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Stochastic Reaction and Diffusion Systems in Molecular Communications: Recent Results and Open Problems

Malcolm Egan , Bayram Cevdet Akdeniz , Bao Quoc Tang
Digital Signal Processing, In press, pp.1-38. ⟨10.1016/j.dsp.2021.103117⟩
Journal articles hal-03233615v1
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Receptor clustering affects signal transduction at the membrane level in the reaction-limited regime.

Bertrand R Caré , Hédi A Soula
Physical Review E : Statistical, Nonlinear, and Soft Matter Physics, 2013, 87 (1), pp.012720. ⟨10.1103/PhysRevE.87.012720⟩
Journal articles hal-00858439v1
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Inferring gene regulatory networks from single-cell data: a mechanistic approach

Ulysse Herbach , Arnaud Bonnaffoux , Thibault Espinasse , Olivier Gandrillon
BMC Systems Biology, 2017, 11 (1), pp.105. ⟨10.1186/s12918-017-0487-0⟩
Journal articles hal-01646910v1
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Cognitive Molecular Communication

Malcolm Egan , Trung Q Duong , Marco Di Renzo , Jean-Marie Gorce , Ido Nevat , et al.
2018 -3rd Workshop on Molecular Communications, Apr 2018, Ghent, Belgium. pp.1-2
Conference papers hal-01728766v1
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Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Sarah Djebali , Julien Lagarde , Philipp Kapranov , Vincent Lacroix , Christelle Borel , et al.
PLoS ONE, 2012, 7, pp.1-22
Journal articles hal-00698428v1

Mathematical modeling of genetic regulatory networks: Stress responses in ıt Escherichia coli

Delphine Ropers , Hidde De Jong , Hans Geiselmann
P. Fu and M. Letterich and S. Panke. Systems Biology and Synthetic Biology, John Wiley & Sons, pp.235-271, 2009
Book sections hal-00793019v1

Modeling and formal verification of biological regulatory networks: an integrative approach

Pedro T. Monteiro , Ana T. Freitas , Delphine Ropers , Radu Mateescu , Hidde De Jong
Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010). First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH10), 2010, Ottawa, Canada
Conference papers hal-00793023v1

A propos du séquençage de génomes

François Rechenmann , Joanna Jongwane
Interstices, 2010
Journal articles hal-00793031v1

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

Sara Berthoumieux , Hidde de Jong , Guillaume Baptist , Corinne Pinel , Caroline Ranquet , et al.
Molecular Systems Biology, 2013, 9 (1), pp.634. ⟨10.1038/msb.2012.70⟩
Journal articles hal-00793352v1

Le premier article scientifique de l'histoire de l'informatique ?

François Rechenmann
Interstices, 2012
Journal articles hal-00793354v1
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Molecular Communication for Equilibrium State Estimation in Biochemical Processes on a Lab-on-a-Chip

Bayram Cevdet Akdeniz , Malcolm Egan
IEEE Transactions on NanoBioscience, 2021, 20 (2), pp.193 - 201. ⟨10.1109/TNB.2021.3062473⟩
Journal articles hal-03151618v1
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Equilibrium Signaling in Spatially Inhomogeneous Diffusion and External Forces

Malcolm Egan , Bayram Cevdet Akdeniz , Bao Quoc Tang
Preprints, Working Papers, ... hal-02910213v1

First-Order Tests for Toricity

Hamid Rahkooy , Thomas Sturm
Preprints, Working Papers, ... hal-03017907v1

Verification and synthesis using real quantifier elimination

Thomas Sturm , Ashish Tiwari
Proc. ISSAC 2011, Jun 2011, San Jose, United States. pp.329, ⟨10.1145/1993886.1993935⟩
Conference papers hal-03142063v1

Linear Integer Arithmetic Revisited

Martin Bromberger , Thomas Sturm , Christoph Weidenbach
Preprints, Working Papers, ... hal-03145059v1
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MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics

Benjamin Churcheward , Maxime Millet , Audrey Bihouée , Guillaume Fertin , Samuel Chaffron
mSystems, 2022, 7 (4), ⟨10.1128/msystems.00432-22⟩
Journal articles hal-03781944v1

