Mikhail L. Blinov, PhDAssociate Professor, Genetics and Genome Sciences
|
Degree | Institution | Major |
---|---|---|
BSc | Moscow State University | Mathematics |
MSc | Weizmann Institute of Science | Mathematics |
PhD | Weizmann Institute of Science | Mathematics |
Other | Los Alamos National Laboratory | Theoretical Immunology |
Post-Graduate Training
Training | Institution | Specialty |
---|---|---|
Postdoctoral | Los Alamos National Laboratory | Theoretical Immunology |
Awards
Name of Award/Honor | Awarding 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 Award | IEEE 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 Award | Los Alamos National Laboratory |
The National Academy of Sciences (U.S.) Travel Grant | |
Weizmann Institute of Science Fellowships | Weizmann Institute of Science |
International Science Foundation Grant | Independent Moscow University |
International Science Foundation Student Grant for Distinguished Successes in Studies | Moscow State University |
Name & Description | Category | Role | Type | Scope | Start Year | End Year |
---|---|---|---|---|---|---|
Systems Biology Area of Concentration (AoC) BioMedical Graduate Program | Education Committee | Director | UConn Health | University | 2019 | |
Graduate Program Committee (GPC) | Education Committee | Member | UConn Health | University | 2019 | |
COMBINE 2019/SBGN workshop | Workshop/Conference | Organizer | International | 2019 | 2019 | |
Reviewer for BMC Bioinformatics, Bioinformatics, PLOS CB, PLOS One, Transactions on Modeling and Computer Simulation, npj Systems Biology and Applications, Proceedings of the Royal Society B, | Professional/Scientific Journal | Reviewer | External | International | 2019 | |
Advisory Commitee | Advisory Committee | Member | UConn Health | University | 2011 | 2014 |
Reviewer for Molecular BioSystems | Other | External | International | 2010 | ||
CCAM Graduate Recruitment Committee | Education Committee | Member | UConn Health | University | 2010 | |
Admission Committee | Education Committee | Interviewer | UConn Health | University | 2010 | |
Reviewer for InFocus | Other | External | International | 2009 | ||
Reviewer for BMC Systems Biology | Other | External | International | 2008 |
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 Lab Rotation Students: Fall Block 2024, Spring 1 and 2 Block 2025
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
-
bnglViz: online visualization of rule-based models.
Bioinformatics (Oxford, England) 2024 Jun;40(6):
-
Mixed selling of different poultry species facilitates emergence of public-health-threating avian influenza viruses.
Emerging microbes & infections 2023 Dec;12(1):2214255
-
MolClustPy: a Python package to characterize multivalent biomolecular clusters.
Bioinformatics (Oxford, England) 2023 Jun;39(6):
-
Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes.
Frontiers in Network Physiology. 2023 May;31079070
-
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Nucleic acids research 2022 May;
-
The solubility product extends the buffering concept to heterotypic biomolecular condensates.
eLife 2021 Jul;10
-
Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology
Current Opinions in Systems Biology 2021 Jun;27, 100350(100350):
-
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
Nucleic acids research 2021 May;
-
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.
Briefings in bioinformatics 2021 Mar;
-
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Molecular systems biology 2020 Aug;16(8):e9110
-
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Journal of integrative bioinformatics 2020 Jul;
-
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
Journal of integrative bioinformatics 2020 Jun;
-
Systems biology graphical notation markup language (SBGNML) version 0.3.
Journal of integrative bioinformatics 2020 Jun;
-
Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns.
Current biology : CB 2020 Mar;30(5):802-814.e8
-
Two MYB proteins in a self-organizing activator-inhibitor system produce spotted pigmentation patterns
Current Biology. 2020 Jan;
-
ModelBricks-modules for reproducible modeling improving model annotation and provenance.
NPJ systems biology and applications 2019 Oct;537
-
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.
Journal of integrative bioinformatics 2019 Jun;
-
Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging.
The journals of gerontology. Series A, Biological sciences and medical sciences 2018 May;73995
-
Compartmental and Spatial Rule-Based Modeling with Virtual Cell.
