1. Atchuta Srinivas Duddu,Elizabeth Andreas,Harshavardhan BV,Kaushal Grover, Vivek Raj Singh, Kishore Hari,Siddharth Jhunjhunwala,Breschine Cummins, Tomas Gedeon, Mohit Kumar Jolly,Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation, npj Systems Biology and Applications, (2024) 10:123.

  2. Tomas Gedeon, Network topology and interaction logic determine states it supports, npj Systems Biology and Applications, (2024) 10:98
  3. William Duncan, Bree Cummins, Tomas Gedeon, Subnetwork inclusion and switching of multilevel Boolean networks preserve parameter graph structure and dynamics, Front. Appl. Math. Stat.,
    Sec. Mathematical Biology, Vol. 10  (2024). 
  4. Tomas Gedeon, Lattice structures that parameterize regulatory network dynamics, Mathematical Biosciences 374 (2024) 109225
  5. Rodolfo Soca, Tomas Gedeon, Attarian Hrayr, The fundamental role of sleep is the reduction of thermodynamic entropy of the central nervous system, Medical Hypotheses, online 4 April 2024, 111336.
  6. Elizabeth Andreas, Breshine Cummins, Tomas Gedeon, Quantifying robustness of the gap gene network, J. Theor. Biol. 580 (2024), 111720.
  7. Firas Khasawneh,Max Chumley, Andreas Otto, Tomas Gedeon, A nonlinear delay model for metabolic oscillations in yeast cells, Bull. Math. Biol. (2023) 85:122.
  8. Jacob Shea, Lisa Davis, Bright Quaye, Tomas Gedeon, Ribosome abundance control in procaryots, Bull. Math. Biol. (2023) 85:119.
    1.  
  9. Kishore Hari, William Duncan, Mohammed Adil Ibrahim, Mohit Kumar Jolly, Breschine Cummins and Tomas Gedeon, Assessing biological network dynamics: comparing numerical simulations with analytical decomposition of parameter space, npj Systems Biology and Applications (2023) 9:29
  10. Valentina Baldazzi,  Delphine Ropers, Jean-Luc Gouze, Tomas Gedeon, Hidde de Jong, Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains, eLIFE 79815 (2023)
  11. Tomas Gedeon and Bree Cummins, Oscillator death in coupled biochemical oscillators, 
    Mathematics of Control, Signals, and Systems, online April 21, 2023,
  12. Breschine Cummins et. al. Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop,  Synthetic Biology, Volume 8, Issue 1, (2023)
  13. Robin Belton, Bree Cummins,Tomas Gedeon, and Brittany Terese Fasy,  Extremal event graphs: A (stable) tool for analyzing noisy time series data, Foundations of Data Science 5(1): 81-151 (2023) 
  14. Bree Cummins, Marcio Gameiro, Tomas Gedeon, Shane Kepley, Konstantin Mischaikow, Lun Zhang,  Extending combinatorial regulatory network modeling to include activity control and decay modulation, SIADS  21(3) (2022), doi: 10.1137/21M1456832(2022)
  15. T. Gedeon, A. R. Humphries, M. C. Mackey, H-O Walther, Z. Wang, Operon Dynamics with State Dependent Transcription and/or Translation Delays, Journal of Mathematical Biology, 84(2)  (2022).
  16. Burcu Ozay, Shannon Murphy, Esther E.  Stopps,Tomas Gedeon,  and Stephanie E. McCalla, Positive Feedback Drives A Secondary Nonlinear Product Burst During a Biphasic DNA Amplification Reaction,  Analyst, 147, 4450-4461 (2022).
  17. Breschine Cummins,  Francis C. Motta, Robert C. Moseley, Anastasia Deckard, Sophia Campione, Tomas Gedeon, Konstantin Mischaikow, Steven B. Haase, Experimental Guidance for Discovering Genetic Networks through Iterative Hypothesis Reduction on Time Series,  PLoS Comput Biol, 18(10): e1010145 (2022).
  18. Ross Carlson, Ashley Beck, Alissa Bleem, Jeffrey Heys, Tomas Gedeon, Hans Bernstein, Diana Schepens, William Harcombe, Kathryn Pintar, Ashley Schrammeck, Timothy Johnson, and Martina Du, Environment constrains fitness advantages of division of labor in microbial consortia engineered for metabolite push or pull interactions, mSystems 7(4), e00051-22, (2022)
  19.  Peter Crawford-Kahrl, Robert R. Nerem, Bree Cummins and Tomas Gedeon, Genetic networks encode the secrets of their past, J. Theor. Biol. vol. 541, 111092, May 2022.
