David James Sherman

110

Documents

Présentation

Publications

	Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte , Wenfan Cao , Julie Aubert , David James Sherman , Hélène Falentin Metabolic Engineering, 2024, 83, pp.24 - 38. ⟨10.1016/j.ymben.2024.02.014⟩ Article dans une revue hal-04509395v1
	Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing Klara Cerk , Pablo Ugalde-Salas , Chabname Ghassemi Nedjad , Maxime Lecomte , Coralie Muller Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩ Article dans une revue hal-04409251v1
	The functional microbiome of grapevine throughout plant evolutionary history and lifetime Paola Fournier , Lucile Pellan , Didac Barroso-Bergadà , David Bohan , Thierry Candresse Advances in Ecological Research, 2022, Advances in Ecological Research, 67, pp.27-99. ⟨10.1016/bs.aecr.2022.09.001⟩ Article dans une revue hal-03858395v1
	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 Yeast, 2018, 35 (1), pp.141-156. ⟨10.1002/yea.3248⟩ Article dans une revue hal-01585808v1
	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 OENO One, 2017, 51 (3), pp.309 - 322. ⟨10.20870/oeno-one.2017.51.4.1861⟩ Article dans une revue hal-01666981v1
	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
	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
	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 Genome Biology and Evolution, 2015, 7 (6), pp.1506-18. ⟨10.1093/gbe/evv084⟩ Article dans une revue hal-01202801v1
	The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Gotthard Kunze , Claude Gaillardin , Małgorzata Czernicka , Pascal Durrens , Tiphaine Martin Biotechnology for Biofuels, 2014, 7 (1), pp.66. ⟨10.1186/1754-6834-7-66⟩ Article dans une revue pasteur-00988609v1
	Draft genome sequence of Rhodosporidium toruloides CECT1137, an oleaginous yeast of biotechnological interest Nicolas Morin , Xavier Calcas , Hugo Devillers , Pascal Durrens , David James Sherman Genome Announcements, 2014, 2 (4), ⟨10.1128/genomeA.00641-14⟩ Article dans une revue hal-02635833v1
	Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models. Rodrigo Assar , Martín A Montecino , Alejandro Maass , David J Sherman BioSystems, 2014, 121, pp.43-53. ⟨10.1016/j.biosystems.2014.05.007⟩ Article dans une revue hal-01002987v1
	QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite. Adrien Zimmer , Cécile Durand , Nicolás Loira , Pascal Durrens , David James Sherman PLoS ONE, 2014, 9 (1), pp.e86298. ⟨10.1371/journal.pone.0086298⟩ Article dans une revue hal-00986680v1
	Knowledge-based generalization of metabolic models Anna Zhukova , David James Sherman Journal of Computational Biology, 2014, 21 (7), pp.534-47. ⟨10.1089/cmb.2013.0143⟩ Article dans une revue hal-00925881v1
	Diversity and variability of NOD-like receptors in fungi Witold Dyrka , Marina Lamacchia , Pascal Durrens , Bostjan Kobe , Asen Daskalov Genome Biology and Evolution, 2014, in press. ⟨10.1093/gbe/evu251⟩ Article dans une revue hal-01083450v1
	Knowledge-based generalization of metabolic networks: a practical study Anna Zhukova , David James Sherman Journal of Bioinformatics and Computational Biology, 2014, 12(2) (1441001), ⟨10.1142/S0219720014410017⟩ Article dans une revue hal-00906911v1
	A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Pedro Almeida , Carla Gonçalves , Sara Teixeira , Diego Libkind , Martin Bontrager Nature Communications, 2014, 5, pp.4044. ⟨10.1038/ncomms5044⟩ Article dans une revue hal-01002466v1
	Implementing biological hybrid systems: Allowing composition and avoiding stiffness Rodrigo Assar , David James Sherman Applied Mathematics and Computation, 2013 Article dans une revue hal-00853997v1
	Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines. Andrea Romano , Hein Trip , Hugo Campbell-Sills , Olivier Bouchez , David Sherman Genome Announcements, 2013, 1 (1), pp.e00097-12. ⟨10.1128/genomeA.00097-12⟩ Article dans une revue hal-00863284v1
	Speciation of nickel (II) chloride complexes in hydrothermal fluids: In situ XAS study Yuan Tian , Barbara Etschmann , Weihua Liu , Stacey Borg , Yuan Mei Chemical Geology, 2012, 334, pp.345-363. ⟨10.1016/j.chemgeo.2012.10.010⟩ Article dans une revue hal-00761072v1
	Reusing and composing models of cell fate regulation of human bone precursor cells. Rodrigo Assar , Andrea V Leisewitz , Alice Garcia , Nibaldo C Inestrosa , Martín A Montecino BioSystems, 2012, 108 (1-3), pp.63-72. ⟨10.1016/j.biosystems.2012.01.008⟩ Article dans une revue hal-00681022v1
	A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica Nicolás Loira , Thierry Dulermo , Jean-Marc Nicaud , David James Sherman BMC Systems Biology, 2012, 6 (1), pp.35. ⟨10.1186/1752-0509-6-35⟩ Article dans une revue hal-00784406v1
	The Génolevures database Pascal Durrens , Tiphaine Martin , David James Sherman Comptes Rendus Biologies, 2011, 334 (8-9), pp.585-589. ⟨10.1016/j.crvi.2011.05.004⟩ Article dans une revue inria-00539200v1
	Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. André B Canelas , Nicola Harrison , Alessandro Fazio , Jie Zhang , Juha-Pekka Pitkänen Nature Communications, 2010, 1 (9), pp.145. ⟨10.1038/ncomms1150⟩ Article dans une revue inria-00562005v1
	Minimum information about a protein affinity reagent (MIAPAR). Julie Bourbeillon , Sandra Orchard , Itai Benhar , Carl Borrebaeck , Antoine de Daruvar Nature Biotechnology, 2010, 28 (7), pp.650-3. ⟨10.1038/nbt0710-650⟩ Article dans une revue inria-00544750v1
	A community standard format for the representation of protein affinity reagents. David E Gloriam , Sandra Orchard , Daniela Bertinetti , Erik Björling , Erik Bongcam-Rudloff Molecular and Cellular Proteomics, 2010, 9 (1), pp.1-10. ⟨10.1074/mcp.M900185-MCP200⟩ Article dans une revue inria-00544751v1
	Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. David James Sherman , Tiphaine Martin , Macha Nikolski , Cyril Cayla , Jean-Luc Souciet Nucleic Acids Research, 2009, 37, pp.D550-D554. ⟨10.1093/nar/gkn859⟩ Article dans une revue inria-00341578v1
	Comparative genomics of protoploid Saccharomycetaceae Jean-Luc Souciet , Bernard Dujon , Claude Gaillardin , Mark Johnston , Philippe V Baret Genome Research, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩ Article dans une revue inria-00407511v1
	Minimum information requirements : neither bandits in the Attic nor bats in the belfry David James Sherman New Biotechnology, 2009, 25 (4), pp.173-4. ⟨10.1016/j.nbt.2008.12.002⟩ Article dans une revue inria-00407505v1
	Mining the semantics of genome super-blocks to infer ancestral architectures Géraldine Jean , David James Sherman , Macha Nikolski Journal of Computational Biology, 2009, 16 (9), pp.1267-1284. ⟨10.1089/cmb.2008.0046⟩ Article dans une revue inria-00414692v1
	Unusual composition of a yeast chromosome arm is associated with its delayed replication. Célia Payen , Gilles Fischer , Christian Marck , Caroline Proux , David James Sherman Genome Research, 2009, 19, pp.1710-1721. ⟨10.1101/gr.090605.108⟩ Article dans une revue inria-00407518v1
	Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts. Florian Iragne , Macha Nikolski , David James Sherman FEMS Yeast Research, 2008, 8 (1), pp.132-9. ⟨10.1111/j.1567-1364.2007.00290.x⟩ Article dans une revue inria-00202723v1
	Exploratory Simulation of Cell Ageing Using Hierarchical Models Maria Cvijovic , Hayssam Soueidan , Edda Klipp , David James Sherman , Macha Nikolski Genome Informatics Series, 2008, 21, pp.114--125 Article dans une revue hal-00407512v1
