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 (1997) Completely uncoupled and perfectly coupled gene expression in repressible systems. J. Mol. Biol. 266, 538-558. [PubMed Abstract]
  4. 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] 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]
  5. 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)]
  6. 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]
  7. 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]
  8. 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]
  9. 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)]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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)]
  19. 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)]
  20. 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)]
  21. 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 ]
  22. 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]
  23. 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)]
  24. 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)]
  25. 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)]
  26. 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]
  27. 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)]
  28. 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]
  29. 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)]
  30. 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]
  31. 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]
  32. 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] 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)] Transactions on Computational Systems Biology vol. VII in the series
  33. 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]
  34. 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]
  35. 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]
  36. 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]
  37. 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]
  38. B. Goldstein, D. Coombs, J. R. Faeder and W. S. Hlavacek (2008) Kinetic proofreading model. Adv. Exp. Med. Biol. 640, 82-94. In Multichain Immune Recognition Receptor Signaling: From Spatiotemporal Organization to Human Disease (A.B. Sigalov, Editor), Ch. 8. Landes Bioscience, Austin, TX [PubMed Abstract]
  39. T. Lipniacki, B. Hat, J. R. Faeder and W. S. Hlavacek (2008) Stochastic effects and bistability in T cell receptor signaling. J. Theor. Biol. 254, 110-122 [doi:10.1016/j.jtbi.2008.05.001 | PubMed Abstract]
  40. J. Yang, M. I. Monine, J. R. Faeder and W. S. Hlavacek (2008) Kinetic Monte Carlo method for rule-based modeling of biochemical networks. Phys. Rev. E 78, 031910 [doi: 10.1103/PhysRevE.78.031910 | arXiv:0712.3773 | PubMed Abstract]
  41. I. Nemenman, W. S. Hlavacek, J. S. Edwards, J. R. Faeder, Y. Jiang and M. E. Wall (2008) Editorial: selected papers from the First q-bio Conference on Cellular Information Processing. IET Syst. Biol. 2, 203-205. [PubMed Abstract]
  42. D. W. Dreisigmeyer, J. Stajic, I. Nemenman, W. S. Hlavacek and M. E. Wall (2008) Determinants of bistability in induction of the Escherichia coli lac operon. IET Syst. Biol. 2, 293-303. [arXiv:0802.1223 | PubMed Abstract]
  43. W. S. Hlavacek (2009) How to deal with large models? Mol. Syst. Biol. 5:240. [PubMed Abstract | Full Text]
  44. J. R. Faeder, M. L. Blinov and W. S. Hlavacek (2009) Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. 500, 113-167. In Systems Biology (I.V. Maly, Editor) Humana Press, Totowa, NJ, Ch. 5, pp.113-167. ISBN: 978-1-934115-64-0
  45. J. Colvin, M. I. Monine, J. R. Faeder, W. S. Hlavacek, D. D. Von Hoff and R. G. Posner (2009) Simulation of large-scale rule-based models. Bioinformatics 25, 910-917. [PubMed Abstract | DYNSTOC]
  46. B. Hu, G. M. Fricke, J. R. Faeder, R. G. Posner and W. S. Hlavacek (2009) GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics 25, 1457-1460. [PubMed Abstract | Abstract | GetBonNie]
  47. W. S. Hlavacek and J. R. Faeder (2009) The complexity of cell signaling and the need for a new mechanics. Sci. Signal. 2, pe46 [PubMed Abstract | Abstract]
  48. I. Nemenman, W. S. Hlavacek, Y. Jiang and M. E. Wall (2009) Editorial: selected papers from the Second q-bio Conference on Cellular Information Processing. IET Syst. Biol. 3, 297-299. [PubMed Abstract]
  49. M. I. Monine, R. G. Posner, P. B. Savage, J. R. Faeder and W. S. Hlavacek (2010) Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates. Biophys. J. 98, 48-56 [PubMed Abstract]
  50. F. Mu, A. L. Bauer, J. R. Faeder and W. S. Hlavacek (2010) Using systems biology techniques to determine metabolic fluxes and metabolite pool sizes. In Handbook of Chemoinformatics Algorithms (J.-L. Faulon and A. Bender, Editors) Chapman & Hall/CRC Press, Boca Raton, FL, Ch. 15, pp. 399-422. ISBN: 978-1420082920
  51. J. Colvin, M. I. Monine, R. N. Gutenkunst, W. S. Hlavacek, D. D. Von Hoff and R. G. Posner (2010) RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics 11:404 [Full Text | PubMed Abstract]
  52. I. Nemenman, W. S. Hlavacek, Y. Jiang, M. E. Wall, and A. Zilman (2010) Editorial: selected papers from the Third q-bio Conference on Cellular Information Processing. IET Syst. Biol. 4, 331-333 [PubMed Abstract].
