Referenced in PubMed (open access)
Referenced in AMS (American Mathematical Society; subscription required)
Referenced in the DBLP Computer Science Bibliography (open access)

Full List (Reverse Chronological Order)

  1. C.V. Falkenberg., J.H. Carson, and M.L. Blinov. (2017). Multivalent Molecules as Modulators of RNA Granule Size and CompositionBiophys. J. 113(2): 235-245. PMID: 28242011.
  2. M.L. Blinov, J.C. Schaff, D. Vasilescu, I.I. Moraru, J.E. Bloom and L.M. Loew. (2017) Compartmental and spatial rule-based modeling with Virtual Cell (VCell)Biophys. J. 113, 1365-1372.
  3. J.C. Schaff, D. Vasilescu, I.I. Moraru, L.M. Loew, and M.L. Blinov (2017) Rule-based modeling with Virtual CellBioinformatics. 32(18), 2880-2. PMID: 27497444.
  4. M.L. Blinov, J.C. Schaff, O. Ruebenacker, X. Wei, D. Vasilescu, F. Gao, F. Morgan, L. Ye, A. LakshminarayanaL., I.I. Moraru, L.M. Loew (2014) "Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling"Bioinformatics.
  5. C.V. Falkenberg, M.L. Blinov, L.M. Loew (2013) "Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules"Biophys J. 105(11):2451-60. [SuppMat]
  6. K.J. Kesseler, M.L. Blinov, T.C. Elston, W.K. Kauffman, D.A. Simpson (2013) "A predictive mathematical model of the DNA damage G2 checkpoint"J Theor Biol, 320:159-69.
  7. M.L. Blinov, I.I. Moraru (2012) "Logic modeling and the ridiculome under the rug"BMC Biology, 10:92. []
  8. A. Nag, M.I. Monine, B. Goldstein, J.R. Faeder, M.L. Blinov (2012) "Mathematical modeling of Syk activation in allergen-stimulated mast cells and basophils", in the book "Protein Kinases / Book 2", ISBN 979-953-307-890-7.
  9. M.L.Blinov, I.I. Moraru (2012) "Leveraging modeling approaches: reaction networks and rules"Adv Exp Med Biol. 736:517-30.
  10. M.L.Blinov (2011) "Proliferating dynamic modeling in systems biology studies"Mol Biosyst. 7(10):2735-6.
  11. L.A. Chylek, B. Hu, M.L. Blinov, T. Emonet, J.R. Faeder, B. Goldstein, R.N. Gutenkunst, J.M. Haugh, T. Lipniacki, R.G. Posner, J. Yang, W.S. Hlavacek. (2011) "Guidelines for visualizing and annotating rule-based models"Mol Biosyst. 7(10):2779-95.
  12. A. Nag, M.I. Monine, M.L. Blinov, B. Goldstein (2010) "A detailed mathematical model predicts serial engagement of IgE-FceRI complexes can enhance Syk activation in mast cells"J.Immunol. 185(6):3268-76.
  13. O. Ruebenacker O, M. Blinov (2010) "Using views of Systems Biology Cloud: application for model building."Theory Biosci. 130: 45-54.
  14. E. Demir et al. (2010) BioPAX - A Community Standard for Pathway Data SharingNature Biotechnology. 28(9):935-42 []
  15. M.L.Blinov, O. Ruebenacker, J.C.Schaff, I.I.Moraru (2010) "Modeling without Borders: Creating and Annotating VCell Models Using the Web"Lecture Notes in Bionformatics 6053, 3-17.
  16. B.J.Mayer, M.L.Blinov, L.M. Loew (2009) "Molecular Machines or Pleiomorphic Ensembles: Signaling Complexes Revisited"J. Biol. 8(9), 81.
  17. O. Ruebenacker, I.I.Moraru, J.C.Schaff, M.L.Blinov (2009 ) "Integrating BioPAX knowledge with SBML models"IET Systems Biology, 3(5), 317-328.
  18. J. R. Faeder, M. L. Blinov, and W. S. Hlavacek (2009). Rule-Based Modeling of Biochemical Systems with BioNetGen. In Methods in Molecular Biology: Systems Biology, 500:113-67.
  19. M. L. Blinov, O. Ruebenacker and I. I. Moraru (2008) Complexity and Modularity of Intracellular Networks - A Systematic Approach for Modeling and Simulation. IET Systems Biology, 2(5), 363-368. [Abstract]
  20. I.I. Moraru, J.C. Schaff, B.M. Slepchenko, M.L. Blinov, F. Morgan, A. Lakshminarayana, F. Gao, Y. Li, and L.M. Loew (2008). Virtual Cell modelling and simulation software environmentIET Systems Biology, 2(5), 352-362. [Abstract]
  21. Y. Igarashi, E. Heureux, K. S. Doctor, P. Talwar, S. Gramatikova, K. Gramatikoff, Y. Zhang, M. Blinov, S. S. Ibragimova, S. Boyd, B. Ratnikov, P. Cieplak, A. Godzik, J.W. Smith, A. L. Osterman, and A. M. Eroshkin (2008). PMAP: databases for analyzing proteolytic events and pathwaysNucleic Acids Res. 37(Database issue): D611-8. [PubMed]
  22. O. Ruebenacker, I. I. Moraru, J. C. Schaff and M. L. Blinov (2007) Kinetic Modeling Using BioPAX OntologyProceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine: 339-348.
