure, TertiaryRec A RecombinasesSequence Homology, Amino AcidConceptsRegulatory protein-protein interactionsDNA damage-inducible proteinProtein-protein interactionsY-family DNA polymerasesFamily DNA polymerasesMutagenic phenotypeOpen active siteDinBRecAMutagenic potentialDNA polymeraseFrameshift mutagenesisProteinStructural modelingActive siteEukaryotesOrthologsArchaeaUmuDMutagenesisPolymerasePhenotypeBacteriaSitesEvolution
2005
ACTIVE 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