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Standardized benchmarking in the quest for orthologs

Adrian M Altenhoff , Brigitte Boeckmann , Salvador Capella-Gutiérrez , Daniel A Dalquen , Todd Deluca , et al.
Nature Methods, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩
Journal articles hal-01636892v1
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Méthodes avancées de raisonnement en logique propositionnelle : application aux réseaux métaboliques

Martin Morterol
Intelligence artificielle [cs.AI]. Université Paris-Saclay, 2016. Français. ⟨NNT : ⟩
Theses tel-01486750v1
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Conception, modélisation et simulation in silico d'un nanosystème biologique artificiel pour le diagnostic médical

Marc Bouffard
Bio-informatique [q-bio.QM]. Université Paris Saclay (COmUE), 2016. Français. ⟨NNT : 2016SACLS302⟩
Theses tel-01400244v1
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Traitement de données bioinformatiques massives (Big Data)

Sarah Cohen-Boulakia , Patrick Valduriez
[Rapport de recherche] RR-8915, Inria Sophia Antipolis; LRI - CNRS, University Paris-Sud. 2016, pp.8
Reports hal-01321033v1
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Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways

Alexandra Zaharia , Bernard Labedan , Christine Froidevaux , Alain Denise
SeqBio 2016, Nov 2016, Nantes, France
Conference papers hal-01745390v1
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Unfolding of Parametric Boolean Networks

Juraj Kolčák , David Šafránek , Stefan Haar , Loïc Paulevé
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⟩
Conference papers hal-01354109v2
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Qualitative dynamics semantics for SBGN process description

Adrien Rougny , Christine Froidevaux , Laurence Calzone , Loïc Paulevé
BMC Systems Biology, 2016, ⟨10.1186/s12918-016-0285-0⟩
Journal articles hal-01332679v1
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Pint, a static analyzer for dynamics of Automata Networks

Loïc Paulevé
14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Sep 2016, Cambridge, United Kingdom.
Conference poster hal-01366730v1
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Goal-Oriented Reduction of Automata Networks

Loïc Paulevé
14th International Conference on Computational Methods in Systems Biology (CMSB 2016), Sep 2016, Cambridge, United Kingdom. pp.252-272, ⟨10.1007/978-3-319-45177-0_16⟩
Conference papers hal-01149118v2
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Identification of Bifurcations in Biological Regulatory Networks using Answer-Set Programming

Louis Fippo Fitime , Olivier Roux , Carito Guziolowski , Loïc Paulevé
Constraint-Based Methods for Bioinformatics Workshop, Sep 2016, Toulouse, France
Conference papers hal-01361350v1
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Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

Simon Boitard , Willy Rodríguez , Flora Jay , Stefano Mona , Frederic Austerlitz
conférence Jaques Monod "Coalescence des approches théoriques et expérimentales en génomique évolutive et biologie des systèmes", 2016, Roscoff, France
Conference papers hal-01604024v1
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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent J. Henry , Arnaud Ferré , Christine Froidevaux , Anne Goelzer , Vincent V. Fromion , et al.
IC2016 - Ingénierie des Connaissances, Jun 2016, Montpellier, France
Conference papers hal-01442727v1
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The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect

Jorgelindo da Veiga Moreira , Minoo Hamraz , Mohammad Abolhassani , Erwan Bigan , Sabine Pérès , et al.
Metabolites, 2016, 6 (4), 12 p. ⟨10.3390/metabo6040033⟩
Journal articles hal-01417967v1
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Prédiction de structure tridimensionnelle de molécules d’ARN par minimisation de regret

Mélanie Boudard
Informatique et théorie des jeux [cs.GT]. Université Paris Saclay (COmUE), 2016. Français. ⟨NNT : 2016SACLV026⟩
Theses tel-01315684v1
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Méthodes qualitatives pour la construction et l'analyse des réseaux moléculaires SBGN

Adrien Rougny
Bio-informatique [q-bio.QM]. Université Paris Saclay (COmUE), 2016. Français. ⟨NNT : 2016SACLS325⟩
Theses tel-01391465v1
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Effective and Efficient Similarity Search in Scientific Workflow Repositories

Johannes Starlinger , Sarah Cohen-Boulakia , Sanjeev Khanna , Susan Davidson , Ulf Leser
Future Generation Computer Systems, 2016, 56, pp.584-594. ⟨10.1016/j.future.2015.06.012⟩
Journal articles hal-01170597v1
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Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming

Max Ostrowski , Loïc Paulevé , Torsten Schaub , Anne Siegel , Carito Guziolowski
Journal articles hal-01354075v1
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Relationship between the Reprogramming Determinants of Boolean Networks and their Interaction Graph

Hugues Mandon , Stefan Haar , Loïc Paulevé
Fifth International Workshop on Hybrid Systems Biology (HSB 2016), Oct 2016, Grenoble, France. pp.113-127, ⟨10.1007/978-3-319-47151-8_8⟩
Conference papers hal-01354079v1
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Necessary and sufficient conditions for protocell growth

Erwan Bigan , Loïc Paulevé , Jean-Marc Steyaert , Stéphane S. Douady
Journal of Mathematical Biology, 2016, ⟨10.1007/s00285-016-0998-0⟩
Journal articles hal-01338156v1
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Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

Simon Boitard , Willy Rodríguez , Flora Jay , Stefano Mona , Frédéric Austerlitz
PLoS Genetics, 2016, 12 (3), pp.e1005877. ⟨10.1371/journal.pgen.1005877⟩
Journal articles hal-01310742v1
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Reconstructing dynamic molecular states from single-cell time series

Lirong Huang , Loïc Paulevé , Christoph Zechner , Michael Unger , Anders S. Hansen , et al.
Journal of the Royal Society Interface, 2016, 13 (122), ⟨10.1098/rsif.2016.0533⟩
Journal articles hal-01362502v1
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Homology ­modeling of complex structural RNAs

Wei Wang​ , Matthieu Barba​ , Philippe Rinaudo​ , Alain Denise , Yann Ponty
JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France
Conference papers hal-01332642v1
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Variations de la taille d’une population : estimation à partir de génomes entiers.

Simon Boitard , Willy Rodríguez , Flora Jay , Stefano Mona , Frédéric Austerlitz
GDR AIEM, Nov 2016, Montpellier, France
Conference papers hal-01605807v1