David James Sherman

111

Documents

Presentation

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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles hal-01202801v1
	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⟩ Journal articles hal-01002466v1
	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⟩ Journal articles hal-01002987v1
	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⟩ Journal articles pasteur-00988609v1
	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⟩ Journal articles hal-01083450v1
	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⟩ Journal articles hal-00925881v1
	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⟩ Journal articles hal-02635833v1
	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⟩ Journal articles hal-00986680v1
	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⟩ Journal articles hal-00906911v1
	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⟩ Journal articles hal-00863284v1
	Implementing biological hybrid systems: Allowing composition and avoiding stiffness Rodrigo Assar , David James Sherman Applied Mathematics and Computation, 2013 Journal articles hal-00853997v1
	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⟩ Journal articles hal-00784406v1
	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⟩ Journal articles 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⟩ Journal articles hal-00681022v1
	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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles inria-00544751v1
	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⟩ Journal articles inria-00407505v1
	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⟩ Journal articles 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⟩ Journal articles inria-00407511v1
	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⟩ Journal articles 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⟩ Journal articles inria-00407518v1
	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⟩ Journal articles inria-00341569v1
	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 Journal articles hal-00407512v1
	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⟩ Journal articles inria-00202723v1
	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 Journal articles 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⟩ Journal articles hal-00306585v1
	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⟩ Journal articles inria-00202434v1
	Extrapolation of metabolic pathways as an aid to modelling completely sequenced Florian Iragne , Macha Nikolski , David Sherman FEMS Yeast Research, 2007, pp.132-139 Journal articles hal-00306592v1
	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⟩ Journal articles inria-00202721v1
	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⟩ Journal articles 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⟩ Journal articles 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⟩ Journal articles inria-00202436v1
	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⟩ Journal articles inria-00202722v1
	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 Journal articles hal-00306577v1
	Genome evolution in yeasts. Bernard Dujon , David Sherman , Gilles Fischer , Pascal Durrens , Serge Casaregola Nature, 2004, 430 (6995), pp.35-44. ⟨10.1038/nature02579⟩ Journal articles hal-00104411v1
	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⟩ Journal articles 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⟩ Journal articles inria-00202437v1
	Squeezing Intermediate Construction in Equational Programs Alain Miniussi , David James Sherman Lecture Notes in Computer Science, 1996, 1110, pp.284 -302 Journal articles 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 Journal articles hal-00389567v1

	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 Conference papers hal-03781287v1
	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 Conference papers hal-03857848v2
	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 Conference papers hal-03857781v1
	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 Conference papers hal-03694338v1
	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 Conference papers hal-03531761v1
	Diversity and Domestication in Oenological Yeasts David James Sherman Moscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia Conference papers hal-01212044v1
	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 Conference papers hal-01203357v1
	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 Conference papers hal-00867373v1
	Knowledge-based zooming for metabolic models Anna Zhukova , David James Sherman JOBIM, Jul 2013, Toulouse, France Conference papers hal-00859437v1
	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 Conference papers hal-00938262v1
	Knowledge-based generalization of metabolic networks: An applicational study Anna Zhukova , David James Sherman Moscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia Conference papers hal-00859440v1
	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 Conference papers hal-00686072v1
	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 Conference papers hal-00652903v1
	Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style Natalia Golenetskaya , David James Sherman SeqBio 2011, Dec 2011, Lille, France Conference papers hal-00654797v1
	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 Conference papers hal-00646867v1
	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 Conference papers hal-00653518v1
	Addressing scaling-out challenges for comparative genomics David James Sherman , Natalia Golenetskaya Moscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia Conference papers hal-00649189v1
	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 Conference papers inria-00617419v1
	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 Conference papers 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 Conference papers inria-00524386v1
	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⟩ Conference papers inria-00541215v1
	High-performance comparative annotation David James Sherman , Nicolás Loira , Natalia Golenetskaya Bioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia Conference papers inria-00563533v1
	Methods for understanding function and history in small eukaryote genomes David James Sherman Colloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France Conference papers inria-00563529v1
	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 Conference papers inria-00563519v1
	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 Conference papers inria-00404135v1
	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 Conference papers inria-00409534v1
	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 Conference papers inria-00524390v1
	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 Conference papers 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 Conference papers inria-00401915v1
	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 Conference papers 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 Conference papers inria-00407631v1
	Genomic Exploration of the Hemiascomycetous Yeasts David James Sherman 3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia Conference papers inria-00350570v1
	Bases de données et fouille de données chez les levures hémiascomycètes David James Sherman Conférence FungEffector, May 2007, Bordeaux, France Conference papers 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 Conference papers inria-00350567v1
	BioRica: A multi model description and simulation system Hayssam Soueidan , David James Sherman , Macha Nikolski F0SBE, 2007, Germany. pp.279-287 Conference papers 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 Conference papers 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 Conference papers 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 Conference papers inria-00401921v1
	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 Conference papers inria-00407495v1
	Mining the Hemiascomycete Yeasts David James Sherman Yeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria Conference papers inria-00407492v1
	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 Conference papers 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 Conference papers 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 Conference papers 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 Conference papers 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 Conference poster hal-04423917v1
	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. Conference poster hal-04236775v1
	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 Conference poster hal-03839337v1
	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. Conference poster hal-04252041v1
	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 Conference poster hal-03533795v1
	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 Conference poster 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 Conference poster hal-03533786v1
	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⟩ Conference poster 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 Conference poster hal-01171745v1
	Three-level representation of metabolic networks Anna Zhukova , David James Sherman Journées EDMI, Nov 2014, Bordeaux, France Conference poster 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 Conference poster 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 Conference poster 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 Conference poster hal-00652929v1

