William S. Hlavacek

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William S. Hlavacek

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PUBLICATIONS (Chronological Order)

  1. W. S. Hlavacek and M. A. Savageau (1995) Subunit structure of regulator proteins influences the design of gene circuitry: analysis of perfectly coupled and completely uncoupled circuits. J. Mol. Biol. 248, 739-755. [PubMed Abstract]
  2. W. S. Hlavacek and M. A. Savageau (1996) Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol. 255, 121-139. [PubMed Abstract]
  3. W. S. Hlavacek and M. A. Savageau (1996) Comparison of completely uncoupled and perfectly coupled gene expression in repressible biosynthetic systems. In Methodologies for the Conception, Design, and Application of Intelligent Systems: Proceedings of the 4th International Conference on Soft Computing (T. Yamakawa and G. Matsumoto, eds.), vol. 1, pp. 167-179. World Scientific, Singapore. [ISBN:9810228457]
  4. W. S. Hlavacek and M. A. Savageau (1997) Completely uncoupled and perfectly coupled gene expression in repressible systems. J. Mol. Biol. 266, 538-558. [PubMed Abstract]
  5. W. S. Hlavacek and M. A. Savageau (1998) Method for determining natural design principles of biological control circuits. J. Intell. Fuzzy Syst. 6, 147-160. [Abstract]
  6. R. G. Posner, J. Bold, Y. Bernstein, J. Rasor, J. Braslow, W. S. Hlavacek and A. S. Perelson (1998) Measurement of receptor crosslinking at the cell surface via multiparameter flow cytometry. Proc. SPIE 3256, 132-143. [Reprint (pdf)]
  7. W. S. Hlavacek, A. S. Perelson, B. Sulzer, J. Bold, J. Paar, W. Gorman and R. G. Posner (1999) Quantifying aggregation of IgE-FcεRI by multivalent antigen. Biophys. J. 76, 2421-2431. [PubMed Abstract | Full Text]
  8. W. S. Hlavacek, R. G. Posner and A. S. Perelson (1999) Steric effects on multivalent ligand-receptor binding: exclusion of ligand sites by bound cell surface receptors. Biophys. J. 76, 3031-3043. [PubMed Abstract | Full Text]
  9. W. S. Hlavacek, C. Wofsy and A. S. Perelson (1999) Dissociation of HIV-1 from follicular dendritic cells during HAART: mathematical analysis. Proc. Natl. Acad. Sci. USA 96, 14681-14686. [PubMed Abstract | Full Text]
  10. W. S. Hlavacek, N. I. Stilianakis and A. S. Perelson (2000) Influence of follicular dendritic cells on HIV dynamics. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 1051-1058. [PubMed Abstract | doi:10.1098/rstb.2000.0642 | Reprint (pdf)]
  11. W. S. Hlavacek, N. I. Stilianakis, D. W. Notermans, S. A. Danner and A. S. Perelson (2000) Influence of follicular dendritic cells on decay of HIV during antiretroviral therapy. Proc. Natl. Acad. Sci. USA 97, 10966-10971. [PubMed Abstract | Full Text]
  12. W. S. Hlavacek, A. Redondo, H. Metzger, C. Wofsy and B. Goldstein (2001) Kinetic proofreading models for cell signaling predict ways to escape kinetic proofreading. Proc. Natl. Acad. Sci. USA 98, 7295-7300. [PubMed Abstract | Full Text]
  13. W. S. Hlavacek, J. K. Percus, O. E. Percus, A. S. Perelson and C. Wofsy (2002) Retention of antigen on follicular dendritic cells and B lymphocytes through complement-mediated multivalent ligand-receptor interactions: theory and application to HIV treatment. Math. Biosci. 176, 185-202. [PubMed Abstract]
  14. B. Goldstein, J. R. Faeder, W. S. Hlavacek, M. L. Blinov, A. Redondo and C. Wofsy (2002) Modeling the early signaling events mediated by FcεRI. Mol. Immunol. 38, 1213-1219. [PubMed Abstract]
  15. R. G. Posner, P. B. Savage, A. S. Peters, A. Macias, J. DelGado, G. Zwartz, L. A. Sklar and W. S. Hlavacek (2002) A quantitative approach for studying IgE-FcεRI aggregation. Mol. Immunol. 38, 1221-1228. [PubMed Abstract]
  16. W. S. Hlavacek, A. Redondo, C. Wofsy and B. Goldstein (2002) Kinetic proofreading in receptor-mediated transduction of cellular signals: receptor aggregation, partially activated receptors, and cytosolic messengers. Bull. Math. Biol. 64, 887-911. [PubMed Abstract]
  17. 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 model. J. Immunol. 170, 3769-3781. [PubMed Abstract | Full Text]
  18. M. E. Wall, W. S. Hlavacek and M. A. Savageau (2003) Design principles for regulator gene expression in a repressible gene circuit. J. Mol. Biol. 332, 861-876. [PubMed Abstract]
  19. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, A. S. Perelson and B. Goldstein (2003) The complexity of complexes in signal transduction. Biotechnol. Bioeng. 84, 783-794. [PubMed Abstract | Reprint (pdf)]