  53. J. Yang, X. Meng and W. S. Hlavacek (2010) Rule-based modeling and simulation of biochemical systems with molecular finite automata. IET Syst. Biol. 4, 453-466. [PubMed Abstract | arXiv:1007.1315]
  54. A. L. Bauer, W. S. Hlavacek, P. J. Unkefer and F. Mu (2010) Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. PLoS Comput. Biol. 6:e1001007. [PubMed Abstract]
  55. N. W. Lemons, B. Hu and W. S. Hlavacek (2011) Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 12:45. [PubMed Abstract]
  56. F. Mu, C. J. Unkefer, P. J. Unkefer and W. S. Hlavacek (2011) Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds. Bioinformatics 27, 1537-1545. [PubMed Abstract]
  57. J. Yang and W. S. Hlavacek (2011) Scaffold-mediated nucleation of protein signaling complexes: elementary principles. Math. Biosci. 232, 164-173. [PubMed Abstract | arXiv:1105.4688]
  58. I. Nemenman, J. R. Faeder, W. S. Hlavacek, Y. Jiang, M. E. Wall and A. Zilman (2011) Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing. Phys. Biol. 8:050301. [Abstract]
  59. J. Yang and W. S. Hlavacek (2011) The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems. Phys. Biol. 8:055009. [Abstract]
  60. 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 and W. S. Hlavacek (2011) Guidelines for visualizing and annotating rule-based models. Mol. BioSyst. 7, 2779-2795. [PubMed Abstract | OmniGraffle stencil package]
  61. W. S. Hlavacek (2011) Two challenges of systems biology. In Handbook of Statistical Systems Biology (M. P. H. Stumpf, D. J. Balding and M. A. Girolami, Editors) Wiley, Chichester, UK, Ch. 1, pp. 3-14. ISBN: 978-0-470-71086-9 (Print) [Online ISBN: 9781119970606]
  62. A. Chaudhary, K. Ganguly, S. Cabantous, G. S. Waldo, S. N. Micheva-Viteva, K. Nag, W. S. Hlavacek and C.-S. Tung (2012) The Brucella TIR-like protein TcpB interacts with the death domain of MyD88. Biochem. Biophys. Res. Commun. 417, 299-304. [PubMed Abstract]
  63. D. Barua, W. S. Hlavacek and T. Lipniacki (2012) A computational model for early events in B cell antigen receptor signaling: analysis of the roles of Lyn and Fyn. J. Immunol. 189, 646-658. [PubMed Abstract]
  64. M. S. Creamer, E. C. Stites, M. Aziz, J. A. Cahill, C. W. Tan, M. E. Berens, D. D. Von Hoff, W. S. Hlavacek and R. G. Posner (2012) Visualization, annotation and simulation of a large rule-based model for ErbB receptor signaling. BMC Syst. Biol. 6:107. [Full Text | PubMed Abstract]
  65. I. Nemenman, S. Gnanakaran, W. S. Hlavacek, Y. Jiang, B. Munsky, M. E. Wall and J. R. Faeder (2012) The Fifth q-bio Conference on Cellular Information Processing. Phys. Biol. 9:050201. [Full Text]
  66. M. Maienschein-Cline, A. R. Dinner, W. S. Hlavacek and F. Mu (2012) Improved predictions of transcription factor binding sites using physicochemical features of DNA. Nucleic Acids Res. 40:e175. [Full Text | PubMed Abstract]
  67. K. R. Martin,* D. Barua,* A. L. Kauffman, L. M. Westrate, R. G. Posner, W. S. Hlavacek and J. P. MacKeigan (2013) Computational model for autophagic vesicle dynamics in single cells. Autophagy 9, 74-92. *These authors contributed equally. [Full Text | PubMed Abstract]
  68. K. Nowak-Lovato, L. B. Alexandrov, A. Banisadr, A. L. Bauer, A. R. Bishop, A. Usheva, F. Mu, E. Hong-Geller, K. Ø. Rasmussen, W. S. Hlavacek and B. S. Alexandrov (2013) Binding of nucleoid-associated protein Fis to DNA is regulated by DNA breathing dynamics. PLOS Comput. Biol. 9:e1002881. [Full Text | PubMed Abstract]
  69. W. S. Hlavacek, C. J. Unkefer, F. Mu and P. J. Unkefer (2013) Method for predicting enzyme-catalyzed reactions. United States Patent 8,401,797.
