Photo of Mikhail L. Blinov, Ph.D.

Mikhail L. Blinov, Ph.D.

Assistant Professor, Genetics and Genome Sciences
Associate Director, Graduate Program in Cell Analysis and Modeling
Academic Office Location:
Center for Cell Analysis and Modeling
UConn Health
263 Farmington Avenue
Farmington, CT 06030
Phone: 860-679-6081
Fax: 860 679-1039
Email: blinov@uchc.edu
Website(s):

Genetics & Developmental Biology Graduate Program

Center for Cell Analysis and Modeling

Blinov Lab Page

Education
DegreeInstitutionMajor
B.Sc.The Moscow State University Mathematics
M.Sc.The Weizmann Institute of ScienceMathematics
Ph.D.The Weizmann Institute of Science Mathematics
OtherLos Alamos National LaboratoryTheoretical Immunology

Post-Graduate Training
TrainingInstitutionSpecialty
PostdoctoralLos Alamos National LaboratoryTheoretical Immunology

Awards
Name of Award/HonorAwarding Organization
Certificate of Recognition for contribution to the teaching program in Community Based Education, Academic Year 2008-2009
First Runner-Up for the Inter/Multidisciplinary Research Paper AwardIEEE Bioinformatics and Bioengineering
Certificate of Recognition for contribution to the teaching program in Community Based Education, Academic Year 2007-2008
“BioNetGen” software nominated by Los Alamos National Lab for 2004 R&D 100 competition.
Student Distinguished Performance AwardLos Alamos National Laboratory
The National Academy of Sciences (US) Travel Grant
Weizmann Institute of Sciences FellowshipsWeizmann Institute of Sciences
International Science Foundation Grant Independent Moscow University
International Science Foundation Student Grant for distinguished successes in studiesMoscow State University
Name & DescriptionCategoryRoleTypeScopeStart YearEnd Year
Admission CommitteeEducation CommitteeMemberUConn HealthUniversity20122013
Admission CommitteeEducation CommitteeMemberUConn HealthUniversity20112012
Advisory CommiteeAdvisory CommitteeMemberUConn HealthUniversity20112014
Admission CommiteeEducation CommitteeInterviewerUConn HealthUniversity20102011
Reviewer for Molecular BioSystemsOtherExternalInternational2010
CCAM Graduate Recruitment CommitteeEducation CommitteeMemberUConn HealthUniversity2010
Reviewer for InFocusOtherExternalInternational2009
Reviewer for BMC Systems BiologyOtherExternalInternational2008

1. Computational modeling: Signal transduction networks often exhibit combinatorial complexity: the number of protein complexes and modification states that potentially can be generated during the response to a signal is large, because signaling proteins contain multiple sites of modification and interact with multiple binding partners. If the number of species is large enough, manual specification becomes impossible. A rule-based description provides a way to specify a biological system using a set of rules. Using rule-based approach, we do mathematical modeling of signal transduction network in a single cell. Specifically, we are interested in describing activities and interactions among domains of biomolecules (e.g. phosphorylation of specific tyrosine residues, interactions between SH2 domain and phosphotyrosine) for receptor signaling and proteins-dna interactions.


2. Technology: We are developing software for rule-based modeling called BioNetGen (http://vcell.org/bionetgen). BioNetGen specification language can describe a broad range of biological effects. We are working on representing and visualizing protein-protein interactions as a set of rules.


3. Bioinformatics: Multiple public databases provide a variety of resources: thousands of substances and interactions, hundreds of ready to use models, links to reference materials (data and/or publications), etc. Mathematical modeling can be used to integrate this complex data and create quantitative, testable predictions based on the current state of knowledge of a biological process. Data retrieval, visualization, flexible querying, and model annotation for future reuse, are some of the important requirements for modeling-based research in the modern age. We develop Systems Biology Linker (SyBiL, http://vcell.org/sybil) for simultaneous querying of multiple systems biology knowledge bases and data sources, such as web repositories, databases, and user files, and converting the extracted and refined data into model elements.

Accepting students for Lab Rotations: Summer '16, Fall '16, Spring '17


Students who wish to learn how to apply modeling to their own biological system of interest are more than welcome. In addition the following projects are available:


1. We are interested in effect of mulattions in BCL11B protein on IL2 transctiption, and crosstalk with NF-kappaB pathway. Rotation project will involve computational modeling with the BioNetGen and Virtual Cell software.


