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Mimoza: web-based semantic zooming and navigation in metabolic networks

 Anna Zhukova , David James Sherman
BMC Systems Biology, 2015, 9, pp.10. ⟨10.1186/s12918-015-0151-5⟩
Article dans une revue hal-01123715v1
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Linking phylogenetic similarity and pollution sensitivity to develop ecological assessment methods: a test with river diatoms

 François Keck , Agnes Bouchez , Alain Franc , Frédéric Rimet
Journal of Applied Ecology, 2016, 53 (3), pp.856-864. ⟨10.1111/1365-2664.12624⟩
Article dans une revue hal-01426853v1
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The impact of parasitism on resource allocation in a fungal host: the case of Cryphonectria parasitica and its mycovirus, Cryphonectria Hypovirus 1

 Jérémie Brusini , Marta L. Wayne , Alain Franc , Cécile Robin
Ecology and Evolution, 2017, 7 (15), pp.5967-5976. ⟨10.1002/ece3.3143⟩
Article dans une revue hal-01608310v1
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Exact and approximate inference in graphical models: variable elimination and beyond

 Nathalie Dubois Peyrard , Simon de Givry , Alain Franc , Stephane Robin , Régis Sabbadin , et al.
2015
Pré-publication, Document de travail hal-01197655v1
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Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations

 Warren Albertin , Maria Chernova , Pascal Durrens , Erwan Guichoux , David James Sherman , et al.
Yeast, 2018, 35 (1), pp.141-156. ⟨10.1002/yea.3248⟩
Article dans une revue hal-01585808v1
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Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936

 Pascal Durrens , Christophe C. Klopp , Nicolas Biteau , Valérie Fitton-Ouhabi , Karine Dementhon , et al.
Genome Announcements, 2017, 5 (31), pp.e00724-17. ⟨10.1128/genomeA.00724-17⟩
Article dans une revue hal-01583349v1
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Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

 Hugo Campbell-Sills , Mariette El Khoury , Marion Favier , Andrea Romano , Franco Biasioli , et al.
Genome Biology and Evolution, 2015, 7 (6), pp.1506-18. ⟨10.1093/gbe/evv084⟩
Article dans une revue hal-01202801v1
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Deriving Gene Associations for Metabolic Models

 Razanne Issa , David James Sherman
[Research Report] RR-9246, Inria Bordeaux Sud-Ouest. 2018
Rapport hal-01976744v1
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Deciphering the language of fungal pathogen recognition receptors

 Witold Dyrka , Pascal Durrens , Sven J Saupe , Mathieu Paoletti , David James Sherman
EMBO Young Scientists Forum 2015, Jul 2015, Warsaw, Poland. , 2015
Poster de conférence hal-01171745v1
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Deciphering the language of fungal pathogen recognition receptors

 Witold Dyrka , Pascal Durrens , Mathieu Paoletti , Sven J Saupe , David James Sherman
8th Symposium of the Polish Bioinformatics Society, Polish Bioinformatics Society, Sep 2015, Lublin, Poland
Communication dans un congrès hal-01203357v1
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Plastome data reveal multiple geographic origins of Quercus Group Ilex

 Marco Cosimo Simeone , Guido W. Grimm , Alessio Papini , Federico Vessella , Simone Cardoni , et al.
PeerJ, 2016, 4, pp.e1897. ⟨10.7717/peerj.1897⟩
Article dans une revue hal-01426766v1
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E-Biothon: an experimental platform for BioInformatics

 Michel Daydé , Benjamin Depardon , Alain Franc , Jean-François Gibrat , Romaric Guillier , et al.
International Conference on Computer Science and Information Technologies, Sep 2015, Yerevan, Armenia. ⟨10.1109/CSITechnol.2015.7358239⟩
Communication dans un congrès hal-01207320v1
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Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana

 Sylvain Poque , Gaëlle Pagny , Laurence Ouibrahim , Aurélie Chague , Jean-Philippe Eyquard , et al.
BMC Plant Biology, 2015, 15 (159), pp.159. ⟨10.1186/s12870-015-0559-5⟩
Article dans une revue hal-01262384v1
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Nonlinear Mapping and Distance Geometry

 Alain Franc , Pierre Blanchard , Olivier Coulaud
[Research Report] RR-9210, Inria Bordeaux Sud-Ouest. 2018, pp.14
Rapport hal-01897104v2

Exact or approximate inference in graphical models: why the choice is dictated by the treewidth, and how variable elimination can be exploited

 Nathalie Dubois Peyrard Peyrard , Marie-Josée Cros , Simon de Givry , Alain Franc , Stephane S. Robin , et al.
Australian and New Zealand Journal of Statistics, 2019, 61 (2), pp.89-133. ⟨10.1111/anzs.12257⟩
Article dans une revue hal-02433018v1
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diagno-syst: a tool for accurate inventories in metabarcoding