  70. Y. Liu, D. Barua, P. Liu, B. S. Wilson, J. M. Oliver, W. S. Hlavacek and A. K. Singh (2013) Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLOS ONE 8:e60159. [Full Text | PubMed Abstract]
  71. N. Kozer,* D. Barua,* S. Orchard, E. C. Nice, A. W. Burgess, W. S. Hlavacek and A. H. A. Clayton (2013) Exploring higher-order EGFR oligomerisation and phosphorylation—a combined experimental and theoretical approach. *These authors contributed equally. Mol. BioSyst. 9, 1849-1863. [Full Text | PubMed Abstract]
  72. I. Nemenman, J. R. Faeder, S. Gnanakaran, W. S. Hlavacek, Y. Jiang, B. Munsky and M. E. Wall (2013) Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Phys. Biol.
    73. 10:030301 (4 pages). [Full Text | PubMed Abstract]
  73. L. A. Chylek, E. C. Stites, R. G. Posner and W. S. Hlavacek (2013) Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools, Vol. 1, Ch. 9, pp. 273-300 (A. Prokop and B. Csukás, Editors), Springer, Dordrecht. ISBN: 978-94-007-6802-4 (Print) ISBN: 978-94-007-6803-1 (Online) [Full Text]
  74. D. Barua and W. S. Hlavacek (2013) Modeling the effect of APC truncation on destruction complex function in colorectal cancer cells. PLOS Comput. Biol. 9:e1003217 (18 pages). [Full Text | PubMed Abstract]
  75. L. A. Chylek, L. A. Harris, C.-S. Tung, J. R. Faeder, C. F. Lopez and W. S. Hlavacek (2014) Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip. Rev. Syst. Biol. Med. 6, 13-36 [Full Text | PubMed Abstract]
  76. N. Kozer, D. Barua, C. Henderson, E. C. Nice, A. W. Burgess, W. S. Hlavacek and A. H. A. Clayton (2014) Recruitment of the adaptor protein Grb2 to EGFR tetramers. Biochemistry 53, 2594-2604 [PubMed Abstract | Full Text]
  77. L. M. Westrate,* J. A. Drocco,* K. R. Martin, W. S. Hlavacek and J. P. MacKeigan (2014) Mitochondrial morphological features are associated with fission and fusion events. *These authors contributed equally. PLOS ONE 9:e95265 [PubMed Abstract | Full Text]
  78. L. A. Chylek, D. A. Holowka, B. A. Baird and W. S. Hlavacek (2014) An interaction library for the FcεRI signaling network. Front. Immunol. 5:172 [PubMed Abstract | Abstract]
  79. O. Resnekov, B. Munsky and W. S. Hlavacek (2014) Perspective on the q-bio Summer School and Conference: 2007–2014 and beyond. Quant. Biol. 2, 54-58 [Full Text]
  80. A. Mahajan, D. Barua, P. Cutler, D. S. Lidke, F. A. Espinoza, C. Pehlke, R. Grattan, Y. Kawakami, C.-S. Tung, A. R. M. Bradbury, W. S. Hlavacek and B. S. Wilson (2014) Optimal aggregation of FcεRI with a structurally-defined trivalent ligand overrides negative regulation driven by phosphatases. ACS Chem. Biol. 9, 1508-1519 [PubMed Abstract | Abstract]
  81. I. Nemenman, J. R. Faeder, S. Gnanakaran, W. S. Hlavacek, B. Munsky and M. E. Wall (2014) Special issue dedicated to the Seventh q-bio Conference: meeting report and preface. Phys. Biol. 11:040301 [PubMed Abstract]
  82. L. A. Chylek,* V. Akimov,* J. Dengjel,* K. T. G. Rigbolt, B. Hu, W. S. Hlavacek and B. Blagoev (2014) Phosphorylation site dynamics of early T-cell receptor signaling. PLOS ONE 9: e104240. *These authors contributed equally. [PubMed Abstract | Full Text]
  83. L. A. Chylek, B. S. Wilson and W. S. Hlavacek (2014) Modeling biomolecular site dynamics in immunoreceptor signaling systems. Adv. Exp. Med. Biol. 844, 245-262. [PubMed Abstract] In A Systems Biology Approach to Blood, Ch. 12, pp. 245-262 (S. J. Corey, M. Kimmel and J. N. Leonard, Editors), Springer. ISBN: 978-1-4939-2095-5 (Print) ISBN: 978-1-4939-2095-2 (Online)
  84. P. Szymańska, K. R. Martin, J. P. MacKeigan, W. S. Hlavacek and T. Lipniacki (2015) Computational analysis of an autophagy/translation switch based on mutual inhibition of MTORC1 and ULK1. PLOS ONE 10: e0116550 [PubMed Abstract | Full Text]