Biophysical journal 2017 Oct;113(7):1365-1372
-
Multivalent Molecules as Modulators of RNA Granule Size and Composition.
Biophysical journal 2017 Feb;113235-245
-
Rule-based modeling with Virtual Cell.
Bioinformatics (Oxford, England) 2016 Sep;32(18):2880-2
-
Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules.
Biophysical journal 2013 Dec;105(11):2451-60
-
Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Bioinformatics (Oxford, England) 2013 Nov;30(2):292-4
-
A predictive mathematical model of the DNA damage G2 checkpoint.
Journal of theoretical biology 2013 Mar;320159-69
-
Leveraging modeling approaches: reaction networks and rules.
Advances in experimental medicine and biology 2012 Jan;736517-30
-
Logic modeling and the ridiculome under the rug.
BMC biology 2012 Jan;1092
-
Guidelines for visualizing and annotating rule-based models.
Molecular bioSystems 2011 Oct;7(10):2779-95
-
Proliferating dynamic modeling in systems biology studies.
Molecular bioSystems 2011 Oct;7(10):2735-6
-
Using views of Systems Biology Cloud: application for model building.
Theory in biosciences = Theorie in den Biowissenschaften 2011 Mar;130(1):45-54
-
A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells.
Journal of immunology (Baltimore, Md. : 1950) 2010 Sep;185(6):3268-76
-
The BioPAX community standard for pathway data sharing.
Nature biotechnology 2010 Sep;28(9):935-42
-
Modeling without borders: Creating and annotating Vcell models using the web.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2010 Jan;6053 LNBI3-17
-
Integrating BioPAX pathway knowledge with SBML models.
IET systems biology 2009 Sep;3(5):317-28
-
Molecular machines or pleiomorphic ensembles: Signaling complexes revisited
Journal of Biology 2009 Jan;8(9):
-
PMAP: databases for analyzing proteolytic events and pathways.
Nucleic acids research 2009 Jan;37(Database issue):D611-8
-
Rule-based modeling of biochemical systems with BioNetGen.
Methods in molecular biology (Clifton, N.J.) 2009 Jan;500113-67
-
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.
IET systems biology 2008 Sep;2(5):363-8
-
Virtual Cell modelling and simulation software environment.
IET systems biology 2008 Sep;2(5):352-62
-
Rules for modeling signal-transduction systems.
Science's STKE : signal transduction knowledge environment 2006 Jul;2006(344):re6
-
Depicting signaling cascades.
Nature biotechnology 2006 Feb;24(2):137-8; author reply 138
-
A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity.
Bio Systems 2006 Jan;83(2-3):136-51
-
Graph theory for rule-based modeling of biochemical networks
Transact. Computat. Syst. Biol. VII in the series Lect. Notes Comput. Sci. 2006 Jan;89-106
-
'On-the-fly' or 'generate-first' modeling?
Nature biotechnology 2005 Nov;23(11):1344-5; author reply 1345
-
Combinatorial complexity and dynamical restriction of network flows in signal transduction.
Systems biology 2005 Mar;2(1):5-15
-
Graphical rule-based representation of signal-transduction networks
ACM Symposium on Applied Computing 2005 Jan;133-140
-
Local Center Conditions for Abel Equation and Cyclicity of it Zero Solution
Contemp. Math. 2005 Jan;38265-82
-
Rule-based modeling of biochemical networks
Complexity 2005 Jan;10(4):22-41
-
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.
Bioinformatics (Oxford, England) 2004 Nov;20(17):3289-91
-
The complexity of complexes in signal transduction.
Biotechnology and bioengineering 2003 Dec;84(7):783-94
-
Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model.
Journal of immunology (Baltimore, Md. : 1950) 2003 Apr;170(7):3769-81
-
Center and Moment Conditions for Rational Abel Equation
Funct. Diff. Equations 2003 Jan;1095-106
-
Modeling the early signaling events mediated by FcepsilonRI.