  20. Peter Crawford-Kahrl, Bree Cummins and Tomas Gedeon, Joint realizability of Monotone Boolean functions, Journal or Theoretical Computer Science, Volume 922, 24 June 2022, pp. 447-474.
  21.  Erika Fox, Bree Cummins, Will Duncan and Tomas Gedeon, Modeling transport regulation in gene regulatory networks, Bulletin of Mathematical Biology (2022), pp. 84:89
  22.  W. Duncan,T.  Gedeon, H. Kokubu, H. Oka and K. Mischaikow, Equilibria and their stability in networks with steep sigmoidal nonlinearities, SIAM J. Appl. Dyn. Syst. 20-4, , pp. 2108-2141(2021)
  23. Sarah P. Hammarlund, T. Gedeon, R. Carlson, W. Harcombe, Limitation by a shared mutualist promotes coexistence of multiple competing partners, Nature Communications 12, 619 (2021).
  24. L. Davis, T. Gedeon, J. Thorenson and K. Weber, Tradeoffs between transcription elongation rate, number, and duration of ubiquitous pauses on rrn operon, Journal of Bioinformatics and Computational Biology 19(5), 2150020 (2021) .
  25. W. Duncan and T. Gedeon,Stability and bifurcations of equilibria in networks with piecewise linear interactions, International Journal of Bifurcation and Chaos (IJBC), 31(11),  Article No. 2130032 (2021).
  26. M. Gameiro, T. Gedeon, S. Kepley and K. Mischaikow,  Rational design of complex phenotype via network models, PLoS Comput Biol 17(7): e1009189 (2021).
  27. Lauren M.Smith, F. Motta, G. Chopra, J. Moch, R. R. Nerem, B. Cummins, K. Roche, Ch. Kelliher, A. Leman, J. Harer, T. Gedeon, N.Waters, S. Haase, An Intrinsic Oscillator Drives the Blood Stage Cycle of the Malaria Parasite, Plasmodium falciparum, Science 368, 754759, 15 May, (2020) .
  28. T. Gedeon, Multi-parameter exploration of dynamics of regulatory networks, BioSystems, vol. 190, April 2020, 1045113.
  29. E. Berry, B. Cummins, R. E. Nerem, L. Smith, S. Haase and T. Gedeon, Using extremal events to characterize noisy time series, Journal of Mathematical Biology vol. 80, p. 1523- 1557 (2020)
  30. N. Ciesielski, S. McCalla, T. Gedeon, Analysis of dynamics of a biphasic isothermal DNA amplification reaction, SIAM J. Appl. Math. , 80(5), 20712097 (2020).
  31. Ying Xin, B. Cummins and T. Gedeon, Multistability in the epitehlial-mesenchymal transition network, BMC Bioinformatics 21, article 71 (2020).
  32. D. Schepens, R.P. Carlson, J. Heys, A. E. Beck and T. Gedeon, Role of resource allocation in emergence of cross-feeding in microbial consortia (PDF), Journal of Theoretical Biology, vol. 467, april 21 2019, p.150-163.
  33. Zane Huttinga, Bree Cummins, and Tomas Gedeon, Combinatorial dynamics for regulatory networks, in Molecular Logic and Computational Synthetic Biology, Madalena Chaves and Manuel A. Martins (Eds.), Theoretical Computer Science and General Issues, vol. 11415 (2019).
  34. Peter Crawford-Kahrl, Bree Cummins, Tomas Gedeon, Comparison of Combinatorial Signatures of Global Network Dynamics Generated by Two Classes of ODE Models, SIAM J. Appl. Dyn. Syst. 18-1 (2019), pp. 418-457
  35. T. Heberling L. Davis and T. Gedeon, Mean escape time for a tilted periodic potential, Commun. Comput. Phys., 25 (2019), pp. 1-40.
  36. N. Ciesielski, B. Ozay, S. McCalla and T. Gedeon, A mathematical model for a biphasic DNA amplification reaction, Interface Royal Society, Volume 16, Issue 154 (2019).