 Jean-Marc Frigerio , Frédéric Rimet , Agnes Bouchez , Emilie Chancerel , Philippe Chaumeil , et al.
2016
Pré-publication, Document de travail hal-01426764v1

Emergence of an integrated city-system in France (XVIIth–XIXth centuries): Evidence from toolset in graph theory

 Anne Bretagnolle , Alain Franc
Historical Methods: A Journal of Quantitative and Interdisciplinary History, 2017, 50 (1), pp.49-65. ⟨10.1080/01615440.2016.1237915⟩
Article dans une revue hal-01603847v1

Modeling and predicting behaviors and dynamics of ecosystems

 Damien Eveillard , Xavier Raynaud , Jérémie Bourdon , Alain Franc , Frédéric Plewniak
Insight on environmental genomics, the high-throughput sequencing revolution, 2016
Chapitre d'ouvrage hal-03823723v1
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Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana

 Vincent Lacoste , Arielle Salmier , Sourakhata Tirera , Alain Franc , Edith Darcissac , et al.
PLoS ONE, 2017, 12 (11), pp.1-25. ⟨10.1371/journal.pone.0186943⟩
Article dans une revue pasteur-01633803v1

Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca)

 Stéphanie Mariette , Fabienne Wong Jun Tai , Guillaume Roch , Aurélien Barré , Aurélie Chague , et al.
New Phytologist, 2016, 209 (2), DOI: 10.1111/nph.13627. ⟨10.1111/nph.13627⟩
Article dans une revue hal-01198840v1

A generic conceptual framework for describing transitions in settlement systems

 Laure Nuninger , Lena Sanders , Arnaud Banos , Frédérique Bertoncello , Anne Bretagnolle , et al.
Sanders L. Settling the World : From Prehistory to the Metropolis Era, Presses universitaires François-Rabelais, Chap 2, 2021, Perspectives Villes et Territoires, 9782869068551. ⟨10.4000/books.pufr.10527⟩
Chapitre d'ouvrage hal-03480382v1

Simuler des transitions : une introduction aux modèles spatio-temporels

 Arnaud Banos , Florent Le Néchet , Ouriachi Marie-Jeanne , Alain Franc
Sanders L. Peupler la terre. De la préhistoire à l'ère des métropoles, Presses universitaires François-Rabelais, pp.89-110, 2017
Chapitre d'ouvrage hal-02202128v1

Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action

 Florian Leese , Agnes Bouchez , Kessy Abarenkov , Florian Altermatt , Angel Borja , et al.
Next Generation Biomonitoring: Part 1, 58, Elsevier, pp.63-99, 2018, Advances In Ecological Research, 978-0-12-813949-3
Chapitre d'ouvrage hal-01984996v1

Pantograph: A template-based method for genome-scale metabolic model reconstruction

 Nicolás Loira , Anna Zhukova , David James Sherman
Journal of Bioinformatics and Computational Biology, 2015, 10, pp.1550006. ⟨10.1142/S0219720015500067⟩
Article dans une revue hal-01123733v1
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Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights

 Hugo Campbell-Sills , Mariette El Khoury , Marine Gammacurta , Cecile Miot-Sertier , Lucie Dutilh , et al.
OENO One, 2017, 51 (3), pp.309 - 322. ⟨10.20870/oeno-one.2017.51.4.1861⟩
Article dans une revue hal-01666981v1
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FMR: Fast randomized algorithms for covariance matrix computations

 Pierre Blanchard , Olivier Coulaud , Eric Darve , Alain Franc
Platform for Advanced Scientific Computing (PASC), Jun 2016, Lausanne, Switzerland. 2016
Poster de conférence hal-01334747v1

Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status

 Bonnie Bailet , Agnes Bouchez , Alain Franc , Jean-Marc Frigerio , François Keck , et al.
Metabarcoding and Metagenomics, 2019, 3, ⟨10.3897/mbmg.3.34002⟩
Article dans une revue hal-02432989v1

Disentangling the processes driving the biogeography of freshwater diatoms: A multiscale approach

 François Keck , Alain Franc , Maria Kahlert
Journal of Biogeography, 2018, 45 (7), pp.1582-1592. ⟨10.1111/jbi.13239⟩
Article dans une revue hal-01982135v1
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phylosignal: an R package to measure, test, and explore the phylogenetic signal

 François Keck , Frédéric Rimet , Agnes Bouchez , Alain Franc
Ecology and Evolution, 2016, 6 (9), pp.2774 - 2780. ⟨10.1002/ece3.2051⟩
Article dans une revue hal-01426773v1

Diversity and Domestication in Oenological Yeasts

 David James Sherman
Moscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia
Communication dans un congrès hal-01212044v1
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