  20. M. E. Wall, W. S. Hlavacek and M. A. Savageau (2004) Design of gene circuits: lessons from bacteria. Nat Rev. Genet. 5, 34-42 [PubMed Abstract | Reprint (pdf) | Online Table S1 (pdf) | EcoTFs]
  21. B. Goldstein, J. R. Faeder and W. S. Hlavacek (2004) Mathematical and computational models of immune-receptor signalling. Nat. Rev. Immunol. 4, 445-456 [PubMed Abstract | Reprint (pdf)]
  22. R. G. Posner, J. M. Paar, A. Licht, I. Pecht, D. H. Conrad and W. S. Hlavacek (2004) Interaction of monoclonal IgE-specific antibody with cell-surface IgE-FcεRI: characterization of equilibrium binding and secretory response. Biochemistry 43, 11352-11360. [PubMed Abstract | doi:10.1021/bi049686o ]
  23. 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 Abstract | doi:10.1093/bioinformatics/bth378 (open access) | BioNetGen]
  24. 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)]
  25. 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. [PubMed Abstract | Abstract | Reprint (pdf)]
  26. 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)]
  27. M. E. Wall, M. J. Dunlop and W. S. Hlavacek (2005) Multiple functions of a feed-forward-loop gene circuit. J. Mol. Biol. 349, 501-514 [PubMed Abstract | doi:10.1016/j.jmb.2005.04.022]
  28. 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.  Available as Los Alamos Technical Report LA-UR-05-4534.  [Reprint (pdf)] Reprinted in Transactions on Computational Systems Biology vol. VII in the series Lect. Notes Comput. Sci. (see below)
  29. 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)]
  30. 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]
  31. 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)]
  32. W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka and W. Fontana (2006) Rules for modeling signal-transduction systems. Sci. STKE 2006, re6. [PubMed Abstract | doi:10.1126/stke.3442006re6]
  33. J. Yang, W. J. Bruno, W. S. Hlavacek and J. E. Pearson (2006) On imposing detailed balance in complex reaction mechanisms. Biophys. J. 91,1136-1141. [PubMed Abstract | doi:10.1529/biophysj.105.071852]
  34. M. L. Blinov, J. Yang, J. R. Faeder and W. S. Hlavacek (2006) Graph theory for rule-based modeling of biochemical networks. Lect. Notes Comput. Sci. 4230, 89-106. [doi:10.1007/11905455_5]
  35. F. Mu, P. J. Unkefer, C. J. Unkefer and W. S. Hlavacek (2006) Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites. Bioinformatics 22, 3082-3088 [PubMed Abstract | doi:10.1093/bioinformatics/btl535]
  36. R. Rubenstein, P. C. Gray, T. J. Cleland, M. S. Piltch, W. S. Hlavacek, R. M. Roberts, J. Ambrosiano and J.-I. Kim (2007) Dynamics of the nucleated polymerization model of prion replication. Biophys. Chem. 125, 360-367 [PubMed Abstract | doi:10.1016/j.bpc.2006.09.011]
  37. I. Nemenman, G. S. Escola, W. S. Hlavacek, P. J. Unkefer, C. J. Unkefer and M. E. Wall (2007) Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann. N. Y. Acad. Sci. 1115, 102-115 [PubMed Abstract]
  38. F. Mu, R. F. Williams, C. J. Unkefer, P. J. Unkefer, J. R. Faeder and W. S. Hlavacek (2007) Carbon fate maps for metabolic reactions. Bioinformatics 23, 3193-3199 [doi:10.1093/bioinformatics/btm498 | PubMed Abstract]
  39. J. S. Edwards, J. R. Faeder, W. S. Hlavacek, Y. Jiang, I. Nemenman and M. E. Wall (2007) q-bio 2007: a watershed moment in modern biology. Mol. Syst. Biol. 3, 148. [doi:10.1038/msb4100193]
  40. B. Goldstein, D. Coombs, J. R. Faeder and W. S. Hlavacek (2008) Kinetic proofreading model. In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease (A.B. Sigalov, Editor), Ch. 8. Landes Bioscience, Austin, TX.
  41. J. R. Faeder, M. L. Blinov and W. S. Hlavacek (in press) Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol.
  42. T. Lipniacki, B. Hat, J. R. Faeder and W. S. Hlavacek (in press) Stochastic effects and bistability in T cell receptor signaling.
    43. J. Theor. Biol. [doi:10.1016/j.jtbi.2008.05.001]
  43. D. W. Dreisigmeyer, J. Stajic, I. Nemenman, W. S. Hlavacek and M. E. Wall (in press) Determinants of bistability in induction of the Escherichia coli lac operon. IET Syst. Biol. [arXiv:0802.1223]
  44. I. Nemenman, W. S. Hlavacek, J. S. Edwards, J. R. Faeder, Y. Jiang and M. E. Wall (in press) Editorial: special issue dedicated to the First q-bio Conference on Cellular Information Processing. IET Syst. Biol.
  45. J. Yang, M. I. Monine, J. R. Faeder and W. S. Hlavacek (submitted) Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys. Rev. E [arXiv:0712.3773]