2. We are interested in modeling of TOG-mediated granule assembly in the A2 RNA trafficking pathway.

Journal Articles

Book Chapters

  • Mathematical Modeling of Syk Activation in Allergen-Stimulated Mast Cells and Basophils
    Nag A, Monine MI, Goldstein B, Faeder JR, Blinov ML Advances in Protein Kinases 2012 Jan;271-312

Conference Papers

  • Rule-based modeling - managing combinatorics of protein complexes and phosphoforms.
    Blinov ML 2008 Jan;
  • XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes.
    Blinov, Michael L; Moraru, Ion I Proceedings / Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE). IEEE International Symposium on Bioinformatics and Bioengineering 2007 Nov;987-994
  • Kinetic Modeling using BioPAX ontology
    Ruebenacker O., Moraru I.I., Schaff J.C., Blinov M.L. Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007 2007 Jan;339-346
  • Modeling and analysis of signal transduction without ignoring combinatorial complexity.
    Blinov ML 2004 Jan;
  • Center and moment conditions for rational Abel equations on a closed curve.
    Blinov ML 2002 Jan;
  • Center and Composition Conditions for Abel Differential Equation, and Rational Curves.
    Blinov ML 1999 Jan;
Title or AbstractTypeSponsor/EventDate/YearLocation
Virtual Cell tutorialOther The COMBINE workshop2012Toronto, Canada
Virtual Cell Modeling Framework: Synergy of Multiple Modeling Tools and Data sourcesPosterICSB meeting2012Toronto, Canada
Combining rule-based and reaction networks modeling approachesPosterComputational Cell Biology Meeting2011Cold Spring Harbor Laboratory, MY
Rule-Based Modeling with BioNetGenOtherComputational Cell Biology Meeting2011Cold Spring Harbor, NY
Bringing data into VCell Modeling Framework: Pathway Commons and SABIO-RKTalkComputational Modeling in Biology Network COMBINE-20112011Heidelberg, Germany
Spatial Modeling of Signaling Networks using VCell (the “Virtual Cell”)TalkCenter for Cancer Systems Biology at Vanderbilt 5th Hands-on Workshop2011Nashville, TN
Modeling without Borders: Creating and Annotating VCell Models Using the WebTalk2010 International Symposium on Bioinformatics Research and Applications (ISBRA2010Storrs, CT
Linking VCell modeling and simulation framework to the world of public databasesPosterThe 11th International Conference on Systems Biology2010Edinburgh, UK
Kinetic proofreading and serial engagement in T-cell receptor signalingPosterThe 11th International Conference on Systems Biology2010Edinburgh, UK
Rule-Based Kinetic Modeling using BioNetGenOtherThe 11th International Conference on Systems Biology2010Edinburgh, UK
Kinetic proofreading and serial engagement in T cell receptor signaling.TalkCCAM seminar2010Farmington, CT
Rule-Based Kinetic Modeling using BioNetGen.OtherThe 11th International Conference on Systems Biology2010Edinburgh, UK
BioPAX and Rule-Based Modeling with BioNetGen.TalkBioPAX Workshop, MSKCC2009New York, NY
Rule-Based Kinetic Modeling of Signal Transduction Networks.OtherThe 10th International Conference on Systems Biology2009Stanford, CA
Latest from the Data Integration Frontier: Using Pathway Data to Build and Annotate Systems Biology Models.OtherThe 10th International Conference on Systems Biology2009Stanford, CA
Rule-Based Modeling.OtherWorkshop on Rule-Based Modeling2009Farmington, CT
Systems Biology Linker (SyBiL) – a tool for analysis of BioPAX pathway data and converting it to SBML format.OtherComputational Cell Biology Meeting2009Cold Spring Harbor, NY
Kinetic Modeling using BioPAX ontology.PosterWorkshop on Emerging Modelling Methodologies in Medicine and Biology2009Edinburgh, UK
Latest from the Data Integration Frontier: Using Pathway Data to Build and Annotate Systems Biology Models.PosterQ-bio meeting2009Santa Fe, NM
Towards Unifying Systems Biology - Using Pathway Data in Biopax Format for SBML Simulators.Poster2009 Biophysical Society Meeting2009Boston, MA
BioNetGen at the Virtual Cell: extending biomolecular interactions to account for combinatorial complexity.PosterNIH All Hands Meeting of National Technology Centers for Networks and Pathways2009Bethesda, MD
Describing rule-based models.TalkStandards and Specifications in Synthetic Biology Workshop2008Seattle, WA
Describing rule-based models.TalkStandards and Specifications in Synthetic Biology Workshop2008Seattle, WA
Systems Biology Graphical Notations – another of many existing standards in Systems Biology.TalkCCAM seminar2008Farmington, CT
Mathematical Modeling of EGFR signaling: accounting for complex formation.TalkGenetics and Developmental Biology Seminar2008Farmington, CT
