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Deposit type : Notice

Odd Gossiping

Guillaume Fertin , Joseph G. Peters , Lynette Raabe , Charlie Xu
Discrete Applied Mathematics, 2017, 216, pp.550-561. ⟨10.1016/j.dam.2016.01.034⟩
Journal articles hal-01314648v1

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore

Benoît Delahaye , Damien Eveillard , Nicholas Bouskill
mSystems, 2017, 2 (6), ⟨10.1128/mSystems.00169-17⟩
Journal articles hal-01658218v1

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks

Vincent Picard , Anne Siegel , Jérémie Bourdon
Journal of Computational Biology, 2017, 24 (8), pp.1--12. ⟨10.1089/cmb.2017.0099⟩
Journal articles hal-01552190v1

SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes

Matthieu David , Guillaume Fertin , Helene Rogniaux-Bonaventure , Dominique Tessier
Journal of Proteome Research, 2017, 16 (8), pp.3030-3038. ⟨10.1021/acs.jproteome.7b00308⟩
Journal articles hal-01607343v1

Sorting permutations by prefix and suffix rearrangements

Carla Negri Lintzmayer , Guillaume Fertin , Zanoni Dias
Journal of Bioinformatics and Computational Biology, 2017, 15 (1), pp.1-46. ⟨10.1142/S0219720017500020⟩
Journal articles hal-01524046v1

Modelling plankton ecosystems in the meta-omics era. Are we ready?

Krzysztof Franciszek Stec , Luigi Caputi , Pier Luigi Buttigieg , Domenico d'Alelio , Federico Matias Ibarbalz et al.
Marine Genomics, 2017, 32, pp.1-17. ⟨10.1016/j.margen.2017.02.006⟩
Journal articles hal-01584309v1

Plankton networks correlated to the biological carbon pump in the global ocean

A.S. Benoiston , L. Bittner , Lionel Guidi , S. Chaffron , D. Eveillard et al.
Journée analyse des réseau, GDR génomique environnementale, 2017, Nantes, France
Conference papers hal-04024048v1

OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques

Marko Budinich , Jérémie Bourdon , Abdelhalim Larhlimi , Damien Eveillard
13th International Conference on Computational Methods in Systems Biology CMSB 2015, Sep 2015, Nantes, France. pp.279-281, ⟨10.1007/978-3-319-23401-4_23⟩
Conference papers hal-02464859v1

Toward a better understanding of the plant microbiota

Victoria Potdevin , Marie Chevallier , Ruben Garrido Oter , Anne Siegel , Stéphane Hacquard et al.
4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France
Conference papers hal-01576743v1

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Marko Budinich , Jérémie Bourdon , Abdelhalim Larhlimi , Damien Eveillard
PLoS ONE, 2017, 12 (2), pp.e0171744
Journal articles hal-01478375v1

Graph matching problems and the NP-hardness of sortedness constraints

Irena Rusu
Theoretical Computer Science, 2017, 695, pp.16 - 27. ⟨10.1016/j.tcs.2017.07.019⟩
Journal articles hal-01708356v1

Modélisation et prédiction du fonctionnement et de la dynamique des écosystèmes

Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frederic Plewniak et al.
La génomique environnemetale : la révolution du séquençage à haut débit, 2016
Book sections hal-01777358v1

The Contig Assembly Problem and Its Algorithmic Solutions

Géraldine Jean , Andreea Radulescu , Irena Rusu
Algorithms for Next-Generation Sequencing Data, pp. 267-298, 2017
Book sections hal-01819204v1

caspo: a toolbox for automated reasoning on the response of logical signaling networks families

Santiago Videla , Julio Saez-Rodriguez , Carito Guziolowski , Anne Siegel
Journal articles hal-01426880v1

Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling

Aristotelis Kittas , Aurélien Delobelle , Sabrina Schmitt , Kai Breuhahn , Carito Guziolowski et al.
FEBS Journal, 2016, 283 (2), pp.350-360. ⟨10.1111/febs.13580⟩
Journal articles hal-02466989v1

Permutation reconstruction from MinMax-Betweenness constraints

Irena Rusu
Discrete Applied Mathematics, 2016, 207, pp.106-119. ⟨10.1016/j.dam.2016.03.008⟩
Journal articles hal-02464904v1

log-Lists and their applications to sorting by transpositions, reversals and block-interchanges

Irena Rusu
Theoretical Computer Science, 2017, 660, pp.1 - 15. ⟨10.1016/j.tcs.2016.11.012⟩
Journal articles hal-01708351v1

Algorithmic Aspects of the Maximum Colorful Arborescence Problem

Guillaume Fertin , Julien Fradin , Géraldine Jean
Theory and Applications of Models of Computation - 14th Annual Conference, Apr 2017, Berne, Switzerland. pp.216-230, ⟨10.1007/978-3-319-55911-7_16⟩
Conference papers hal-01524069v1

Modeling and predicting behaviors and dynamics of ecosystems

Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frédéric Plewniak et al.
Insight on environmental genomics, the high-throughput sequencing revolution, 2016
Book sections hal-03823723v1

Toward the study of metabolic functions in algal holobionts

Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami et al.
4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France
Conference papers hal-01576484v1

L'écologie des systèmes

Damien Eveillard , Anne Siegel , Philippe Vandenkoornhuyse
Mokrane Bouzeghoub et Rémy Mosseri. Les Big Data à Découvert, CNRS éditions, 2017, 978-2-271-11464-8
Book sections hal-01575603v1