  23. M. L. Blinov and I. I. Moraru (2007) XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular ComplexesProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering: 987-994.
  24. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka and W. Fontana (2006) Rules for modeling signal-transduction systemsSci. STKE 2006, re6. [PubMed | doi:10.1126/stke.3442006re6]
  25. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Depicting signaling cascadesNat. Biotechnol. 24, 137-138. [PubMed]
  26. M. L. Blinov R. Faeder, B. Goldstein and W. S. Hlavacek (2006) A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexityBioSystems 83, 136-151 [PubMed | doi:10.1016/j.biosystems.2005.06.014]
  27. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Graph theory for rule-based modeling of biochemical networksTransactions on Computational Systems Biology IV pp. 89-106.
  28. M. L. Blinov, J. R. Faeder, J. Yang, B. Goldstein and W. S. Hlavacek (2005) `On-the-fly' or `generate-first' modeling? Nat. Biotechnol. 23, 1344-1345. [PubMed]
  29. J. R. Faeder*, M. L. Blinov*, B. Goldstein and W. S. Hlavacek (2005) Rule-based modeling of biochemical networksComplexity 10, 22-41. [Abstract]
    * These two authors contributed equally to the manuscript.
  30. J. R. Faeder, M. L. Blinov, B. Goldstein and W. S. Hlavacek (2005) Combinatorial complexity and dynamical restriction of network flows in signal transductionSyst. Biol. 2, 5-15. [Abstract]
  31. J. R. Faeder, M. L. Blinov and W. S. Hlavacek (2005) Graphical rule-based representation of signal-transduction networks. In Proc. 2005 ACM Symp. Appl. Computing (L. M. Liebrock, Editor) ACM Press, New York, NY, pp. 133-140. Presented at The 20th ACM Symposium on Applied Computing, Santa Fe, NM, March 13-17, 2005. []
  32. M. Blinov, M. Briskin, Y. Yomdin (2005) Local Center Conditions for Abel Equation and Cyclicity of it Zero Solution. In Complex analysis and dynamical systems II, Contemp. Math. 382, 65-82. Amer. Math. Soc., Providence, RI.
  33. M. L. Blinov, J. R. Faeder, B. Goldstein and W. S. Hlavacek (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. [PubMed | doi:10.1093/bioinformatics/bth378 | BioNetGen software]
  34. J. R. Faeder, W. S. Hlavacek, I. Reischl, M. L. Blinov, H. Metzger, A. Redondo, C. Wofsy and B. Goldstein (2003) Investigation of early events in FcεRI-mediated signaling using a detailed mathematical modelJ. Immunol. 170, 3769-3781. [PubMed | Full Text]
  35. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, A. S. Perelson and B. Goldstein (2003) The complexity of complexes in signal transductionBiotechnol. Bioeng. 84, 783-794. [PubMed]
  36. M. Blinov, N. Roytvarf, Y. Yomdin (2003) Center and Moment Conditions for Rational Abel EquationFunct. Diff. Equations 10, 95-106
  37. M. Blinov, N. Zehavi, S. Black (2003) A Computer Motivated Study of Problems in Number TheoryThe International Journal of Computer Algebra in Mathematics Education 9, 315-330.
  38. B. Goldstein, J. R. Faeder, W. S. Hlavacek, M. L. Blinov, A. Redondo and C. Wofsy (2002) Modeling the early signaling events mediated by FcεRIMol. Immunol. 38, 1213-1219. [PubMed]
  39. M. Blinov, Y. Yomdin (2001) Center and Composition Conditions for Abel Differential Equation, and rational curvesQualitative Theory of Dynamical Systems 2, 111-127.
  40. M. Blinov, Y. Yomdin. (1999) Generalized center conditions and multiplicities for polynomial Abel equations of small degreesNonlinearity 12, 1013-1028.


  • Blinov M, Faeder J, Hlavacek W, Software and procedures for creating mathematical/computational models of cellular signaling. U.S. Patent Application 20050042663 (2005), available at the U.S. Patent and Trademark Office.
  • Faeder J, Blinov M, Hlavacek W. Graphical procedures for creating mathematical/computational models of cellular signaling. U.S. Patent Application (2006).


  • M.L. Blinov, J.R. Faeder, B. Goldstein, A. Finney and W.S. Hlavacek (2004) "Rule-based modeling of multi-component species." A proposal for SBML Level 3 presented at the 9th SBML Forum [presentation]