Mathematical Modeling of EGFR signaling: accounting for complex formation.TalkGenetics and Developmental Biology Seminar2008Farmington, CT
Modeling of biological networks. TalkUndergrad Research Seminar2008Farmington, CT
Rule-based modeling of coagulation cascade.TalkPhysics in Biology Seminar2008Farmington, CT
Rule-based modeling - managing combinatorics of protein complexes and phosphoforms.TalkBurnham Institute2008San Diego, CA
Mathematical Modeling of signal transduction: tracking protein complex formation around EGFR receptor.TalkGenetics and Developmental Biology Seminar2008Farmington, CT
Modularity and Multistate complexes, TCNP retreat.Talk2008Westbrook, CT
Towards unifying systems biology- using pathway data in BioPAX format for SBML simulators.PosterQ-bio meeting2008Santa Fe, NM
Towards unifying systems biology- using pathway data in BioPAX format for SBML simulators.PosterICSB meeting2008Gothenburg, Sweden
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-component Molecular Complexes.Talk7th IEEE International Symposium on Bioinformatics and Bioengineering2007Boston, MA
Rule-Based kinetic modeling of signal transduction networks.TalkMathematical Biosciences Institute2007Columbus, OH
A rule-based model of F-actin that enumerates branched actin networks.Talk51st Annual Meeting of the Biophysical Society2007Baltimore, MD
Rule-based models: RNA selectivity and Actin filaments.TalkCCAM seminar2007Farmington, CT
Models of protein-protein interactions: language, compilation and executable.TalkCS&E Colloquia, University of Connecticut2007Storrs, CT
Complexity and modularity of intracellular networks – a systematic approach for modeling and simulation.TalkCCAM seminar2007Farmington, CT
Rule-Based Kinetic Modeling of Signal Transduction Networks.OtherThe 8th International Conference on Systems Biology2007San Diego, CA
Rule-Based Modeling using BioNetGen and the Virtual Cell.OtherThe first q-bio conference2007Santa Fe, NM
Rule-Based Modeling using BioNetGen.OtherCSHL meeting on Computational Cell Biology2007Cold Spring Harbor, NJ
Kinetic Modeling using BioPAX ontology.PosterIEEE International Conference on Bioinformatics and Biomedicine (BIBM)2007Silicon Valley, USA
BioNetGen at the Virtual Cell: extending biomolecular interactions to account for combinatorial complexity.Poster51st Annual Meeting of the Biophysical Society2007Baltimore, MD
Modularity and Complexity, TCNP Retreat.Talk2006Westbrook, CT
Rule-based modeling: application to CCAM projects.TalkCCAM seminar2006Farmington, CT
Rule-based Approach for modeling of Biochemical Systems.TalkQCB seminar, University of Connecticut Health Center2006Farmington, CT
Graph Theory for Rule-based Modeling of Biochemical Networks.Talk2005 Workshop at CONCUR2005 international meeting.2005San Francisco, CA
BioNetGen: current state and further development.OtherThe 3rd International Symposium on Computational Cell Biology2005Lenox, MA
Rule-based modeling of multi-component species.Talk9th SBML Forum2004Heidelberg, Germany
Modeling and analysis of combinatorial complexity in signal transduction.TalkUnderstanding Complex Systems Symposium2004Urbana-Champaign, IL
BioNetGen: a modeling tool that handles combinatorial complexity.PosterMathematical Models in Signaling Systems2004Nashville, TN
Modeling and analysis of combinatorial complexity in signal transduction.PosterInternational Conference on Complex Systems (ICCS2004)2004Boston, MA
The EcoTFs Database: Escherichia Coli Transcription Factors and Signals.PosterRECOMB 20042004San Diego, CA
Network model for early events in EGFR signaling that accounts for hundreds of protein complexes and phosphoforms.PosterProceedings of the 4th International Conference on Systems Biology2003St Louis, USA
Networks that govern Complex Formation during Signal Transduction Exibit Narrow Flows.PosterProceedings of the 4th International Conference on Systems Biology2003St Louis, USA
Combinatorial complexity in immunoreceptor signaling.PosterProceedings of the 3rd International Conference on Systems Biology2002Stockholm, Sweden
Database of Models for Ligand-Receptor Binding in XML-based formats.PosterProceedings of the 2nd International Conference on Systems Biology2001Pasadena, USA
A detailed kinetic model of immuno-receptor signaling.PosterProceedings of the 2nd International Conference on Systems Biology2001Pasadena, USA
Analysis of Cell-Signaling Networks: Which Reactions in the Network are Important?PosterBridging the Canyon: Biology at LANL2001Santa Fe, NM
Abel Differential Equation on Rational Curves.TalkSummer School on Dynamics Systems, CIME2000Cetraro, Italy