Education

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

Book Chapters

Conference Papers

Editorials

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