  37. Z. Huttinga, B. Cummins, T. Gedeon and K. Mischaikow, Global dynamics for switching systems and their extensions by linear differential equations (PDF), Physica D 367, p. 19-37, March (2018)
  38. Z. Huttinga, B. Cummins and T. Gedeon, Linear Extensions of a Partial Order Subject to Algebraic Constraints (PDF), SIURO (SIAM Undergraduate Research Online) vol. 11, (2018).
  39. R. Carlson, A. Beck, J. Heys, T. Gedeon, M. Henson, L. Hanley, W. Harcombe, and M. Fields, Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross feeding consortia, Biochemical Society Transactions Feb 22, 2018, BST20170242; (2018)
  40. T. Gedeon, B. Cummins, S. Harker, K. Mischaikow, Identifying Robust Hysteresis in Networks (PDF), PLoS Comput. Biology 14(4): e1006121, (2018)
  41. B. Cummins,T. Gedeon, S. Harker, K. Mischaikow, DSGRN: Examining the Dynamics of Families of Logical Models (PDF), Front. Physiol.,9: 549, (2018) | https://doi.org/10.3389/fphys.2018.00549 (PDF)
  42. B.Cummins, T.Gedeon, S. Harker and K. Mischaikow, Model rejection and parameter reduction via time series, SIAM Journal on Applied Dynamical Systems Vol. 17, No. 2, pp. 1589-1616, (2018).
  43. T. Gedeon, S. Harker, H. Kokubu, K. Mischaikow, H. Oka, Global Dynamics for Steep Sigmoidal Nonlinearities in Two Dimensions (PDF), Physica D, Vol. 339, pp. 18-38 (15 January 2017)
  44. Venters M, Carlson RP, Gedeon T, Heys JJ (2017) Effects of Spatial Localization on Microbial Consortia Growth (PDF). PLoS ONE 12(1): e0168592. doi:10.1371/journal.pone.0168592.
  45. Schepens, D., Beck, A.E., Heys, J.J., Gedeon, T., Carlson, R.P., The Benefits of Resource Partitioning and Division of Labor in Microbial Consortia, Advances in Systems and Synthetic Biology. (editors P. Amar, F. Kepes, V. Norris) EDP Sciences Publishing. pp. 137-148. ISBN 978-2-7598-2116-7, (2017)
  46. Ryan S. Waters, Justin S. A. Perry, SunPil Han, Bibiana Bielekova and Tomas Gedeon, The Effects of Interleukin-2 on Immune Response Regulation (PDF), Mathematical Medicine and Biology (2017) 35(1), 79-119.
  47. B. Cummins, T. Gedeon, S. Harker and K, Mischaikow, Database of Dynamic Signatures Generated by Regulatory Networks (DSGRN) (PDF), in Computational Methods in Systems Biology 2017, editors"Jerome Feret and Heinz Koeppl, Springer (2017), chapter 19, pp. 300-308
  48. T. Gedeon, M. Pernarowski and A. Wilander, Autoinducer feedback in synthetic quorum sensing models (PDF), Bull Math Biol (2016) 78(6), pp 1291-1317
  49. G. Fan, B. Cummins and T. Gedeon, Convergence properties of post-translationally modied protein-protein switching networks with fast decay rates, Bull. Math. Biol, 78(6), (2016), pp. 1077-1120.
  50. T. Heberling, L. Davis, J. Gedeon, M. Morgan and T. Gedeon, A mechanistic model for cooperative behavior of co-transcribing RNA polymerases, PLoS Comp. Biol. August 12 (2016)
  51. B. Cummins, T. Gedeon, S. Harker, K. Mischaikow and K. Mok, Combinatorial representation of parameter space for switching networks (PDF), SIAM Journal on Applied Dynamical Systems 2016, Vol. 15, No. 4, pp. 2176-2212.
  52. B. Cummins, T. Gedeon, and K. Spendlove, On the efficacy of state space reconstruction methods in determining causality (PDF), SIAM J. Appl. Dyn. Syst, 14(1), 335-381, (2015).
  53. P. Kosa, M. Komori, R Waters, T. Wu, I. Cortese, J. Ohayon, K. Fenton, J. Cherup, T. Gedeon and B. Bielekova,Novel composite MRI scale correlates highly with disability in multiple sclerosis patients (PDF), Multiple Sclerosis and Related Disorders 4 (2015) 526535.
