Articles in refereed journals
Published or accepted:
1. Ferreira A, Constantinescu VS, Sagathelyan A*, Hardy SV*, (2024) Distinct forms of structural plasticity of adult-born interneuron spines in the mouse olfactory bulb induced by different odor learning paradigms, Communications Biology, 7(1), 420.
2. Ferreira A, Bressan C, Hardy SV*, Sagathelyan A*, (2022) Deciphering heterogeneous populations of migrating cells based on the computational assessment of their dynamic properties, Stem Cell Reports, 17(4), 911-923.
3. Lavoie M, Saint-Béat B, Strauss J, Guérin S, Allard A, Hardy SV, Falciatore A, Lavaud J, (2020) Genome-Scale Metabolic Reconstruction and in Silico Perturbation Analysis of the Polar Diatom Fragilariopsis cylindrus Predicts High Metabolic Robustness, Biology, 9(30).
4. Pagé Fortin M, Hardy SV, (2018) A Hybrid Model of the Akt-Wnt-mTOR-p70S6K Signalling Network in Neurons, Fundamenta Informaticae, 160(1-2), 1-25
5. Richard A, Desrosiers P, Hardy SV, Doyon N. (2016) Counting Hidden Neural Networks, Journal of Integer Sequences, 19(4), 16.4.7.
6. Azeloglu EU*, Hardy SV*, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R. (2014) Interconnected network motifs control podocyte morphology and kidney function, Science Signaling, 7(311), ra12. pubmed *shared first authorship
7. Hardy, S. & Robillard, P. N. (2008) Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways, Bioinformatics, 24(2), 209-217.
8. Hardy, S. & Robillard, P. N. (2005) Phenomenological and molecular level Petri net modelling and simulation of long-term potentiation, Biosystems, 82:1, 26-38.
Articles in refereed conference proceedings
1. Hardy SV, Pagé Fortin M, Analysis of the Signal Transduction Dynamics Regulating mTOR with Mathematical Modeling, Petri Nets and Dynamic Graphs, BioPPN @ Petri nets 2016. p. 347-361
2. Becutti M., Blätke MA, Falk M, Hardy S.V., Heiner M, Maus C, Nähring C et Rohr C, Dictyostelium discoideum: Aggregation and Synchronisation of Amoebas in Time and Space, Dagstuhl Reports, 4:11, p. 195-213
3. Hardy, S. & Robillard, P. N. (2008) A Petri net framework for the modeling, simulation and data analysis of biological models, 1st North American Simulation Technology Conference. Montréal, Canada. p. 57-63
4. Hardy, S. & Robillard, P. N. (2008) Spectral representation of system dynamics and molecular activity – An engineering perspective of biological models, 4th WSEAS International Conference on Mathematical Biology and Ecology. Acapulco, Mexico. p. 103-107
5.Hardy, S. & Robillard, P. N. (2007) Visualization of the simulation data of biochemical network models: a painted Petri net approach, Summer Computer Simulation Conference. San Diego, USA. p. 802-808
6.Hardy, S. & Robillard, P. N. (2006) Painted Petri Net and Functional Abstraction to Visualize Dynamic Modeling, European Simulation and Modelling Conference. Toulouse, France. p. 340-345
Refereed book chapters:
1.Hardy, S. & Iyengar, R. (2010) Analysis of dynamical models of signaling networks with Petri nets, in Modeling in Systems Biology – The Petri net approach. Ed. Ina Koch, Wolfgang Reisig and Falk Schreiber. Springer-Verlag, p. 225-251.
Refereed abstracts:
1.Hardy S.V et Iyengar R. (2011) Analysis of the regulatory motif dynamic of signaling networks using Petri net-based dynamic graphs, Dagstuhl Reports, 1:4, p. 51.
2.Blätke M.A, Gao Q., Gilber D., Hardy S.V., Heiner M., Kierzek A., Liu F. et Marwan W. (2011) Dictypat project, Dagstuhl Reports, 1:4, p. 61. Special mention for most original contribution
3.Hardy, S.V., Tzavaras, N., Mariottini, C., Wist, A., Seco, J., Blitzer, R.D. & Iyengar, R. (2011) Analysis of the regulatory motifs dynamics identifies new local protein synthesis controls in the long-term potentiation of hippocampal neurons, Computational Cell Biology meeting. Cold Spring Harbor, USA.
19.Barbieri, V., Hardy, S.V., Vaqué J.P., Gutkind J.S & Iyengar, R. (2011) Spatial and temporal relationships between regulatory motifs and the activity of transcription factors in the Gq protein signalling network, Computational Cell Biology meeting. Cold Spring Harbor, USA.
4.Hardy, S. & Iyengar, R. (2009) Analysis of Motif Dynamics within Signaling Networks using Graph Representation of Dynamical Systems, Computational Cell Biology meeting. Cold Spring Harbor, USA.
5.Hardy, S. & Robillard, P. N. (2006) Visualization of biological systems regulatory dynamics. Cold Spring Harbor, USA.
Conference presentations
1.Hardy S.V., Neves, S. & Iyengar, R. (2010) Coupling biochemistry and electrophysiology modeling with MOOSE. Reaction-diffusion workshop, Computational Neuroscience Meeting, 2010 San Antonio, USA.
2.Hardy S. & Iyengar R. (2009) Analysis of signal propagation and crosstalk within signaling networks using animated graph representations of dynamical systems. Dagstuhl Workshop on Formal Methods in Molecular Biology. Dagstuhl, Germany. 2nd place at modeling competition
Thesis
1.Hardy, S. (2007) Méthodes systémiques d'analyse de données de simulation de modèles de voies de signalisation cellulaire, Doctor of philosophy (Ph.D.) Thesis, École Polytechnique de Montréal, 217 pages.
2.Hardy, S. (2004) Modélisation et simulation de systèmes biologiques à l’aide de réseaux de Pétri, Master of Applied Science (M.Sc.A.) Thesis, École Polytechnique de Montréal, 100 pages.