	Fusion and fission of genes define a metric between fungal genomes. Pascal Durrens , Macha Nikolski , David James Sherman PLoS Computational Biology, 2008, 4 (10), pp.e1000200. ⟨10.1371/journal.pcbi.1000200⟩ Article dans une revue inria-00341569v1
	Family relationships: should consensus reign?- consensus clustering for protein families Macha Nikolski , David James Sherman Bioinformatics, 2007, 23, pp.e71--e76. ⟨10.1093/bioinformatics/btl314⟩ Article dans une revue inria-00202434v1
	Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Samuel Kerrien , Sandra Orchard , Luisa Montecchi-Palazzi , Bruno Aranda , Af Quinn BMC Biology, 2007, 5, pp.9;5(1):44 Article dans une revue hal-00306554v1
	ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome Michael J. Taussing , Oda Stoevesandt , Carl a K Borrebaeck , Andrew R Bradbury , Dolores Cahill Nature Methods, 2007, 4, pp.13-17. ⟨10.1038/nmeth0107-13⟩ Article dans une revue hal-00306585v1
	How to decide which are the most pertinent overly-represented features during gene set enrichment analysis Roland Barriot , David James Sherman , Isabelle Dutour BMC Bioinformatics, 2007, 8 (1), ⟨10.1186/1471-2105-8-332⟩ Article dans une revue inria-00202721v1
	Extrapolation of metabolic pathways as an aid to modelling completely sequenced Florian Iragne , Macha Nikolski , David Sherman FEMS Yeast Research, 2007, pp.132-139 Article dans une revue hal-00306592v1
	Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. David James Sherman , Pascal Durrens , Florian Iragne , Emmanuelle Beyne , Macha Nikolski Nucleic Acids Research, 2006, 34 (Database issue), pp.D432-5. ⟨10.1093/nar/gkj160⟩ Article dans une revue hal-00118142v1
	A systematic nomenclature of chromosomal elements for hemiascomycete yeasts Pascal Durrens , David James Sherman Yeast, 2005, 22 (5), pp.337-342. ⟨10.1002/yea.1214⟩ Article dans une revue inria-00202435v1
	ProViz: protein interaction visualization and exploration Florian Iragne , Macha Nikolski , Bertrand Mathieu , David Auber , David James Sherman Bioinformatics, 2005, 21 (2), pp.272-274. ⟨10.1093/bioinformatics/bth494⟩ Article dans une revue inria-00202436v1
	Genome evolution in yeasts. Bernard Dujon , David Sherman , Gilles Fischer , Pascal Durrens , Serge Casaregola Nature, 2004, 430 (6995), pp.35-44. ⟨10.1038/nature02579⟩ Article dans une revue hal-00104411v1
	IntAct: an open source molecular interaction database Henning Hermjakob , Luisa Montecchi-Palazzi , Sugath Mudali , Samuel Kerrien , Sandra Orchard Nucleic Acids Research, 2004, 32, pp.D452--5 Article dans une revue hal-00306577v1
	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale Roland Barriot , Jerome Poix , Alexis Groppi , Aurélien Barré , Nicolas Goffard Nucleic Acids Research, 2004, 32 (12), pp.3581-9. ⟨10.1093/nar/gkh681⟩ Article dans une revue inria-00202722v1
	Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. David Sherman , Pascal Durrens , Emmanuelle Beyne , Macha Nikolski , Jean-Luc Souciet Nucleic Acids Research, 2004, 32 (Database issue), pp.D315-8. ⟨10.1093/nar/gkh091⟩ Article dans une revue inria-00407519v1
	Novel Transporters from Hemiascomycete Yeasts Benoît de Hertogh , Emmanuel Talla , Fredj Tekaia , Emmanuelle Beyne , David James Sherman Journal of Molecular Microbiology and Biotechnology, 2003, 6 (1), pp.19-28. ⟨10.1159/000073405⟩ Article dans une revue inria-00202437v1
	Squeezing Intermediate Construction in Equational Programs Alain Miniussi , David James Sherman Lecture Notes in Computer Science, 1996, 1110, pp.284 -302 Article dans une revue hal-00389564v1
	Improving Arithmetic Performance using Fine-Grain Unfolding Timo Metzemakers , Alain Miniussi , David James Sherman , Robert Strandh Lecture Notes in Computer Science, 1994, pp.324 - 339 Article dans une revue hal-00389567v1

	Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communities Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux Journée GT Bioss 2022, Nov 2022, Nantes, France Communication dans un congrès hal-03857781v1
	Characterizing microbial interactions in controlled and natural microbial communities Maxime Lecomte , Simon Labarthe , David James Sherman , Hélène Falentin , Clémence Frioux Workshop SymBioDiversity, May 2022, Santiago, Chile Communication dans un congrès hal-03857848v2
	Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée. Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard 23ème édition du colloque du Club des Bactéries Lactiques, UMR INRAE - Institut Agro STLO (Science et Technologie du Lait et de l’Œuf), Jun 2022, Rennes, France Communication dans un congrès hal-03694338v1
	Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese. Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard FOODMICRO 2022, Aug 2022, Athènes, Greece Communication dans un congrès hal-03781287v1
	Metabolic modelling deciphers interactions in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe Metaboday 2021, Mar 2021, Bordeaux, France Communication dans un congrès hal-03531761v1
	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
	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
	What is the optimal representation of a generalized metabolic model using SBML and SBGN? Anna Zhukova , David James Sherman COMBINE 2013, Sep 2013, Paris, France Communication dans un congrès hal-00867373v1
	Knowledge-based zooming for metabolic models Anna Zhukova , David James Sherman JOBIM, Jul 2013, Toulouse, France Communication dans un congrès hal-00859437v1
	Knowledge-based generalization of metabolic networks: An applicational study Anna Zhukova , David James Sherman Moscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia Communication dans un congrès hal-00859440v1
	Taming the complexity of 'n-ary' relations in comparative genomics David James Sherman 9th International Conference on Genome Biology and Bioinformatics, Georgia Tech and Emory University, Nov 2013, Atlanta, Georgia, United States Communication dans un congrès hal-00938262v1
	Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid Systems Rodrigo Assar , Martín A Montecino , David James Sherman XII Latin American Congress of Probability and Mathematical Statistics, Mar 2012, Viña del Mar, Chile Communication dans un congrès hal-00686072v1
	Assessing ''last mile'' tools for affinity binder databases Natalia Golenetskaya , David James Sherman 5th ESF Workshop on Affinity Proteomics: Ligand Binders against the Human Proteome, Mar 2011, Alpbach, Austria Communication dans un congrès hal-00653518v1
	Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style Natalia Golenetskaya , David James Sherman SeqBio 2011, Dec 2011, Lille, France Communication dans un congrès hal-00654797v1
	Comparative annotation and scaling-out challenges for paraphyletic strategies David James Sherman , Natalia Golenetskaya , Tiphaine Martin , Pascal Durrens EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Understanding the Complexity of Diversity, EMBO, Oct 2011, San Feliu de Guixols, Spain Communication dans un congrès hal-00652903v1
	Addressing scaling-out challenges for comparative genomics David James Sherman , Natalia Golenetskaya Moscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia Communication dans un congrès hal-00649189v1
	How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock. Aurélie Goulielmakis , Julen Bridier , Aurélien Barré , Olivier Claisse , David Sherman Oeno2011- 9e symposium international d'oenologie de Bordeaux: Actes de colloques du 9e symposium international d'oenologie de Bordeaux, Jun 2011, Bordeaux, France. pp.358-363 Communication dans un congrès hal-00646867v1
	Modeling Stochastic Switched Systems with BioRica Rodrigo Assar , Alice Garcia , David James Sherman Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Institut Pasteur, Jun 2011, Paris, France. pp.297--304 Communication dans un congrès inria-00617419v1
	Reconciling competing models: a case study of wine fermentation kinetics Rodrigo Assar , Felipe A. Vargas , David James Sherman Algebraic and Numeric Biology 2010, Research Institute for Symbolic Computation, Johannes Kepler University of Linz, Jul 2010, Hagenberg, Austria. pp.68--83, ⟨10.1007/978-3-642-28067-2_6⟩ Communication dans un congrès inria-00541215v1
	Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica Nicolás Loira , David James Sherman 11th International Conference on Systems Biology, ICSB, Oct 2010, Edinburgh, United Kingdom Communication dans un congrès hal-00652922v1
	Génolevures, knowledge base and annotation of hemiascomycete yeast genomes Tiphaine Martin , David James Sherman , Pascal Durrens Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, Sep 2010, Montpellier, France Communication dans un congrès inria-00524386v1
	High-performance comparative annotation David James Sherman , Nicolás Loira , Natalia Golenetskaya Bioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia Communication dans un congrès inria-00563533v1
	Two examples of evolutionary algorithms in reconstructing genome evolution David James Sherman Workshop on Evolutionary Algorithms - Challenges in Theory and Practice, INRIA Bordeaux Sud-Ouest, Mar 2010, Bordeaux, France Communication dans un congrès inria-00563519v1