  85. E. C. Stites, M. Aziz, M. S. Creamer, D. D. Von Hoff, R. G. Posner and W. S. Hlavacek (2015) Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys. J. 108, 1819-1829 [PubMed Abstract | Full Text]
  86. L. A. Chylek, L. A. Harris, J. R. Faeder and W. S. Hlavacek (2015) Modeling for (physical) biologists: an introduction to the rule-based approach. Phys. Biol. 12:045007 [PubMed Abstract]
  87. C. C. Valley, D. J. Arndt-Jovin, N. Karedla, M. P. Steinkamp, A. I. Chizhik, W. S. Hlavacek, B. S. Wilson, K. A. Lidke and D. S. Lidke (2015) Enhanced dimerization drives ligand-independent activity of mutant EGFR in lung cancer. Mol. Biol. Cell 26: 4087-4099. [PubMed Abstract | Full Text]
  88. W. S. Hlavacek, S. Gnanakaran, B. Munsky, M. E. Wall, J. R. Faeder, Y. Jiang, I. Nemenman and O. Resnekov (2015) The Eighth q-bio Conference: meeting report and special issue preface. Phys. Biol. 12: 060401. [PubMed Abstract]
  89. B. R. Thomas, L. A. Chylek, J. Colvin, S. Sirimulla, A. H. A. Clayton, W. S. Hlavacek and R. G. Posner (2016) BioNetFit: a fitting tool compatible with BioNetGen, NFsim, and distributed computing environments. Bioinformatics 32: 798-800. [PubMed Abstract | BioNetFit Web site]
  90. Kochańczyk M, Kocieniewski P, Kozłowska E, Jaruszewicz-Błonska J, Sparta B, Pargett M, Albeck JG, Hlavacek WS, Lipniacki T (2017) Relaxation oscillations and hierarchy of feedbacks in MAPK signaling. Sci Rep 7: 38244 [Full Text]
  91. Mahajan A, Youssef LA, Cleyrat C, Grattan R, Lucero SR, Mattison CP, Erasmus MF, Jacobson B, Tapia L, Hlavacek WS, Schuyler M, Wilson BS (2017) Allergen valency, dose and FcεRI occupany set thresholds for secretory responses to Pen a 1 and motivate design of hypoallergens. J Immunol 198: 1034-1046 [Full Text]
  92. Suderman R, Hlavacek WS (2017) TRuML: a translator for rule-based modeling languages. In Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB '17, Boston, MA, August 20-23, 2017), pp. 372-377. ACM Press, New York. [Full Text]
  93. Schwartz SL, Cleyrat C, Olah MJ, Relich PK, Phillips GK, Hlavacek WS, Lidke KA, Wilson BS, Lidke DS (2017) Differential mast cell outcomes are sensitive to FcεRI-Syk binding kinetics. Mol Biol Cell 28: 3397-3414. [Full Text]
  94. Kochańczyk M, Hlavacek WS, Lipniacki T (2017) SPATKIN: a simulator for spatial rule-based modeling of biomolecular site dynamics. Bioinformatics 33: 3667-3669. [Full Text]
  95. Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS, Singh AK (2017) Timescale separation of positive and negative signaling creates history-dependent responses to IgE receptor stimulation. Sci Rep 7: 15586. [Full Text]
  96. Ramanathan RK, Weiss GJ, Posner RG, Rajeshkumar NV, Jameson G, Aziz M, Hoering A, Bolejack V, Maitra A, Fulk M, Stites EC, Hlavacek WS, Gatalica Z, Xiu J, Hidalgo M, Von Hoff DD, Barrett MT (2017) A phase 2 trial of personalized cytotoxic therapy based on tumor immunohistochemistry in previously treated metastatic pancreatic cancer patients. J Gastrointest Oncol 8: 925-935. [Full Text]
  97. Lin YT, Chylek LA, Lemons NW, Hlavacek WS (2018) Using equation-free computation to accelerate network-free stochastic simulation of chemical kinetics. J Phys Chem B 122: 6351-6356 [PubMed Abstract | Full Text]
  98. Rukhlenko OS, Khorsand F, Krstic A, Rozanc J, Alexopoulos LG, Rauch N, Erickson KE, Hlavacek WS, Posner RG, Gómez-Coca S, Rosta E, Fitzgibbon C, Matallanas D, Rauch J, Kolch W, Kholodenko BN (2018) Dissecting RAF inhibitor resistance by structure-based modeling reveals ways to overcome oncogenic RAS signaling. Cell Syst
    99. 7: 161-179. [Full Text | PubMed Abstract]