Source-Target Proximity Analysis in Protein Networks Using Random Walks with Restart; Applications to Cancer Drug Resistance Prediction from Single-Cell Data

Frédéric Cazals , Jérémie Roux , Alain Jean-Marie , Dorian Mazauric , Guilherme Sales Santa Cruz
SophI.A 2019 - Springboard for Artificial Intelligence, Université Côte d'Azur, Nov 2019, Sophia-Antipolis, France
Conference papers hal-02432552v1
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Identification of metabolic network models from incomplete high-throughput datasets

Sara Berthoumieux , Matteo Brilli , Hidde De Jong , Daniel Kahn , Eugenio Cinquemani
Bioinformatics, 2011, 27 (13), pp.i186-i195. ⟨10.1093/bioinformatics/btr225⟩
Journal articles hal-00793039v1

Inferring structure and parameters of genetic regulatory networks: an approach based on hybrid systems

Riccardo Porreca , Samuel Drulhe , Hidde De Jong , Giancarlo Ferrari-Trecate
Workshop on Classification and Forecasting Models, ECOBIOSYS 2009, 2009, Milano, Italy
Conference papers hal-00793016v1

Vers la cellule virtuelle

Hidde De Jong
DocSciences, 2009, 8, pp.20-25
Journal articles hal-00793017v1

From qualitative to quantitative models of gene regulatory networks in bacteria (extended abstract)

Hidde De Jong
Proceedings of 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2010), 2010, Budapest, Hungary
Conference papers hal-00793022v1

Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells

Pedro T. Monteiro , Paulo J. Dias , Delphine Ropers , Arlindo L. Oliveira , Isabel Sà-Correia , et al.
11th International Conference on Systems Biology, ICSB 2010, 2010, Edinburgh, United Kingdom. pp.105
Conference papers hal-00793029v1

Modelling and analysis of protein aggregation - completing pathways in prion (PrP) polymerisation

Stephanie Prigent , Hadjer Wafaa Haffaf
Other publications hal-00958804v1
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Size distribution of amyloid brils. Mathematical models and experimental data.

Stephanie Prigent , Hadjer Wafaa Haffaf , H. T. Banks , M. Hoffmann , Human Rezaei , et al.
International Journal of Pure and Applied Mathematics, 2014, 93 (6), pp.845-878. ⟨10.12732/ijpam.v93i6.10⟩
Journal articles hal-00958785v2
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Microbial community functioning during plant litter decomposition

Simon Schroeter , Damien Eveillard , Samuel Chaffron , Johanna Zoppi , Bernd Kampe , et al.
Scientific Reports, 2022, 12 (1), pp.7451. ⟨10.1038/s41598-022-11485-1⟩
Journal articles hal-03781927v1

Gene regulatory network inference from single-cell data using a self-consistent proteomic field

Ulysse Herbach
Preprints, Working Papers, ... hal-03370228v1

Efficiently and Effectively Recognizing Toricity of Steady State Varieties

Dima Grigoriev , Alexandru Iosif , Hamid Rahkooy , Thomas Sturm , Andreas Weber
Preprints, Working Papers, ... hal-02397107v1

A Linear Algebra Approach for Detecting Binomiality of Steady State Ideals of Reversible Chemical Reaction Networks

Hamid Rahkooy , Ovidiu Radulescu , Thomas Sturm
Computer Algebra in Scientific Computing: 22nd International Workshop - CASC 2020, pp.492-509, 2020, ⟨10.1007/978-3-030-60026-6_29⟩
Book sections hal-02977486v1
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Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain

Caroline Brossas , Anne-Laure Valton , Sergey V Venev , Sabarinadh Chilaka , Antonin Counillon , et al.
EMBO Journal, 2020, ⟨10.15252/embj.201899520⟩
Journal articles hal-03023038v1
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A Molecular Communication Scheme to Estimate the State of Biochemical Processes on a Lab-on-a-Chip

Bayram Cevdet Akdeniz , Malcolm Egan
NanoCoCoA 2020 - 1st ACM International Workshop on Nanoscale Computing, Communication, and Applications, Nov 2020, Virtual Event, Japan. pp.1-6, ⟨10.1145/3416006.3431272⟩
Conference papers hal-03018289v1