	Methods for understanding function and history in small eukaryote genomes David James Sherman Colloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France Communication dans un congrès inria-00563529v1
	The Génolevures website comparative genomic studies on hemiascomycetous yeasts Tiphaine Martin , David James Sherman , Macha Nikolski , Jean-Luc Souciet , Pascal Durrens Comparative Genomics of Eukaryotic Microorganisms 2009, EMBL-EMBO, Oct 2009, San Feliu de Guixols, Spain Communication dans un congrès inria-00524390v1
	The Génolevures online database Tiphaine Martin , Macha Nikolski , David James Sherman , Jean-Luc Souciet , Pascal Durrens Second German/ French/European/ Meeting Yeast and Filamentous Fungi, May 2009, Strasbourg, France Communication dans un congrès inria-00409534v1
	Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios Nikolay Vyahhi , Adrien Goëffon , David James Sherman , Macha Nikolski ACM SIGEVO Conference on Genetic and evolutionary computation, ACM SIGEVO, 2009, Montréal, Canada Communication dans un congrès inria-00407508v1
	Base de données Génolevures : génomique comparative des Hemiascomycetes Tiphaine Martin , David James Sherman , Macha Nikolski , Jean-Luc Souciet , Pascal Durrens Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182 Communication dans un congrès inria-00401915v1
	Hierarchical study of Guyton Circulatory Model Rodrigo Assar , Hayssam Soueidan , David James Sherman JOBIM 2009 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France Communication dans un congrès inria-00404135v1
	An Efficient Probabilistic Population-Based Descent for the Median Genome Problem Adrien Goëffon , Macha Nikolski , David James Sherman GECCO: Genetic And Evolutionary Computation Conference, Aug 2008, Atlanta, United States. pp.315-322 Communication dans un congrès hal-00341672v1
	The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeasts Tiphaine Martin , Pascal Durrens , Emmanuelle Beyne , Macha Nikolski , Florian Iragne First German/French/European/ Meeting Yeast and Filamentous Fungi, May 2008, Strasbourg, France Communication dans un congrès inria-00407631v1
	Genomic Exploration of the Hemiascomycetous Yeasts David James Sherman 3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia Communication dans un congrès inria-00350570v1
	BioRica: A multi model description and simulation system Hayssam Soueidan , David James Sherman , Macha Nikolski F0SBE, 2007, Germany. pp.279-287 Communication dans un congrès hal-00306550v1
	Gene Fusion and Fission Events in Fungal Genomes Pascal Durrens , Macha Nikolski , David James Sherman XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S132 Communication dans un congrès inria-00352592v1
	Gene fusion and fission events in fungus genomes Pascal Durrens , Macha Nikolski , David James Sherman 23rd international conference on yeast genetics and molecular biology, Jul 2007, Melbourne, Australia. pp.S132 Communication dans un congrès inria-00402220v1
	The Génolevures online database Tiphaine Martin , Pascal Durrens , Emmanuelle Beyne , Macha Nikolski , Florian Iragne XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135 Communication dans un congrès inria-00401921v1
	Bases de données et fouille de données chez les levures hémiascomycètes David James Sherman Conférence FungEffector, May 2007, Bordeaux, France Communication dans un congrès inria-00352600v1
	Reconstruction and visualization of genome rearrangements within the Kuyveromyces Géraldine Jean , David James Sherman , Macha Nikolski ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Oct 2007, San Feliu de Guixols, Spain. pp.44 Communication dans un congrès inria-00350567v1
	Mining the Hemiascomycete Yeasts David James Sherman Yeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria Communication dans un congrès inria-00407492v1
	The Génolevures database David James Sherman Yeast Genome 10th Anniversary, Académie Royale des Sciences, des Letters et des Beaux-Arts de Belgique, Sep 2006, Brussels, Belgium Communication dans un congrès inria-00407495v1
	Génolevures complete genomes provide data and tools for com- parative genomics of hemiascomycetous yeasts David James Sherman ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain Communication dans un congrès inria-00407502v1
	A whole-cell proteomics approach for comparing hemiascomycete yeast genomes Emmanuelle Beyne , Jean-Paul Lasserre , Stéphane Claverol , David James Sherman , Marc Bonneu ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain Communication dans un congrès inria-00407503v1
	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale Roland Barriot , Jérôme Poix , Alexis Groppi , Aurélien Barré , Nicolas Goffard Actes des 5ème Journées Ouvertes Biologie Informatique Mathématiques à Montréal (Canada), 2004, Canada. pp.3581-3589 Communication dans un congrès hal-00307645v1
	Factotum: Automatic and systematic sharing support for systems analyzers David James Sherman , Nicolas Magnier Tools and Algorithms for the Construction and Analysis of Systems (TACAS'98), Mar 1998, Lisbon, Portugal Communication dans un congrès inria-00334475v1

	Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing Carole Belliardo , Samuel Mondy , Arthur Pere , Claire Lemaitre , Riccardo Vicedomini Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024 Poster de conférence hal-04423917v1
	Characterising competition and cooperation potentials in microbial communities using discrete models of metabolism. An exploratory analysis Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux JOBIM 2022 - JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES, Jul 2022, Rennes, France Poster de conférence hal-03839337v1
	Dynamic Flux Balance Analysis with Metamodels Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou JOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. Poster de conférence hal-04236775v1
	Dynamic Flux Balance Analysis with Metamodels Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom. Poster de conférence hal-04252041v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe JOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Poster de conférence hal-03533781v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe MPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States Poster de conférence hal-03533786v1
	Modelling metabolic network dynamics in a cheese bacterial community Maxime Lecomte , David James Sherman , Hélène Falentin , Clémence Frioux , Simon Labarthe CMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France Poster de conférence hal-03533795v1
	Identification by QTL mapping of new genes and their allelic forms conferring robustness to environmental variations in wine fermentation Philippe Marullo , Maria Marti Raga , Adrien Zimmer , Emilien Peltier , Marina Bely 27. International Conference on Yeast Genetics and Molecular Biology, Sep 2015, Terme, Italy. , Yeast, Volume 32, Issue S1, 2015, Abstracts of the 27th International Conference on Yeast Genetics and Molecular Biology. ⟨10.1002/yea.3092⟩ Poster de conférence hal-02742176v1
	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
	Three-level representation of metabolic networks Anna Zhukova , David James Sherman Journées EDMI, Nov 2014, Bordeaux, France Poster de conférence hal-01081711v1
	Biological Knowledge, Problem Detecting, Model Reﬁnement and Diagnostics Anna Zhukova , David James Sherman EMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology 2012, Apr 2012, Cambridge, United Kingdom. 2012 Poster de conférence hal-00867375v1
	Mixed-formalism hierarchical modeling and simulation with BioRica Alice Garcia , David James Sherman 11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446 Poster de conférence inria-00529669v1
	Reconstruction and validation of the genome-scale metabolic model of Yarrowia lipolytica iNL750 David James Sherman , Nicolás Loira Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), Sep 2010, Montpellier, France. 2010 Poster de conférence hal-00652929v1

