Publications

  1. D. Murrugarra, A. Veliz-Cuba, B. Aguilar, S. Arat, R. Laubenbacher "Modeling Stochasticity and Variability in Gene Regulatory Networks" EURASIP Journal on Bioinformatics and Systems Biology, 2012
  2. F. Hinkelmann and R. Laubenbacher, Boolean models of bistable biological systems, Journal of Discrete and Continuous Dynamical Systems - Series S (DCDS-S) 4-6 December 2011 special issue on Biomathematics, DOI: 10.3934/dcdss.2011.4.1443
  3. ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra, F. Hinkelmann, M. Brandon, B. Guang, R. McNeill, G. Blekherman, A. Veliz-Cuba, R. Laubenbacher, BMC Bioinformatics, 2011, DOI: 10.1186/1471-2105-12-295http://dx.doi.org/10.1186/1471-2105-12-295
  4. F. Hinkelmann, D. Murrugarra, A. Jarrah, R. Laubenbacher, A Mathematical Framework for Agent Based Models of Complex Biological Networks, Bulletin of Mathematical Biology, Volume 73, Number 7, 1583-1602, DOI: 10.1007/s11538-010-9582-8
  5. R. Laubenbacher and D. Pengelley, “Voici ce que j’ai trouvé:” Sophie Germain’s grand plan to prove Fermat’s Last Theorem, Historia Mathematica, 2009, in press.
  6. E. Dimitrova, P. Vera-Licona, J. McGee, R. Laubenbacher, Comparison of data discretization methods for inference of biochemical networks, J. Comp. Biol., 2009, in press.
  7. A. Jarrah, R. Laubenbacher, A. Veliz-Cuba, The dynamics of conjunctive and disjunctive Boolean network models, Bull. Math. Biol., 2009, in press. (ArXiv 0805.0275)
  8. R. Robeva and R. Laubenbacher, Mathematical biology education: beyond calculus, Science 325, No. 5940, pp. 542-543, July 31, 2009.
  9. R. Laubenbacher and A. Jarrah, Algebraic models in systems biology, Methods in Enzymology, 467, 163-196, 2009.
  10. R. Laubenbacher, E. Dimitrova, L.D. Garcia, F. Hinkelmann, A. Jarrah, B. Stigler, M. Stillman, P. Vera-Licona, Parameter estimation for Boolean models, J. Theor. Comp. Sci. 2010, DOI: 10.1016/j.tcs.2010.04.034
  11. R. Laubenbacher, V. Hower, A. Jarrah, S. V. Torti, V. Shulaev, P. Mendes, F. M. Torti, and S. Akman, A systems biology view of cancer, Biochim Biophys Acta, 2009, 1796(2):129-39.
  12. R. Laubenbacher, A. S. Jarrah, E. Dimitrova. B. Stigler, and P. Vera-Licona, 15th IFAC Symposium on System Identification, St. Malo, France, July 2009.
  13. V. Hower, P. Mendes, F. M. Torti, R. Laubenbacher, S. Akman, V. Shulaev, and S. V. Torti, A General Map of Iron Metabolism and Tissue-specific Subnetworks, Molecular Biosystems 5 (5) 422-443, 2009.
  14. R. Laubenbacher and B. Sturmfels, Computer algebra in systems biology, The American Mathematical Monthly, 2009, in press.
  15. E. Sontag, A. Veliz-Cuba, R. Laubenbacher, and A. Jarrah. (2008). The effect of negative feedback loops on the dynamics of Boolean networks. Biophysical Journal, 95 (2):518-26.
  16. P. V. Licona and R. Laubenbacher, Inference of ecological interaction networks, Annales Zoologici Fennici, 2008; 45: 459-464.
  17. V. G. Romanovski, A. S. Jarrah, and R. Laubenbacher. The Cyclicity Problem for Two-dimensional Polynomial Systems, Differential Equations and Control Processes 2008; (Electronic journal, ISSN 1817-2172, http://gamma.niimm.spb.su/diffjournal/j/RU/numbers/2008.2/article.74.html)
  18. V. Choi, Y. Huang, V. Lam, D. Potter, R. Laubenbacher, and K. Duca, (2008). Using formal concept analysis for microarray data comparison, Journal of Bioinformatics and Computational Biology 6 (1). PMID: 18324746.
  19. A. Martins, P. Vera-Licona, and R. Laubenbacher. ‘Model your genes the mathematical way’ –a mathematical biology workshop for secondary school teachers, Teaching Mathematics and its Applications 2008; 27: 91-101.
  20. M. Shapiro, K. Duca, E. Delgado-Eckert, V. Hadinoto, Jarrah A., R. Laubenbacher, K. Lee, N. Polys, and D. Thorley-Lawson (2008). A Virtual Look at Epstein-Barr Virus Infection: Simulation Mechanism. Journal of Theoretical Biology. Feb 16 [Epub ahead of print] PMID: 18371986.
