1. B. Goldstein, J.R. Faeder, W.S. Hlavacek, M.L. Blinov, A. Redondo & C. Wofsy (2002) Modeling the early signaling events mediated by Fc&epsilonRI. Mol. Immunol. 38, 1213-1219. [PubMed Abstract]
(Our first rule-based model for a signal-transduction system. This work led us to realize the effect of combinatorial complexity.)
2. J.R. Faeder, W.S. Hlavacek, I. Reischl, M.L. Blinov, H. Metzger, A. Redondo, C. Wofsy & B. Goldstein (2003) Investigation of early events in Fc&epsilonRI-mediated signaling using a detailed mathematical model. J. Immunol. 170, 3769-3781. [PubMed Abstract | Suppl. material]
(Elaboration of our first rule-based model. This work led us to realize that a general-purpose software tool, like BioNetGen, would be useful.)
3. W.S. Hlavacek, J.R. Faeder, M.L. Blinov, A.S. Perelson & B. Goldstein (2003) The complexity of complexes in signal transduction. Biotechnol. Bioeng. 84, 783-794. [PubMed Abstract | Reprint (pdf)]
(A review about how the features of protein interactions give rise to combinatorial complexity and how this complexity cause difficulties when modeling signal-transduction systems.)
4. B. Goldstein, J.R. Faeder & W.S. Hlavacek (2004) Mathematical and computational models of immune-receptor signalling. Nat. Rev. Immunol. 4, 445-456. [PubMed Abstract | Reprint (pdf)]
(A review about modeling of signal transduction in the immune system, including use of rule-based modeling techniques.)
5. M.L. Blinov, J.R. Faeder, B. Goldstein & W.S. Hlavacek (2004) BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics 20, 3289-3291. [doi:10.1093/bioinformatics/bth378 (open access) | PubMed Abstract | BioNetGen]
(The first report of BioNetGen (version 1.0))
6. M.L. Blinov, J.R. Faeder, B. Goldstein, A. Finney & W.S. Hlavacek (2004) Rule-based modeling of multi-component species. A proposal for SBML Level 3 presented at the 9th SBML Forum. [Proposal (pdf)]
(A proposal for extending SBML to incorporate rules for biomolecular interactions)
7. 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. [doi.acm.org/10.1145/1066677.1066712 | Reprint (pdf)]
(Introduction of conventions for using graphs in rule-based modeling of biomolecular interactions.)
8. J. R. Faeder, M. L. Blinov, B. Goldstein and W. S. Hlavacek (2005) Combinatorial complexity and dynamical restriction of network flows in signal transduction. Syst. Biol. 2, 5-15. [Abstract | Reprint (pdf)]
9. J. R. Faeder, M. L. Blinov, B. Goldstein and W. S. Hlavacek (2005) Rule-based modeling of biochemical networks. Complexity 10, 22-41. [Abstract | Reprint (pdf)]
(A detailed description of procedures of rule-based modeling and BioNetGen (version 1.1).)
10. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2005) Graph theory for rule-based modeling of biochemical networks. In Proc. BioCONCUR 2005 (B. Mishra and C. Priami, Editors) 1st paper, pp. 1-19.  Presented at BioCONCUR 2005, San Francisco, CA, August 27, 2005.  Also available as Los Alamos Technical Report LA-UR-05-4534.  [Reprint (pdf)] To be reprinted in an upcoming issue of Transactions on Computational Systems Biology in the series Lect. Notes Comput. Sci.
(Refinement of graphical conventions and a detailed description of graph-based procedures of rule-based modeling. First mention of BioNetGen2 (alpha version).)
11. 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 Abstract | Reprint (pdf)]
(Commentary about on-the-fly and generate-first approaches to modeling. It should be noted that we think Moleculizer is a very cool software tool.)
12. M. L. Blinov, J. 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 complexity. BioSystems 83, 136-151 [PubMed Abstract | doi:10.1016/j.biosystems.2005.06.014]
13. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Depicting signaling cascades. Nat. Biotechnol. 24, 137-138. [PubMed Abstract | Reprint (pdf)]
(Commentary about formal approaches to visualization of proteins and protein interactions (It should be noted that we think process diagrams and related formalisms nicely complement graphical reaction rules). )