  99. Munsky B, Hlavacek WS, Tsimring LS, Editors (2018) Quantitative Biology: Theory, Computational Methods, and Models. The MIT Press, Cambridge, MA. ISBN: 978-0-262-03808-9
  100. Chylek LA, Holowka DA, Baird BA, and Hlavacek WS (2018) Quantitative modeling of mast cell signaling. In Systems Immunology: An Introduction to Modeling Methods for Scientists (Das J, Jayaprakash C, Editors), CRC Press, Boca Raton, FL, Ch 13, pp 213-226. ISBN-13: 978-1-4987-1740-3
  101. Mitra ED, Dias R, Posner RG, Hlavacek WS (2018) Using both qualitative and quantitative data to improve parameter identification for systems biology models. Nat Commun 9: 3901. [Full Text | PubMed Abstract]
  102. Civciristov S, Ellisdon AM, Suderman R, Pon CK, Evans BA, Kleifeld O, Charlton SJ, Hlavacek WS, Canals M, Halls ML (2018) Pre-assembled GPCR signaling complexes mediate unique cellular responses to ultralow ligand concentrations. Sci Signal 11: eaan1188. [Full Text | PubMed Abstract]
  103. Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS (2019) Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. PLOS Comput Biol 15: e1006706. [Full Text | PubMed Abstract]
  104. Shirin A, Klickstein IS, Feng S, Lin YT, Hlavacek WS, Sorrentino F (2019) Prediction of optimal drug schedules for controlling autophagy. Sci Rep 9: 1428. [Full Text | PubMed Abstract]
  105. Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN (2019) New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling. Semin Cancer Biol 54: 162-173. [PubMed Abstract]
  106. Suderman R, Fricke GM, Hlavacek WS (2019) Using RuleBuilder to graphically define and visualize BioNetGen-language patterns and reaction rules. Methods Mol Biol 1945: 33-42. doi: 10.1007/978-1-4939-9102-0_2 [PubMed Abstract | Preprint]
  107. Hlavacek WS, Csicsery-Ronay JA, Baker LR, Ramos Álamo M del C, Ionkov A, Mitra ED, Suderman R, Erickson KE, Dias R, Colvin J, Thomas BR, Posner RG (2019) A step-by-step guide to using BioNetFit. Methods Mol Biol 1945: 391-419. doi: 10.1007.978-1-4939-9102-0_18 [PubMed Abstract | Preprint]
  108. Hlavacek WS, Editor (2019) Modeling Biomolecular Site Dynamics: Methods and Protocols. Humana Press, New York. ISBN: 978-1-4939-9100-6
  109. Lin YT, Feng S, Hlavacek WS (2019) Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks. J Chem Phys 150: 244101. [PubMed Abstract | Preprint | 10.1063/1.5096774]
  110. Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS (2019) Generalizing Gillespie's direct method to enable network-free simulations. Bull Math Biol 81: 2822-2848. [PubMed Abstract | Preprint]
  111. Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS (2019) PyBioNetFit and the Biological Property Specification Language. iScience 19: 1012-1036. [PubMed Abstract | Full Text | GitHub Page]
  112. Mitra ED, Hlavacek WS (2019) Parameter estimation and uncertainty quantification for systems biology models. Curr Opin Syst Biol 18: 9-18. [Full Text | Free Access Link (until January 16, 2020)]
  113. Salazar-Cavazos E, Franco Nitta C, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS (2020) Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell doi: 10.1091/mbc.E19-09-0548 [PubMed Abstract | Full Text | Preprint]
  114. Mitra ED, Hlavacek WS (2020) Bayesian inference using qualitative observations of underlying continuous variables. Bioinformatics doi: 10.1093/bioinformatics/btaa084 [PubMed Abstract | Full Text | Preprint]
  115. Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Luci D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, SBML Community* (submitted) SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol *91 additional co-authors including W.S.H.