  54. T. Gedeon and P. Murphy, Dynamics of simple food webs (PDF), Bull. Math. Biol. Volume 77, Issue 10 (2015), 1833-1853.
  55. L.Davis, J. Gedeon, T. Gedeon and J. Thorenson, Traffic flow model for bio-polymerization processes (PDF), Journal of Mathematical Biology, Volume 68, Issue 3, February 2014, pp 667-700, published online Feb 2013, doi:0.1007/s00285-013-0651-0.
  56. D. P. Patterson, B. Schwarz, R. Waters, T. Gedeon and T. Douglas, Developing Advanced Biomimetic Nanocatalysts: Encapsulation of Synthetic Metabolons Within the Bacteriophage P22 (PDF), ACS Chem. Biol,volume 9, issue 2, year 2014, pp. 359 - 365.
  57. E. Harvey, J. Heys and T. Gedeon, Quantifying the effects of the division of labour in metabolic pathways (PDF) , J. Theor. Biol. 360 (2014), 222-242.
  58. L. Davis, T. Gedeon and J. Thorenson, Discontinuous Galerkin calculations for a nonlinear PDE model of DNA transcription with short, transient and frequent pausing (PDF), J. Comput. Math. vol.32 (6), 2014, 601-629.
  59. L. Davis, T. Gedeon and J. Thorenson, Parameter Studies for a Nonlinear Continuum Model of Transcription, 21st International Symposium on Mathematical Theory of Networks and Systems July 7-11, 2014. Groningen, The Netherlands. p. 68-75, (2014).
  60. K. Spendlove, J. Berwald and T. Gedeon, Predicting High-Codimension Critical Transitions in Dynamical Systems Using Active Learning (PDF), Mathematical and Computer Modelling of Dynamical Systems, Volume 19 (6), 2013, pp. 557-574.
  61. T. Gedeon, A.E. Parker and A. G. Dimitrov, The mathematical structure of information bottleneck methods (PDF), Entropy 2012 14(3), 456-479; doi:10.3390/e14030456
  62. J. Brown and T. Gedeon, Structure of the afferent terminals in terminal ganglion of a cricket and persistent homology (PDF), PLoS ONE 7(5): e37278. doi:10.1371/journal.pone.0037278, 2012
  63. J. Berwald, T. Gedeon and J. Sheppard, Using machine learning to predict catastrophes in dynamical systems (PDF), J. Computational and Applied Mathematics, 236(9), March 2012, 2235-2245.
  64. P. Bokes and T. Gedeon, Delayed protein synthesis reduces the correlation between mRNA and protein fluctuations (PDF), Biophys. J. 103(3), August 8 2012, pp. 377-385
  65. T. Gedeon, G. Cummins and J. Heys, Effect of model selection on prediction of periodic behavior in gene regulatory networks (PDF), Bull. Math. Biology 74(8), 2012,
  66. J. Heys, P.K. Rajaraman, T. Gedeon and J.P. Miller, A model of filiform hair distribution on the cricket cercus (PDF), PLoS ONE 7(10): e46588, doi:10.1371/journal.pone.0046588 2012
  67. Z. Arai, M. Gameiro, T. Gedeon, H. Kokubu, K. Mischaikow and H. Oka, Graph-based topogical approximation of saddle-node bifurcation in maps (PDF), RIMS Kokyuroku Bessatsu, B 31 (2012), pp.225-241
  68. B. Cummins and T. Gedeon, Assessing the mechanical response of groups of arthropod filiform flow sensors, In Frontiers in Sensing, F. Barth, J. Humprhey and M. Srinavasan (eds.), Springer-Verlag 2012.
  69. A. Wright, T. Gedeon and N. Richter, On the movement of vertex points in the simple GA (PDF), FOGA 2011 (Foundations of genetic Algorithms), 193-208 (2011)
  70. Z. Aldworth, A. Dimitrov, G. Cummins, T. Gedeon and J.P. Miller, Temporal coding in a nervous system (PDF), PLoS Comput. Biol. 7(5) e1002041 (2011)
  71. J. P. Miller, S. Krueger, J. Heys and T. Gedeon, Quantitative characterization of the filiform mechanosensory hair array on the cricket cercus (PDF), PloS ONE 6(11) e27873. doi:10.1371/journal.pone.0027873 (2011).
