Publications list

Preprints

  • Sadeghimanesh A, Feliu E (2018) The multistationarity structure of networks with intermediates and a binomial core network. Submitted. Available on arXiv.
  • Feliu E*, Helmer M* (2018) Multistationarity for Fewnomial Chemical Reaction Networks Submitted. Available on arXiv.
  • Sáez M, Wiuf C, Feliu E (2018) Nonnegative linear elimination for chemical reaction networks. Submitted. Available on arXiv.
  • Sadeghimanesh A, Feliu E (2018) Groebner bases of reaction networks with intermediate species. Submitted. Available on arXiv.
  • Hansen MC, Wiuf C (2018) Existence of a Unique Quasi-stationary Distribution for Stochastic Reaction Networks. Submitted. Available on arXiv.

2018

  • Ferragut A, Valls C, Wiuf C. (2018) On the Liouville integrability of Edelstein's reaction system in R3. Chaos Soliton Fract 108: 129-135.
  • Wiuf C. (2018) Some properties of the conditioned reconstructed process with Bernoulli sampling. Theor Pop Biol 122: 36-45.
  • Sáez M, Feliu E, Wiuf C (2018) Graphical criteria for positive solutions to linear systems. Linear Algebra and its Applications, 552 pp 166-193.
  • Feliu E, Cappelletti D, Wiuf C (2018) Node Balanced Steady States: Unifying and Generalizing Complex and Detailed Balanced Steady States. Mathematical Biosciences, 301 pp 68-82.
  • Soraggi S, Wiuf C, Albrechtsen, A. (2018) Powerful inference with the D-statistic on low-coverage whole-genome data. G3 8: 551-566.

2017

  • Conradi C*, Feliu E*, Mincheva M*, Wiuf C* (2017) Identifying parameter regions for multistationarity. PLOS Computational Biology, 13(10): e1005751.
  • David F. Anderson, Daniele Cappelletti, Thomas G. Kurtz (2017) Finite time distributions of stochastically modeled chemical systems with absolute concentration robustness. SIAM J. Appl. Dyn. Syst., 16(3), 1309–1339.
  • Mahdia A, Ferragut A, Valls C, Wiuf C. 2017 Conservation laws in biochemical reaction networks. SIAM J Appl Dyn Syst 16(4): 2213-2232.
  • Cappelletti D, Wiuf C. 2017 Uniform approximation of solutions by elimination of intermediate species in deterministic reaction networks. SIAM J Appl Dyn Syst 16(4): 2259-2286.
  • Vincent M, Mundbjerg K, Pedersen JS, Liang G, Jones PA, Orntoft TF, Sorensen KD, Wiuf C. 2017 EpiG: statistical inference and profiling of DNA methylation from whole-genome bisulphite sequencing data. Genome Biol 18: 38.
  • Marcondes de Freitas M, Wiuf C, Feliu E (2017) Intermediates and Generic Convergence to Equilibria. Bulletin of Mathematical Biology. 79:7, pp. 1662-1686. DOI: 10.1007/s11538-017-0303-4.
  • Marcondes de Freitas M, Feliu E, Wiuf C (2017) Intermediates, Catalysts, Persistence, and Boundary Steady States. Journal of Mathematical Biology. 74:4, pp. 887–932. arxiv:1509.06034.
  • Sáez M, Wiuf C, Feliu E (2017) Graphical reduction of reaction networks by linear elimination of species. Journal of Mathematical Biology. 74:1, pp. 195-237. arxiv:1509.03153.

2016

  • Song F, Sáez M, Wiuf C, Feliu E, Soyer OS (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of the Royal Society Interface, 13:121. DOI: 10.1098/rsif.2016.0524.
  • Feliu E (2016) Sobre las soluciones positivas de sistemas de polinomios parametrizados en biología. (in spanish). La Gaceta de la Real Sociedad Matemática Española.
  • Widder S, Allen R, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft J-U, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Grosskopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS. (2016) Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME Journal, advanced online publication.
  • Cappelletti D, Wiuf C (2016) Elimination of intermediate species in multiscale stochastic reaction networks. Ann Appl Probat, advanced online publication..
  • Cappelletti D, Wiuf C (2016) Product-form Poisson-like distributions and complex balanced reaction systems. SIAM J Appl Math, 76:411-432.
  • Müller S*, Feliu E*, Regensburger G*, Conradi C, Shiu A, Dickenstein A (2016) Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry.  Foundations of Computational Mathematics, 16:1, pp 69-97.