Molecular immunology 2002 Sep;38(16-18):1213-9
-
Center and Composition Conditions for Abel Differential Equation, and rational curves
Qualitative Theory of Dynamical Systems 2001 Jan;2111-127
-
Center and Composition Conditions for Abel Differential Equation, and Rational Curves.
1999 Jan;
-
Generalized center conditions and multiplicities for polynomial Abel equations of small degrees
Nonlinearity 1999 Jan;12(4):1013-1028
Book Chapters
-
Mathematical Modeling of Syk Activation in Allergen-Stimulated Mast Cells and Basophils
Advances in Protein Kinases 2012 Jan;271-312
Conference Papers
-
Rule-based modeling - managing combinatorics of protein complexes and phosphoforms.
2008 Jan;
-
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes.
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
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.
2004 Jan;
-
Center and moment conditions for rational Abel equations on a closed curve.
2002 Jan;
Title or Abstract | Type | Sponsor/Event | Date/Year | Location |
---|---|---|---|---|
Systems Biology Graphical Notations | Talk | COVID-19 map community | 2021 | COVID-19 map community, Online |
ComModelMatch community for collaboration among modelers and experimentalist | Talk | Finding Your Inner Modeler Workshop | 2021 | Finding Your Inner Modeler Workshop, online |
VCell modeling and simulation environment | Lecture | COMBINE | 2021 | COMBINE, online |
Rule-based modeling using VCell | Lecture | Computational Cell Biology workshop | 2021 | Computational Cell Biology workshop, online |
The Systems Biology Graphical Notations: a standardized representation of biological maps | Talk | COMBINE 2020 | 2020 | COMBINE 2020, online |
ModelBricks - Well-annotated, reusable component mechanisms to be assembled into models | Talk | COMBINE 2020 | 2020 | COMBINE 2020, online |
SBGNBricks - A tool to describe recurring concepts in molecular networks | Talk | COMBINE 2020 | 2020 | COMBINE 2020, online |
Introduction to Systems Biology using VCell software | Lecture | Vitatutas Magnus University | 2019 | Vitatutas Magnus University, Kaunas, Lithuania |
Virtual Cell: Modeling and Visualization of Reaction Rules | Talk | COMBINE 2019 | 2019 | COMBINE 2019, Heidelberg, Germany |
Matching computational and modeling expertise among biologists | Talk | FYIM workshop | 2019 | FYIM workshop, Birminghem, Alabama, US |
VCell: compartmental and spatial modeling and simulation using reactions and reaction rules | Talk | CSHL meeting | 2019 | CSHL, NY, USA |
Virtual Cell tutorial | Other | The COMBINE workshop | 2012 | Toronto, Canada |
Virtual Cell Modeling Framework: Synergy of Multiple Modeling Tools and Data sources | Poster | ICSB meeting | 2012 | Toronto, Canada |
Combining rule-based and reaction networks modeling approaches | Poster | Computational Cell Biology Meeting | 2011 | Cold Spring Harbor Laboratory, MY |
Rule-Based Modeling with BioNetGen | Other | Computational Cell Biology Meeting | 2011 | Cold Spring Harbor, NY |
Bringing data into VCell Modeling Framework: Pathway Commons and SABIO-RK | Talk | Computational Modeling in Biology Network COMBINE-2011 | 2011 | Heidelberg, Germany |
Spatial Modeling of Signaling Networks using VCell (the “Virtual Cell”) | Talk | Center for Cancer Systems Biology at Vanderbilt 5th Hands-on Workshop | 2011 | Nashville, TN |
Modeling without Borders: Creating and Annotating VCell Models Using the Web | Talk | 2010 International Symposium on Bioinformatics Research and Applications (ISBRA | 2010 | Storrs, CT |
Linking VCell modeling and simulation framework to the world of public databases | Poster | The 11th International Conference on Systems Biology | 2010 | Edinburgh, UK |