  72. T. Gedeon, C. Bodelon and A. Kuenzi, Hantavirus transmission in sylvan and peridomestic environment (PDF), Bull. of Mathematical Biology 72:3, pp.541 (2010), DOI 10.1007/s11538-009-9460-4
  73. T. Gedeon, Oscillations in monotone systems with negative feedback (PDF), SIAM Dynamical Systems vol.9, No.1, (2010)
  74. Ch. Hayes and T. Gedeon, Hyperbolicity of the fixed point set for the simple genetic algorithm (PDF), Theoretical Computer Science 411 (2010), pp. 2368-2383.
  75. M. Campanelli and T. Gedeon, Somitogenesis clock-wave initiation requires differential decay and multiple binding sites for clock protein, a (PDF) PLoS Comput. Biol. 6(4) e10000728 (2010)
  76. E. Boczko, T. Gedeon, C. Stowers and T. Young, ODE, RDE and SDE models of cell cycle dynamics and clustering in yeast (PDF) J. Biological Dynamics, Vol.4, No.4, July 2010, 328-345
  77. A. Dimitrov, A. Parker and T. Gedeon, Symmetry breaking in soft clustering decoding of neural codes (PDF), IEEE Transactions on Information Theory,Vol. 56, No. 2, Feb 2010, 901-927.
  78. P. De Leenheer, J. Dockery, T. Gedeon and S. Pilyugin, The chemostat with lateral gene transfer (PDF), Journal of Biological Dynamics, Vol. 4, (6), p.607-620 (2010)
  79. P. De Leenheer, J. Dockery, T. Gedeon and S. Pilyugin, Senescence and antibiotic resistance in an age-structured population model (PDF), J. of Math. Biology, 61(4) 475-499 (2010)
  80. T. Gedeon and G. Hines, Multi-valued characteristics and Morse decompositions (PDF), J. Differential Equations, vol. 247, 4, pp. 1013-1042 (2009)
  81. T. Gedeon, K. Mischaikow, K. Patterson and E. Traldi, When activators repress and repressors activate: a qualitative analysis of Shea-Ackers model (PDF), Bulletin of Mathematical Biology, 70:6 (2008), p. 1660-1683. doi 10.1007/s11538-008-9313-6
  82. T. Gedeon, K. Mischaikow, K. Patterson and E. Traldi, Binding cooperativity in phage lambda is not sufficient to produce an effective switch (PDF), Biophysical J. 94(9), May 2008
  83. J.J. Heys, T. Gedeon, B.C. Knott and Y. Kim, Modeling arthropod hair motion using the penalty immersed boundary method (PDF), Journal of Biomechanics, Vol. 41, Issue 5, Pages 977-984, February 2008.
  84. T. Gedeon,C. Campion, A. Parker and Z. Aldworth, Annealing an information type cost function computes the normalized cut, (PDF) Pattern Recognition 41 (2):592-606, February 2008
  85. B. Cummins, T. Gedeon, I. Klapper and R. Cortez, Interaction between arthropod filiform hairs in a fluid enviroment, (PDF), Journal of Theoretical Biology, Volume 247, Issue 2, 21 July 2007, Pages 266-280
  86. M. Gameiro, T. Gedeon, W. Kallies, H. Kokubu, K. Mischaikow and H. Oka, Topological horseshoes of travelling waves for fast-slow predator-prey system (PDF), Journal of Dynamics and Diff. Eq., Volume 19, Number 3,September, 623-654. (2007) online first 10.1007/s10884-006-9013-6.
  87. T. Gedeon, Ch. Hayes and R. Swanson, Genericity of the fixed point set for the infinite population genetic algorithm (PDF), in Foundations of genetic algorithms, LCNS No. 4436, Springer-Verlag 2007.
  88. E. Boczko, T. Gedeon and K. Mischaikow, Dynamics of a simple regulatory switch (PDF),Journal of Mathematical Biology 55: No. 5-6 (2007), DOI 10.1007/s00285-007-0102-x.