  21. D. Camacho, P. Vera-Licona, P. Mendes, and R. Laubenbacher. Comparison of reverse engineering methods using an in silico network. Annals of the New York Academy of Sciences, 2007; 1115:73-89.
  22. A. Jarrah and R. Laubenbacher. Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions, Proc. of the Second Intl.Conf. on Algebraic Biology, 2007; LNCS 4545, pp. 15-22.
  23. A. Jarrah, B. Raposa and R. Laubenbacher. Nested Canalyzing, Unate Cascade, and Polynomial Functions. Physica D: Nonlinear, 2007; Vol. 233 (2), 167-174.
  24. B. Stigler, A. Jarrah, M. Stillman, and R. Laubenbacher R. Reverse-Engineering of Dynamic Networks, Annals of the New York Academy of Sciences. 2007; Vol. 1115, 168-177.
  25. E. Dimitrova, A. Jarrah, B. Stigler, and R. Laubenbacher. A Groebner Fan based Method for Biochemical Network in Proceedings of ISSAC’2007, ACM Press, pp.122-126
  26. K.Duca, M.Shapiro, E.Delgado-Eckert, V. Hadinoto, A. Jarrah, R. Laubenbacher & D.A. Thorley-Lawson. A Virtual Look at Epstein–Barr Virus Infection: Biological Interpretations. PLoS Pathog 2007; 3(10): 1388-400.
  27. F. Castiglione, K.A. Duca , A.S. Jarrah, R. Laubenbacher, D. Hochberg, D.A. Thorley-Lawson, Simulating Epstein-Barr virus infection with C-ImmSim, Bioinformatics 2007; 23 (11): 1371-1377.
  28. A. Jarrah, R. Laubenbacher, B. Stigler, and M. Stillman, Reverse-engineering polynomial dynamical systems, Adv. In Appl. Math. 2007; 39:477–489.
  29. V. Choi, Y. Huang, V. Lam, D. Potter, R. Laubenbacher, and K. Duca, Using formal concept analysis for microarray data comparison, 5th Asia-Pacific Biocomputing Conference, 2006.
  30. O. Colon-Reyes, A. Jarrah, R. Laubenbacher, and B. Sturmfels, Fixed points of monomial dynamical systems over finite fields, Complex Systems 2006 16:333-342.
  31. R. Laubenbacher, B. Pareigis, Update schedules of sequential dynamical systems, Discrete Applied Mathematics 2006; 154:980-994.
  32. L. Garcia, A. S. Jarrah, and R. Laubenbacher, Sequential dynamical systems over words, Applied Math and Comp. 2006; 174:500-510.
  33. E. Babson, H. Barcelo, M. de Longueville, and R. Laubenbacher, Homotopy theory of graphs, J. Alg. Comb. 2006; 24:31-44.
  34. O. Colon-Reyes, R. Laubenbacher, B. Pareigis, Boolean Monomial Dynamical Systems, Annals of Combinatorics 2004; 8: 425-439.
  35. A. Jarrah, H. Vastani, K. Duca, and R. Laubenbacher, An optimal control problem for in vitro virus competition, Proc. Of the 43rd IEEE Conference on Decision and Control, Bahamas, Dec. 2004.
  36. A. Jarrah, R. Laubenbacher, Generic Cohen-Macaulay monomial ideals. Ann. Comb. 2004; 8: 45-61.
  37. R. Laubenbacher and B. Stigler, A computational algebra approach to the reverse-engineering of gene regulatory networks, J. Theor. Biol. 2004; 229:523-537.
  38. N. F. Polys, D. A. Bowman, C. North, R. Laubenbacher, and K. Duca, PathSim Visualizer: an information rich virtual environment framework for systems biology, Proc. SIGGRAPH Web3D Session, Los Angeles, 2004.
  39. A. Jarrah, R. Laubenbacher, and V. Romanovski, The Sibirsky component of the center variety of polynomial differential systems, J. Symbolic Comput. 2003; 35: 577-589.
  40. R. Laubenbacher, A computational algebra approach to reverse-engineering of biological systems, Proceedings of the Intl. Symposium on Symbolic and Algebraic Computation, Assoc. Comp. Mach., 2003.
  41. R. Laubenbacher and B. Pareigis, Decomposition and simulation of sequential dynamical systems, Advances in Applied Math 2003, 30: 655-678.
  42. G. McGrath, R. Laubenbacher, and D. Pengelley, Lagrange and the solution of numerical equations, Historia Mathematica 2001; 28: 220-231.
  43. E. Aguirre, A. Jarrah, R. Laubenbacher, A. Ortiz-Navarro, and R. Torrez, Generic ideals and the Moreno-Socias conjecture, Proceedings of the 2001 International Symposium on Symbolic and Algebraic Computation, ACM, New York, 2001.
  44. R. Laubenbacher and B. Pareigis, Equivalence relations on finite dynamical systems, Advances in Applied Math 2001; 237-251
  45. H. Barcelo, X. Kramer, R. Laubenbacher, and C. Weaver, Foundations of a connectivity theory for simplicial complexes, Advances in Applied Math 2001; 26: 97-128.