2015

  • Kothamanchu VB*, Feliu E*, Cardelli L, Soyer OS (2015) Unlimited multistability and Boolean logic in microbial signaling. Journal of the Royal Society Interface, 12:108.
  • Anderson D, Craciun G, Gopalkrishnan M, Wiuf C (2015) Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks. Bull Math Biol 77: 1744-1769.
  • Feliu E, Wiuf C (2015) Finding the positive feedback loops underlying multi-stationarity. BMC Systems Biology, 9:22.
  • Jovanovic G, Sheng X, Ale A, Feliu E, Harrington HA, Kirk P, Wiuf C, Buck M, Stumpf MPH (2015) Phosphorelay of non-orthodox two component systems functions through a bi-molecular mechanism in vivo: the case of ArcB. Molecular Biosystems. DOI: 10.1039/C4MB00720D.
  • Feliu E (2015) Injectivity, multiple zeros, and multistationarity in reaction networks.  Proceedings of the Royal Society A, 41:2173. DOI: 10.1098/rspa.2014.0530. 

2014

  • Amin M, Kothamachu VB, Feliu E, Scharf BE, Porter SL, Soyer OS (2014) Phosphate sink containing two-component signaling systems as tunable threshold devices. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1003890

2013

  • Kothamachu VB, Feliu E, Wiuf C, Cardelli L, Soyer OS (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLOS Computational Biology, doi:10.1371/journal.pcbi.1003322.
  • Wiuf C, Feliu E (2013) Power-law Kinetics and Determinant Criteria for the Preclusion of Multistationarity in Networks of Interacting Species. SIAM Journal on Applied Dynamical Systems, 12 pp. 1685-1721.
  • Feliu E, Wiuf C (2013) A computational method to preclude multistationarity in networks of interacting species. Bioinformatics, 29 pp. 2327-2334.
  • Feliu E, Wiuf C (2013) Simplifying Biochemical Models With Intermediate Species. Journal of the Royal Society Interface, 10:20130484.
  • Harrington H*, Feliu E*, Wiuf C, Stumpf MPH (2013) Cellular compartments cause multistability in biochemical reaction networks and allow cells to process more information. Biophysical Journal, 104:8 pp 1824-1831.
  • Feliu E, Wiuf C (2013) Variable elimination in post-translational modification reaction networks with mass-action kinetics. Journal of Mathematical Biology, 66:1 pp 281-310.

2012

  • Feliu E, Wiuf C (2012) Preclusion of switch behavior in reaction networks with mass-action kinetics. Applied Mathematics and Computation. 219:4, pp 1449-67.
  • Feliu E, Wiuf C (2012) Variable elimination in chemical reaction networks with mass action kinetics. SIAM Journal on Applied Mathematics. 72:4 pp 959–981.
  • Feliu E, Wiuf C (2012) Enzyme sharing as a cause of multistationarity in signaling systems. Journal of the Royal Society Interface, 9:71 pp 1224-32.
  • Knudsen M, Feliu E, Wiuf C (2012) Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using Mathematical Models. Journal of Theoretical Biology, 300 pp 7-18.
  • Feliu E, Knudsen M, Wiuf C (2012) Signaling cascades: consequences of varying substrate and phosphatase levels. Advances in Systems Biology in Advances in Experimental Medical Biology series. Vol 736, Part 1, pp 81-94. Eds. II Goryanin, AB Goryachev. Springer.
  • Feliu E, Knudsen M, Andersen LN, Wiuf C (2012) An Algebraic Approach to Signaling Cascades with n Layers. Bulletin of Mathematical Biology, 74:1, pp 45-72.