  89. S. Harker, C.R. Vogel and T. Gedeon, A multilinear optimization problem associated with correspondence maximization, (PDF) Journal of Mathematical Imaging and Vision 29:49-62 (2007)
  90. T. Gedeon and E. Sontag, Oscillation in multi-stable monotone system with slowly varying positive feedback (PDF), J.Diff. Eq. Volume 239, Issue 2, 15 August 2007, Pages 273-295
  91. T. Gedeon and D. Arathorn, Convergence in map finding circuits (PDF), Journal of Math. Imaging Vis. 29, p. 235-248, (2007)
  92. K. Patterson,T. Gedeon, K. Mischaikow and Traldi, E., Why does the positive regulation in bacteriophage affect isomerization of the RNAP-DNA complex? (PDF), Proc. Appl. Math. Mech. 2007 7(1):1120101-1120102.T. Gedeon, E. Boczko and K. Mischaikow, Dynamics of transport mediated switch (PDF), Proc. Appl. Math. Mech. 2007 7(1):1120103-1120104.
  93. B. Cummins and T. Gedeon, A refined model of viscous coupling between filiform hairs in the cricket cercal system, Proceedings of IMECE2007, #41075, (2007)
  94. T. Gedeon, J.J. Heys, B.C. Knott and J. Mulder-Rosi, Modeling insect hair motion using the penalty immersed boundary method (PDF), Proceedings of IMECE2007, #41076, (2007)
  95. Gedeon, T., Mischaikow, K., Patterson, K., and Traldi, E., When Activators Repress and Repressors Activate: A Qualitative Analysis of the Shea-Ackers Model, The Eighth International Conference on Systems Biology (ICSB-2007) Proceedings, 2007.
  96. A. Dimitrov and T. Gedeon, Effects of stimulus transformations on estimates of sensory neuron functions (PDF), Journal of Computat. Neurosci. (2006) 20:265-283
  97. T. Gedeon, Hiroshi Kokubu, Kontantin Mischaikow and Hiroe Oka, The Conley index for fast-slow systems II: Multi dimensional slow variable (PDF), J. Differential Equations 225 (2006) 242-307.
  98. T. Gedeon and K. Mischaikow, Singular boundary value problems via the Conley index (PDF), Topological Methods in Nonlinear Analysis vol. 28., No.2 (2006) 263-284.
  99. Structure Theorems and the Dynamics of Nitrogen Catabolite Repression in Yeast (PDF) (For supplemental material click here (PDF)) (with E. Boczko, T. Cooper, K. Mischaikow, D. Murdock, S. Pratap and S Wells) Proceedings of National Academy of Science 2005 102: 5647-5652; published online before print as 10.1073/pnas.0501339102
  100. Z. Aldworth, J.P. Miller, T. Gedeon, G. Cummins and A. Dimitrov, Dejittered spike-conditioned stimulus waveforms yield improved estimates of neuronal feature sensitivity and Spike-Timing Precision of Sensory Interneurons (PDF), The Journal of Neuroscience, June 1, (2005), 25(22):5323-5332; doi:10.1523/JNEUROSCI.0359-05.2005
  101. Finding neural codes using random projections (PDF), (B. Mumey, A. Sarkar, T.G, A. Dimitrov and J. Miller) Neurocomputing 58-60:19-25 (2004)
  102. Bifurcation structure of a class of S_N-invariant constrained optimization problems (PDF), (T.G.and A. Parker) J. Dynamics and Differential Equations, vol. 16, 3, (2004), 629-678.
  103. Phase locking in integrate-and-fire models with refractory periods and modulation (PDF), (T. G. and Matt Holzer), J. Math. Biology, Volume 49, Number 6, 577 - 603, (2004)
  104. Derivation of natural stimulus feature set using a data-diven model (PDF), (A. Dimitrov,T.G, B. Mumey, R. Snider, Z. Aldworth, A. Parker and J. P. Miller), ICCS 2003, P.M.A., Sloot et. al Eds., Springer-Verlag, Berlin, pp. 337-345.
  105. Analysis of neural coding using quantization with an information-based distortion measure (PDF), ( A. Dimitrov, J. Miller,T.G, Z. Aldworth and A. Parker) Network 14, pp. 151-176, (2003)
  106. Attractor reconstruction from interspike intervals is incomplete (PDF) (with Matt Holzer and Mark Pernarowski) Physica D, vol. 178/3-4, 149-172, (2003)
  107. Annealing and the rate distortion problem (PDF) ( Al Parker, T.G and Alex Dimitrov) In S. Thrun, S. Becker and K. Obermayer, editors, Advances in Neural Information Processing Systems 15 (PDF), 969-976, MIT Press, 2003.