Kinetic proofreading and serial engagement in T-cell receptor signaling | Poster | The 11th International Conference on Systems Biology | 2010 | Edinburgh, UK |
Rule-Based Kinetic Modeling using BioNetGen | Other | The 11th International Conference on Systems Biology | 2010 | Edinburgh, UK |
Kinetic proofreading and serial engagement in T cell receptor signaling. | Talk | CCAM seminar | 2010 | Farmington, CT |
Rule-Based Kinetic Modeling using BioNetGen. | Other | The 11th International Conference on Systems Biology | 2010 | Edinburgh, UK |
BioPAX and Rule-Based Modeling with BioNetGen. | Talk | BioPAX Workshop, MSKCC | 2009 | New York, NY |
Rule-Based Kinetic Modeling of Signal Transduction Networks. | Other | The 10th International Conference on Systems Biology | 2009 | Stanford, CA |
Latest from the Data Integration Frontier: Using Pathway Data to Build and Annotate Systems Biology Models. | Other | The 10th International Conference on Systems Biology | 2009 | Stanford, CA |
Rule-Based Modeling. | Other | Workshop on Rule-Based Modeling | 2009 | Farmington, CT |
Systems Biology Linker (SyBiL) – a tool for analysis of BioPAX pathway data and converting it to SBML format. | Other | Computational Cell Biology Meeting | 2009 | Cold Spring Harbor, NY |
Kinetic Modeling using BioPAX ontology. | Poster | Workshop on Emerging Modelling Methodologies in Medicine and Biology | 2009 | Edinburgh, UK |
Latest from the Data Integration Frontier: Using Pathway Data to Build and Annotate Systems Biology Models. | Poster | Q-bio meeting | 2009 | Santa Fe, NM |
Towards Unifying Systems Biology - Using Pathway Data in Biopax Format for SBML Simulators. | Poster | 2009 Biophysical Society Meeting | 2009 | Boston, MA |
BioNetGen at the Virtual Cell: extending biomolecular interactions to account for combinatorial complexity. | Poster | NIH All Hands Meeting of National Technology Centers for Networks and Pathways | 2009 | Bethesda, MD |
Describing rule-based models. | Talk | Standards and Specifications in Synthetic Biology Workshop | 2008 | Seattle, WA |
Describing rule-based models. | Talk | Standards and Specifications in Synthetic Biology Workshop | 2008 | Seattle, WA |
Systems Biology Graphical Notations – another of many existing standards in Systems Biology. | Talk | CCAM seminar | 2008 | Farmington, CT |
Mathematical Modeling of EGFR signaling: accounting for complex formation. | Talk | Genetics and Developmental Biology Seminar | 2008 | Farmington, CT |
Mathematical Modeling of EGFR signaling: accounting for complex formation. | Talk | Genetics and Developmental Biology Seminar | 2008 | Farmington, CT |
Modeling of biological networks. | Talk | Undergrad Research Seminar | 2008 | Farmington, CT |
Rule-based modeling of coagulation cascade. | Talk | Physics in Biology Seminar | 2008 | Farmington, CT |
Rule-based modeling - managing combinatorics of protein complexes and phosphoforms. | Talk | Burnham Institute | 2008 | San Diego, CA |
Mathematical Modeling of signal transduction: tracking protein complex formation around EGFR receptor. | Talk | Genetics and Developmental Biology Seminar | 2008 | Farmington, CT |
Modularity and Multistate complexes, TCNP retreat. | Talk | 2008 | Westbrook, CT | |
Towards unifying systems biology- using pathway data in BioPAX format for SBML simulators. | Poster | Q-bio meeting | 2008 | Santa Fe, NM |
Towards unifying systems biology- using pathway data in BioPAX format for SBML simulators. | Poster | ICSB meeting | 2008 | Gothenburg, Sweden |
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-component Molecular Complexes. | Talk | 7th IEEE International Symposium on Bioinformatics and Bioengineering | 2007 | Boston, MA |
Rule-Based kinetic modeling of signal transduction networks. | Talk | Mathematical Biosciences Institute | 2007 | Columbus, OH |
