@article(alfieri2011modeling, author = "R. Alfieri and E. Bartocci and E. Merelli and L. Milanesi", year = "2011", title = "Modeling the cell cycle: From deterministic models to hybrid systems", journal = "Biosystems", volume = "105", pages = "34--40", doi = "10.1016/j.biosystems.2011.03.002", ) @article(baldazzi2011qualitative, author = "V. Baldazzi and P. T. Monteiro and M. Page and D. Ropers and J. Geiselmann and H. Jong", year = "2011", title = "Qualitative Analysis of Genetic Regulatory Networks in Bacteria", journal = "Understanding the Dynamics of Biological Systems", pages = "111--130", doi = "10.1007/978-1-4419-7964-3-6", ) @article(batt2008symbolic, author = "G. Batt and H. De Jong and M. Page and J. Geiselmann", year = "2008", title = "Symbolic reachability analysis of genetic regulatory networks using discrete abstractions", journal = "Automatica", volume = "44", number = "4", pages = "982--989", doi = "10.1016/j.automatica.2007.08.004", ) @article(reinitzparallel, author = "K.W. Chu and Y. Deng and J. Reinitz", year = "1999", title = "Parallel Simulated Annealing by Mixing of States 1", journal = "Journal of Computational Physics", volume = "148", number = "2", pages = "646--662", doi = "10.1006/jcph.1998.6134", ) @article(csisz2006analysis, author = "A. Csik{\'a}sz-Nagy and D. Battogtokh and K. C. Chen and B. Nov{\'a}k and J. J. Tyson", year = "2006", title = "Analysis of a generic model of eukaryotic cell-cycle regulation", journal = "Biophysical Journal", volume = "90", number = "12", pages = "4361--4379", doi = "10.1529/biophysj.106.081240", ) @article(dantzig1955generalized, author = "G. B. Dantzig and A. Orden and P. Wolfe", year = "1955", title = "The generalized simplex method for minimizing a linear form under linear inequality restraints", journal = "Pacific Journal of Mathematics", volume = "5", number = "2", pages = "183--195", doi = "10.2140/pjm.1955.5.183", ) @book(di2008piecewise, author = "M. Di Bernardo", year = "2008", title = "{Piecewise-smooth dynamical systems: theory and applications}", publisher = "Springer Verlag", doi = "10.1007/978-1-84628-708-4", ) @article(drulhe2008switching, author = "S. Drulhe and G. Ferrari-Trecate and H. de Jong", year = "2008", title = "The switching threshold reconstruction problem for piecewise-affine models of genetic regulatory networks", journal = "IEEE Transactions on Automatic Control", volume = "53", pages = "153--165", doi = "10.1109/TAC.2007.911326", ) @incollection(gorban-dynamic, author = "A. N. Gorban and O. Radulescu", year = "2008", title = "{Dynamic and static limitation in reaction networks, revisited }", editor = "David West Guy B. Marin and Gregory S. Yablonsky", booktitle = "Advances in Chemical Engineering - Mathematics in Chemical Kinetics and Engineering", series = "Advances in Chemical Engineering", volume = "34", publisher = "Elsevier", pages = "103--173", doi = "10.1016/S0065-2377(08)00003-3", ) @incollection(grosu2007learning, author = "Radu Grosu and S Mitra and Pei Ye and Emilia Entcheva and IV Ramakrishnan and Scott A Smolka", year = "2007", title = "Learning cycle-linear hybrid automata for excitable cells", booktitle = "Hybrid Systems: Computation and Control", publisher = "Springer", pages = "245--258", doi = "10.1007/978-3-540-71493-4\_21", ) @article(lam1988efficient, author = "Jimmy Lam and Jean-Marc Delosme", year = "1988", title = "An efficient simulated annealing schedule: derivation", journal = "Yale University, New Haven, Connecticut, Technical Report", volume = "8816", doi = "10.1.1.74.4461", ) @article(lincoln2004symbolic, author = "P. Lincoln and A. Tiwari", year = "2004", title = "Symbolic systems biology: Hybrid modeling and analysis of biological networks", journal = "Hybrid Systems: Computation and Control", pages = "147--165", doi = "10.1007/978-3-540-24743-2-44", ) @article(mishra2009intelligently, author = "B. Mishra", year = "2009", title = "Intelligently deciphering unintelligible designs: algorithmic algebraic model checking in systems biology", journal = "Journal of The Royal Society Interface", volume = "6", number = "36", pages = "575--597", doi = "10.1098/rsif.2008.0546", ) @article(noel2013, author = "V. Noel and D. Grigoriev and S. Vakulenko and O. Radulescu", title = "Tropicalization and tropical equilibrations of chemical reactions", journal = "Contemporary Mathematics, in press; arXiv : 1303.3963", ) @article(SASB2011, author = "V. Noel and D. Grigoriev and S. Vakulenko and O. Radulescu", year = "2012", title = "{Tropical geometries and dynamics of biochemical networks. Application to hybrid cell cycle models}", journal = "Electronic Notes in Theoretical Computer Science", volume = "284", pages = "75--91", doi = "10.1016/j.entcs.2012.05.016", ) @inproceedings(noel2010, author = "V. Noel and S. Vakulenko and O. Radulescu", year = "2010", title = "Piecewise smooth hybrid systems as models for networks in molecular biology", booktitle = "Proceedings of JOBIM 2010", publisher = "Jobim, Montpellier", ) @article(noel2011, author = "V. Noel and S. Vakulenko and O. Radulescu", year = "2011", title = "Algorithm for identification of piecewise smooth hybrid systems: application to eukaryotic cell cycle regulation", journal = "Lecture Notes in Computer Science", volume = "6833", pages = "225--236", doi = "10.1007/978-3-642-23038-7-20", ) @article(noel2012hybrid, author = "Vincent Noel and Dima Grigoriev and Sergei Vakulenko and Ovidiu Radulescu", year = "2012", title = "Hybrid models of the cell cycle molecular machinery", journal = "Electronic Proceedings in Theoretical Computer Science", volume = "92", pages = "88--105", doi = "10.4204/EPTCS.92.7", ) @article(porreca2008structural, author = "R. Porreca and S. Drulhe and H. Jong and G. Ferrari-Trecate", year = "2008", title = "Structural identification of piecewise-linear models of genetic regulatory networks", journal = "Journal of Computational Biology", volume = "15", number = "10", pages = "1365--1380", doi = "10.1089/cmb.2008.0109", ) @article(radulescu2008robust, author = "O. Radulescu and A. N. Gorban and A. Zinovyev and A. Lilienbaum", year = "2008", title = "Robust simplifications of multiscale biochemical networks", journal = "BMC systems biology", volume = "2", number = "1", pages = "86", doi = "10.1186/1752-0509-2-86", ) @article(ropers2011model, author = "D. Ropers and V. Baldazzi and H. de Jong", year = "2011", title = "{Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli}", journal = "IEEE/ACM Transactions on Computational Biology and Bioinformatics", volume = "8", number = "1", pages = "166--181", doi = "10.1109/TCBB.2009.49", ) @article(savageau1987recasting, author = "Alexander Orden Savageau, M. A. anGeorge Bernard Dantzig and E. O. Philip Wolfed Voit", year = "1987", title = "Recasting nonlinear differential equations as S-systems: a canonical nonlinear form", journal = "Mathematical biosciences", volume = "87", number = "1", pages = "83--115", doi = "10.1016/0025-5564(87)90035-6", ) @article(singhania2011hybrid, author = "R. Singhania and R. M. Sramkoski and J. W. Jacobberger and J. J. Tyson", year = "2011", title = "A hybrid model of mammalian cell cycle regulation", journal = "PLoS computational biology", volume = "7", number = "2", pages = "e1001077", doi = "10.1371/journal.pcbi.1001077", ) @article(ye2008modelling, author = "P. Ye and E. Entcheva and SA Smolka and R. Grosu", year = "2008", title = "Modelling excitable cells using cycle-linear hybrid automata", journal = "Systems Biology, IET", volume = "2", number = "1", pages = "24--32", doi = "10.1049/iet-syb:20070001", )