2024
Identifying topologically associating domains using differential kernels
Maisuradze L, King M, Surovtsev I, Mochrie S, Shattuck M, O’Hern C. Identifying topologically associating domains using differential kernels. PLOS Computational Biology 2024, 20: e1012221. PMID: 39008525, PMCID: PMC11249266, DOI: 10.1371/journal.pcbi.1012221.Peer-Reviewed Original ResearchConceptsTopologically associating domainsHi-C mapsFalse discovery rateChromatin conformation capture techniquesEnhancer-promoter interactionsLow false discovery rateSelf-interacting regionsStructure of chromatinRegulate gene expressionAverage contact probabilitiesHi-CLocus IDNA transcriptionGene expressionChromatinDiscovery rateContact probabilityBiological phenomenaState-of-the-artKernel-based techniqueComputer visionReplicationCorrelated changesDisease statesCapture techniques
2016
Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter
Arias‐Cartin R, Dobihal GS, Campos M, Surovtsev IV, Parry B, Jacobs‐Wagner C. Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter. The EMBO Journal 2016, 36: 301-318. PMID: 28011580, PMCID: PMC5286365, DOI: 10.15252/embj.201695513.Peer-Reviewed Original ResearchConceptsNucleoid-associated proteinsDNA replicationNovel nucleoid-associated proteinGene expressionReplication fork passageGlobal gene expressionCell cycle regulationDNA-binding activityCell cycle progressionChromosome dynamicsFork passageChromosome segregationPleiotropic defectsChromosomal biasCaulobacter crescentusAsymmetric localizationReplication forksCellular functionsCycle regulationGenomic techniquesQuantitative cell imagingCell divisionGapRCycle progressionCell cycle
2010
Spatial organization of the flow of genetic information in bacteria
Montero Llopis P, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C. Spatial organization of the flow of genetic information in bacteria. Nature 2010, 466: 77-81. PMID: 20562858, PMCID: PMC2896451, DOI: 10.1038/nature09152.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCaulobacter crescentusChaperoninsChromosomes, BacterialDiffusionDNA, BacterialEndoribonucleasesEscherichia coliGene Expression Regulation, BacterialIn Situ Hybridization, FluorescenceLac OperonProtein BiosynthesisRibosomesRNA StabilityRNA TransportRNA, BacterialRNA, MessengerTranscription, GeneticConceptsSites of transcriptionC. crescentusCaulobacter crescentusEukaryotic cellsCellular physiologyMRNA decayMature mRNAMRNA processesRNase EMRNA substratesMRNA localizationGenetic informationGene expressionBacterial cellsEscherichia coliQuantitative fluorescenceCrescentusSitu hybridizationSpatial organizationMRNABacteriaLimited dispersionCellsTranscriptionTranslation