  108. Information distortion and neural coding, (PDF) (T.G, Al Parker and Alex Dimitrov), Canadian Applied Math. Q. vol 10, 1, 33-70, (2003).
  109. Attractors in continuous-time switching networks (PDF) Communications on Pure and Applied Analysis (CPAA) vol. 2, No. 2, 187-209, (2003).
  110. Chaotic solutions in slowly varying perturbations of Hamiltonian systems with applications to shallow water sloshing (PDF) (with Hiroshi Kokubu, Konstantin Mischaikow and Hiroe Oka) J. of Dynamics and Diff. Eq., vol. 14, 1, (2002)
  111. Upper-semicontinuity properties of the discretization of scalar differential delay equation: An improvement (PDF) (with G. Hines) Journal of Diff. Equations 179, 369-383 (2002),
  112. Non-uniform quantization of neural spike sequences through an information distortion measure (PDF), Neurocomputing 38-40, 175-181 (2001). (by A. G. Dimitrov, J.P. Miller, Z. Aldworth, and T. Gedeon)
  113. The global dynamics of neural networks with infinite gain (PDF) Physica D, 146, (2000), 200-212.
  114. Continuity of resetting curves for FitzHugh-Nagumo equations on a circles (PDF) (with Leon Glass) Fields Institute Communications, Vol.21, (1999).
  115. Structure and dynamics of artificial neural networks (PDF) Fields Institute Communications, Vol.21, (1999).
  116. Upper-semicontinuity properties of the discretization of scalar differential delay equation (PDF) (with Gwendolen Hines) JDE 151, (1999), 36-78.
  117. Additive neural networks and periodic patterns (PDF) Neural Networks 12 (1999), 617-626. (only old version available here because of copy rights. Write me to get the final version of the paper)
  118. The Conley index for fast-slow systems I: One dimensional slow variable (PDF) (with Kontantin Mischaikow, Hiroshi Kokubu, Hiroe Oka and Jim Reineck) J. Dynam. Diff. Eq. 11 (1999), 427-470.
  119. A Lyapunov function for tridiagonal competitive-cooperative systems (PDF) (with Bernold Fiedler), SIAM J. Math. Anal. 30, No. 3, (1999), 469-478.
  120. A class of convergent neural networks (PDF) (with Bernold Fiedler) Physica D 111 (1998), 288-294.
  121. Cyclic feedback systems (PDF) Memoirs of AMS, vol. 134, No. 637 (1998)
  122. Dynamics of cyclic feedback systems (PDF) (with Konstantin Mischaikow) Resenhas IME-USP, Vol.1, No. 4, 495-515. (1994)
  123. Structure of the global attractor of cyclic feedback systems ( with Konstantin Mischaikow ) J. Dynam. Diff. Eq. 7, 141-190. (1995)
  124. Shadowing property of continuous maps, Proceedings of the AMS, 115, 1(1992) ( with Milan Kuchta)
  125. Stable and non-stable non-chaotic maps of the interval, Math. Slovaca 41, 1991, 4, 379-391.
  126. A counterexample to a Fedorenko statement, Acta Math. Univ. Comenianae,vol. LX, 1(1991), pp. 15-18.
  127. Generic chaos can be large, Acta Math. Univ. Comenianae, LIV-LV-1988
  128. There are no chaotic mappings with residual scrambled sets, Bull. Austral. Math. Soc. 36 (1987),411-416

Under review

    1. Bree Cummins, Marcio Gameiro, Tomas Gedeon, Shane Kepley, Konstantin Mischaikow, Lun Zhang,  Extending combinatorial regulatory network modeling to include activity control and decay modulation,  arXiv:2111.01399 [math.DS]
    2. Valentina Baldazzi, Tomas Gedeon, Delphine Ropers, Jean-Luc Gouze, Hidde de Jong, Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.
    3. Robin Belton, Bree Cummins, Brittany Fasy and Tomas Gedeon, Extremal events graphs; A (stable) tool for analyzing noisy time series
    4. Tomas Gedeon and Bree Cummins, Oscillator death in coupled biochemical oscillators,  Mathematics of Control, Signals, and Systems.
    5. Burcu Ozay, Shannon Murphy, Esther E.  Stopps,Tomas Gedeon,  and Stephanie E. McCalla, A Secondary Nonlinear Product Burst During a Biphasic DNA Amplification Reaction