	Databases and Ontologies for Affinity Binders David James Sherman , Natalia Golenetskaya 2010 Other publications inria-00563531v1
	Protein Families in Yeasts David James Sherman 2006 Other publications 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 Preprints, Working Papers, ... hal-04088301v2
	Deciphering the language of fungal pathogen recognition receptors Witold Dyrka , Pascal Durrens , Mathieu Paoletti , Sven J Saupe , David J Sherman 2014 Preprints, Working Papers, ... hal-01083421v1

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

	TANGO models: numerical multi-omics reconciliation of bacterial fermentation in cheese production Julie Aubert , Hélène Falentin , Clémence Frioux , Simon Labarthe , Maxime Lecomte 2024, ⟨swh:1:dir:0a1da28c523c2f32e1214b5d1c1a60ac17ec29df;origin=https://forgemia.inra.fr/tango/tango_models.git;visit=swh:1:snp:722365d9bf1004d05edfe63717763283d4adf26f;anchor=swh:1:rev:bc0bd9895942ed6d82faa9553c1f0a32f60cbbef⟩ Software hal-04562266v1

David James Sherman

Presentation

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.

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

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

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

Diversity and variability of NOD-like receptors in fungi

Knowledge-based generalization of metabolic models

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

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

Knowledge-based generalization of metabolic networks: a practical study

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

Implementing biological hybrid systems: Allowing composition and avoiding stiffness

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

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.

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.

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

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

Comparative genomics of protoploid Saccharomycetaceae

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

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

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

Exploratory Simulation of Cell Ageing Using Hierarchical Models

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

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

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

Extrapolation of metabolic pathways as an aid to modelling completely sequenced

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

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

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

IntAct: an open source molecular interaction database

Genome evolution in yeasts.

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

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

Characterizing microbial interactions in controlled and natural microbial communities

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

Metabolic modelling deciphers interactions in a cheese bacterial community

Diversity and Domestication in Oenological Yeasts

Deciphering the language of fungal pathogen recognition receptors

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

Knowledge-based zooming for metabolic models

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

Knowledge-based generalization of metabolic networks: An applicational study

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

Comparative annotation and scaling-out challenges for paraphyletic strategies

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

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

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

Addressing scaling-out challenges for comparative genomics

Modeling Stochastic Switched Systems with BioRica

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

Génolevures, knowledge base and annotation of hemiascomycete yeast genomes

Reconciling competing models: a case study of wine fermentation kinetics

High-performance comparative annotation

Methods for understanding function and history in small eukaryote genomes

Two examples of evolutionary algorithms in reconstructing genome evolution

Hierarchical study of Guyton Circulatory Model

The Génolevures online database

The Génolevures website comparative genomic studies on hemiascomycetous yeasts

Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios

Base de données Génolevures : génomique comparative des Hemiascomycetes