Publications

Léa Guyon, Jérémy Guez, Evelyne Heyer, Raphaëlle Chaix. Modeling the influence of human social organizations on genetic diversity. RTP Evolutionary human sciences 2021, French Society for Evolutionary Human Sciences, Nov 2021, Montpellier, France. ⟨hal-03972083⟩

Ferdinand Petit, Jérémy Guez, Fanny Pouyet, Evelyne Heyer, Bruno Toupance, et al.. Impact of Cultural Transmission of Reproductive Success on whole-genome data: simulation study and ABC inference. Probabilistic Modelling in Genomics 2022, Mar 2022, Oxford, United Kingdom. ⟨hal-03970627⟩

Ferdinand Petit, Jérémy Guez, Fanny Pouyet, Bruno Toupance, Evelyne Heyer, et al.. Topological comparison of coalescent tree inference tools.. Congress of the European Society for Evolutionary Biology, Aug 2022, Prague (Czech Republic), Czech Republic. ⟨hal-03970653⟩

Arnaud Quelin, Jérémy Guez, Ferdinand Petit, Flora Jay, Frédéric Austerlitz. Inference of the Cultural Transmission of Reproductive Success from human genomic data: ABC and machine learning methods. 2023 Alphy & AIEM Joint Meeting, Jan 2023, Grenoble, France. ⟨hal-03960408⟩

Stéphanie Chevalier. Inférence logique de réseaux booléens à partir de connaissances et d'observations de processus de différenciation cellulaire. Bio-informatique [q-bio.QM]. Université Paris-Saclay, 2022. Français. ⟨NNT : 2022UPASG061⟩. ⟨tel-03917566⟩

Coline Gianfrotta, Vladimir Reinharz, Olivier Lespinet, Dominique Barth, Alain Denise. On the predictibility of A-minor motifs from their local contexts. RNA Biology, 2022, 19 (1), pp.1208-1227. ⟨10.1080/15476286.2022.2144611⟩. ⟨hal-03864666⟩

Harshad Ugamraj, Kevin Dang, Laure-Hélène Ouisse, Benjamin Buelow, Eduardo Chini, et al.. TNB-738, a biparatopic antibody, boosts intracellular NAD+ by inhibiting CD38 ecto-enzyme activity. mAbs, Taylor & Francis, 2022, 14 (1), ⟨10.1080/19420862.2022.2095949⟩. ⟨hal-03684683⟩

Apolline Petit, Jeremy Guez, Arnaud Le Rouzic. Correlated stabilizing selection shapes the topology of gene regulatory networks. 2022. ⟨hal-03813178⟩

Frédérique Bassino, Mathilde Bouvel, Valentin Féray, Lucas Gerin, Adeline Pierrot. Scaling limit of graph classes through split decomposition. 2022. ⟨hal-03797906⟩

Loïc Paulevé, Nathalie Théret. 6th International Workshop on Static Analysis and Systems Biology (SASB 2015) . Loïc Paulevé; Nathalie Theret. SASB, Sep 2015, Saint-Malo, France. 326, Elsevier, pp.88, 2016, Electronic Notes in Theoretical Computer Science. ⟨hal-01385704⟩

Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise. Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways. SeqBio 2016, Nov 2016, Nantes, France. ⟨hal-01745390⟩

Juraj Kolčák, David Šafránek, Stefan Haar, Loïc Paulevé. Unfolding of Parametric Boolean Networks. 7th International Workshop on Static Analysis and Systems Biology (SASB 2016), Sep 2016, Edimbourg, United Kingdom. pp.67-90, ⟨10.1016/j.entcs.2018.03.009⟩. ⟨hal-01354109v2⟩

Lirong Huang, Loïc Paulevé, Christoph Zechner, Michael Unger, Anders S. Hansen, et al.. Reconstructing dynamic molecular states from single-cell time series. Journal of the Royal Society Interface, the Royal Society, 2016, 13 (122), ⟨10.1098/rsif.2016.0533⟩. ⟨hal-01362502⟩

Frédérique Bassino, Mathilde Bouvel, Adeline Pierrot, Carine Pivoteau, Dominique Rossin. An algorithm computing combinatorial specifications of permutation classes. Discrete Applied Mathematics, Elsevier, 2017, 224, pp.16-44. ⟨10.1016/j.dam.2017.02.013⟩. ⟨hal-01175234⟩

Sabine Pérès, Mario Jolicœur, Cécile Moulin, Philippe Dague, Stefan Schuster. How important is thermodynamics for identifying elementary flux modes?. PLoS ONE, Public Library of Science, 2017, 12 (2), ⟨10.1371/journal.pone.0171440⟩. ⟨hal-01709642⟩

Adeline Pierrot, Dominique Rossin. 2-Stack Sorting is Polynomial. Theory of Computing Systems, Springer Verlag, 2017, 60 (3), pp.552 – 579. ⟨10.1007/s00224-016-9743-8⟩. ⟨hal-01758837⟩

Sabine Pérès, Philippe Dague, Mario Jolicœur, Stefan Schuster. Computing EFMs consistent with equilibrium constants. Metabolic Pathway Analysis MPA 2017, Jul 2017, Bozeman, United States. ⟨hal-01676892⟩

Loïc Paulevé, Philippe Dague. Journées BIOSS-IA 2017. 2017. ⟨hal-01666094⟩

Michael Martin, Flora Jay, Sergi Castellano, Montgomery Slatkin. Determination of genetic relatedness from low-coverage human genome sequences using pedigree simulations. Molecular Ecology, Wiley, 2017, 26 (16), pp.4145 – 4157. ⟨10.1111/mec.14188⟩. ⟨hal-01676698⟩

Thomas Chatain, Loïc Paulevé. Goal-Driven Unfolding of Petri Nets. 28th International Conference on Concurrency Theory (CONCUR 2017), Sep 2017, Berlin, Germany. ⟨10.4230/LIPIcs.CONCUR.2017.14⟩. ⟨hal-01392203v2⟩

Hugues Mandon, Stefan Haar, Loïc Paulevé. Temporal Reprogramming of Boolean Networks. CMSB 2017 – 15th conference on Computational Methods for Systems Biology, Sep 2017, Darmstadt, Germany. pp.179 – 195, ⟨10.1007/978-3-319-67471-1_11⟩. ⟨hal-01589251⟩

Loïc Paulevé. Pint: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface. CMSB 2017 – 15th conference on Computational Methods for Systems Biology, Sep 2017, Darmstadt, Germany. pp.370 – 316, ⟨10.1007/978-3-319-67471-1_20⟩. ⟨hal-01589248⟩

Nicolas Levy, Aurélien Naldi, Céline Hernandez, Gautier Stoll, Denis Thieffry, et al.. Prediction of Mutations to Control Pathways Enabling Tumour Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial). Frontiers in Physiology, Frontiers, 2018, 9, pp.787. ⟨10.1101/319780⟩. ⟨hal-01809081⟩

Vladimir Reinharz, Antoine Soulé, Eric Westhof, Jérôme Waldispühl, Alain Denise. Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families. Nucleic Acids Research, Oxford University Press, 2018. ⟨hal-01745345⟩