	Databases and Ontologies for Affinity Binders David James Sherman , Natalia Golenetskaya 2010 Autre publication scientifique inria-00563531v1
	Protein Families in Yeasts David James Sherman 2006 Autre publication scientifique inria-00407493v1

	Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte , Wenfan Cao , Julie J. Aubert , David James Sherman , Hélène Falentin 2023 Pré-publication, Document de travail hal-04088301v2
	Deciphering the language of fungal pathogen recognition receptors Witold Dyrka , Pascal Durrens , Mathieu Paoletti , Sven J Saupe , David J Sherman 2014 Pré-publication, Document de travail hal-01083421v1

	Deriving Gene Associations for Metabolic Models Razanne Issa , David James Sherman [Research Report] RR-9246, Inria Bordeaux Sud-Ouest. 2018 Rapport hal-01976744v1

David James Sherman

Présentation

Publications

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling

Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations

Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights

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

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

Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Draft genome sequence of Rhodosporidium toruloides CECT1137, an oleaginous yeast of biotechnological interest

Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models.

QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.

Knowledge-based generalization of metabolic models

Diversity and variability of NOD-like receptors in fungi

Knowledge-based generalization of metabolic networks: a practical study

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.

Implementing biological hybrid systems: Allowing composition and avoiding stiffness

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines.

Speciation of nickel (II) chloride complexes in hydrothermal fluids: In situ XAS study

Reusing and composing models of cell fate regulation of human bone precursor cells.

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

The Génolevures database

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.

Minimum information about a protein affinity reagent (MIAPAR).

A community standard format for the representation of protein affinity reagents.

Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

Comparative genomics of protoploid Saccharomycetaceae

Minimum information requirements : neither bandits in the Attic nor bats in the belfry

Mining the semantics of genome super-blocks to infer ancestral architectures

Unusual composition of a yeast chromosome arm is associated with its delayed replication.

Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts.

Exploratory Simulation of Cell Ageing Using Hierarchical Models

Fusion and fission of genes define a metric between fungal genomes.

Family relationships: should consensus reign?- consensus clustering for protein families

Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

How to decide which are the most pertinent overly-represented features during gene set enrichment analysis

Extrapolation of metabolic pathways as an aid to modelling completely sequenced

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.

A systematic nomenclature of chromosomal elements for hemiascomycete yeasts

ProViz: protein interaction visualization and exploration

Genome evolution in yeasts.

IntAct: an open source molecular interaction database

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

Novel Transporters from Hemiascomycete Yeasts

Squeezing Intermediate Construction in Equational Programs

Improving Arithmetic Performance using Fine-Grain Unfolding

Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communities

Characterizing microbial interactions in controlled and natural microbial communities

Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée.

Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese.

Metabolic modelling deciphers interactions in a cheese bacterial community

Deciphering the language of fungal pathogen recognition receptors

Diversity and Domestication in Oenological Yeasts

What is the optimal representation of a generalized metabolic model using SBML and SBGN?

Knowledge-based zooming for metabolic models

Knowledge-based generalization of metabolic networks: An applicational study

Taming the complexity of 'n-ary' relations in comparative genomics

Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid Systems

Assessing ''last mile'' tools for affinity binder databases

Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style

Comparative annotation and scaling-out challenges for paraphyletic strategies

Addressing scaling-out challenges for comparative genomics

How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock.

Modeling Stochastic Switched Systems with BioRica

Reconciling competing models: a case study of wine fermentation kinetics

Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica

Génolevures, knowledge base and annotation of hemiascomycete yeast genomes

High-performance comparative annotation

Two examples of evolutionary algorithms in reconstructing genome evolution

Methods for understanding function and history in small eukaryote genomes

The Génolevures website comparative genomic studies on hemiascomycetous yeasts

The Génolevures online database

Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios

Base de données Génolevures : génomique comparative des Hemiascomycetes

Hierarchical study of Guyton Circulatory Model