A rule-based model of F-actin that enumerates branched actin networks. | Talk | 51st Annual Meeting of the Biophysical Society | 2007 | Baltimore, MD |
Rule-based models: RNA selectivity and Actin filaments. | Talk | CCAM seminar | 2007 | Farmington, CT |
Models of protein-protein interactions: language, compilation and executable. | Talk | CS&E Colloquia, University of Connecticut | 2007 | Storrs, CT |
Complexity and modularity of intracellular networks – a systematic approach for modeling and simulation. | Talk | CCAM seminar | 2007 | Farmington, CT |
Rule-Based Kinetic Modeling of Signal Transduction Networks. | Other | The 8th International Conference on Systems Biology | 2007 | San Diego, CA |
Rule-Based Modeling using BioNetGen and the Virtual Cell. | Other | The first q-bio conference | 2007 | Santa Fe, NM |
Rule-Based Modeling using BioNetGen. | Other | CSHL meeting on Computational Cell Biology | 2007 | Cold Spring Harbor, NJ |
Kinetic Modeling using BioPAX ontology. | Poster | IEEE International Conference on Bioinformatics and Biomedicine (BIBM) | 2007 | Silicon Valley, USA |
BioNetGen at the Virtual Cell: extending biomolecular interactions to account for combinatorial complexity. | Poster | 51st Annual Meeting of the Biophysical Society | 2007 | Baltimore, MD |
Modularity and Complexity, TCNP Retreat. | Talk | 2006 | Westbrook, CT | |
Rule-based modeling: application to CCAM projects. | Talk | CCAM seminar | 2006 | Farmington, CT |
Rule-based Approach for modeling of Biochemical Systems. | Talk | QCB seminar, University of Connecticut Health Center | 2006 | Farmington, CT |
Graph Theory for Rule-based Modeling of Biochemical Networks. | Talk | 2005 Workshop at CONCUR2005 international meeting. | 2005 | San Francisco, CA |
BioNetGen: current state and further development. | Other | The 3rd International Symposium on Computational Cell Biology | 2005 | Lenox, MA |
Rule-based modeling of multi-component species. | Talk | 9th SBML Forum | 2004 | Heidelberg, Germany |
Modeling and analysis of combinatorial complexity in signal transduction. | Talk | Understanding Complex Systems Symposium | 2004 | Urbana-Champaign, IL |
BioNetGen: a modeling tool that handles combinatorial complexity. | Poster | Mathematical Models in Signaling Systems | 2004 | Nashville, TN |
Modeling and analysis of combinatorial complexity in signal transduction. | Poster | International Conference on Complex Systems (ICCS2004) | 2004 | Boston, MA |
The EcoTFs Database: Escherichia Coli Transcription Factors and Signals. | Poster | RECOMB 2004 | 2004 | San Diego, CA |
Network model for early events in EGFR signaling that accounts for hundreds of protein complexes and phosphoforms. | Poster | Proceedings of the 4th International Conference on Systems Biology | 2003 | St Louis, USA |
Networks that govern Complex Formation during Signal Transduction Exibit Narrow Flows. | Poster | Proceedings of the 4th International Conference on Systems Biology | 2003 | St Louis, USA |
Combinatorial complexity in immunoreceptor signaling. | Poster | Proceedings of the 3rd International Conference on Systems Biology | 2002 | Stockholm, Sweden |
Database of Models for Ligand-Receptor Binding in XML-based formats. | Poster | Proceedings of the 2nd International Conference on Systems Biology | 2001 | Pasadena, USA |
A detailed kinetic model of immuno-receptor signaling. | Poster | Proceedings of the 2nd International Conference on Systems Biology | 2001 | Pasadena, USA |
Analysis of Cell-Signaling Networks: Which Reactions in the Network are Important? | Poster | Bridging the Canyon: Biology at LANL | 2001 | Santa Fe, NM |
Abel Differential Equation on Rational Curves. | Talk | Summer School on Dynamics Systems, CIME | 2000 | Cetraro, Italy |