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
2009
Mathematical modeling of a minimal protocell with coordinated growth and division
Surovtsev I, Zhang Z, Lindahl P, Morgan J. Mathematical modeling of a minimal protocell with coordinated growth and division. Journal Of Theoretical Biology 2009, 260: 422-429. PMID: 19501600, DOI: 10.1016/j.jtbi.2009.06.001.Peer-Reviewed Original ResearchConceptsCellular componentsDaughter cellsWhole-cell modeling frameworkParental cellsCell cycle engineMinimal protocellWhole-cell modelsContractile ringCoordinated growthCell shapeCell cycleCellular geometryMembrane areaProtocellsMolecular-level mechanismsCellsSimultaneous doublingCytokinesisCell volume
2004
A framework for whole-cell mathematical modeling
Morgan J, Surovtsev I, Lindahl P. A framework for whole-cell mathematical modeling. Journal Of Theoretical Biology 2004, 231: 581-596. PMID: 15488535, DOI: 10.1016/j.jtbi.2004.07.014.Peer-Reviewed Original ResearchLaminin-binding protein as a cellular receptor for the equine Venezuelan encephalomyelitis virus: Report 2. Inhibition of replication of equine Venezuelan encephalomyelitis virus by blocking laminin-binding protein on the surface of Vero cells.
Bondarenko E, Protopopova E, Konovalova S, Surovtsev I, Mal'tsev V, Loktev V. Laminin-binding protein as a cellular receptor for the equine Venezuelan encephalomyelitis virus: Report 2. Inhibition of replication of equine Venezuelan encephalomyelitis virus by blocking laminin-binding protein on the surface of Vero cells. Molecular Genetics, Microbiology And Virology 2004, 36-40. PMID: 15025003.Peer-Reviewed Original ResearchConceptsLaminin-binding proteinVero cellsVirus replicationEncephalomyelitis virusVEE virusVEE virus infectionVirion penetrationVirus infectionFITC-labeled antibodiesRabbit polyclonal antibodyVero cell surfaceInhibition of replicationRecombinant LBPCell surfaceCellular receptorsVirusPossible inhibitionSuch cellsPolyclonal antibodiesReport 2Scanning cytometryAntibodiesCellsInhibitionInhibition of replication of Venezuelan equine encephalomyelitis with polyclonal antibodies to laminin-binding protein.
Bondarenko E, Protopopova E, Surovtsev I, Shvalov A, Loktev V. Inhibition of replication of Venezuelan equine encephalomyelitis with polyclonal antibodies to laminin-binding protein. Problems Of Virology 2004, 49: 32-7. PMID: 15529862.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell LineChlorocebus aethiopsDose-Response Relationship, DrugDrug DesignEncephalitis Virus, Venezuelan EquineEncephalomyelitis, Venezuelan EquineHumansImmune SeraImmunization, PassiveRabbitsReceptors, LamininRecombinant ProteinsTemperatureVero CellsViral Envelope ProteinsVirus ReplicationConceptsCytopathic effectLaminin-binding proteinVero cellsViral glycoprotein E2Presence of antibodiesNew antiviral drugsVenezuelan equine encephalomyelitis virusPolyclonal rabbit antibodiesAntiviral drugsEquine encephalomyelitis virusInfection inhibitionInhibition of replicationVenezuelan equine encephalomyelitisGlycoprotein E2Encephalomyelitis virusTC-83AntibodiesSpecific antibodiesRabbit antibodiesPK cellsInhibitionSuch cellsPolyclonal antibodiesEquine encephalomyelitisGradual attenuation
2003
Laminin-binding protein (LBP) as a cellular receptor for the virus of Venezuelan equine encephalomyelitis (VEE): Part 1. A study of the interaction between VEE virus virions and the human recombinant LBP.
Bondarenko E, Protopopova E, Konovalova S, Sorokin A, Kachko A, Surovtsev I, Loktev V. Laminin-binding protein (LBP) as a cellular receptor for the virus of Venezuelan equine encephalomyelitis (VEE): Part 1. A study of the interaction between VEE virus virions and the human recombinant LBP. Molecular Genetics, Microbiology And Virology 2003, 36-9. PMID: 14664162.Peer-Reviewed Original Research
2000
Mathematical Modeling the Kinetics of Cell Distribution in the Process of Ligand–Receptor Binding
SUROVTSEV I, RAZUMOV I, NEKRASOV V, SHVALOV A, SOINI J, MALTSEV V, PETROV A, LOKTEV V, CHERNYSHEV A. Mathematical Modeling the Kinetics of Cell Distribution in the Process of Ligand–Receptor Binding. Journal Of Theoretical Biology 2000, 206: 407-417. PMID: 10988026, DOI: 10.1006/jtbi.2000.2136.Peer-Reviewed Original Research
1999
Particle classification from light scattering with the scanning flow cytometer
Shvalov A, Surovtsev I, Chernyshev A, Soini J, Maltsev V. Particle classification from light scattering with the scanning flow cytometer. Cytometry 1999, 37: 215-220. PMID: 10520202, DOI: 10.1002/(sici)1097-0320(19991101)37:3<215::aid-cyto8>3.0.co;2-3.Peer-Reviewed Original ResearchConceptsScanning flow cytometerParticle refractive indexRefractive indexLight scattering signalsPolystyrene particlesParticle identificationOptical propertiesLight-scattering patternsScattering signalsMilk fat particlesSingle particleParticle parametersParticle classificationIndicatricesIndicatrixParticle typesParticle sortingParticlesAcquisition of traceParticle-based immunoassayParticle recognitionMeasurementsFluorescent measurementsComplete characterizationSize deviation