David James Sherman

Présentation

My research develops computer science techniques for large-scale comparative genomics and hierarchical modeling of biological systems to better understand the mechanisms of eukaryote genome evolution and the ways that genes and proteins cooperate to realize cellular functions. In my research team we develop tools and algorithms for comparative genomics of eukaryotic microorganisms, inference of interaction and metabolic networks, and construction of hierarchical stochastic models of cell behavior, using techniques from data-mining, modeling, combinatorial analysis and formal methods.

Publications

Article dans une revue (49)

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling Maxime Lecomte,Wenfan Cao,Julie Aubert,David James Sherman,Hélène Falentinet al. 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 Mulleret al. 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 Candresseet al. Advances in Ecological Research, 2022, Advances in Ecological Research, 67, pp.27-99. ⟨10.1016/bs.aecr.2022.09.001⟩ Article dans une revue (article de synthèse) 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 Shermanet al. 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 Dutilhet al. 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
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 Biasioliet al. Genome Biology and Evolution, 2015, 7 (6), pp.1506-18. ⟨10.1093/gbe/evv084⟩ Article dans une revue hal-01202801v1
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
Draft genome sequence of &lt;em&gt;Rhodosporidium toruloides&lt;/em&gt; CECT1137, an oleaginous yeast of biotechnological interest Nicolas Morin,Xavier Calcas,Hugo Devillers,Pascal Durrens,David James Shermanet al. 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 Shermanet al. PLoS ONE, 2014, 9 (1), pp.e86298. ⟨10.1371/journal.pone.0086298⟩ Article dans une revue hal-00986680v1
The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Gotthard Kunze,Claude Gaillardin,Małgorzata Czernicka,Pascal Durrens,Tiphaine Martinet al. Biotechnology for Biofuels, 2014, 7 (1), pp.66. ⟨10.1186/1754-6834-7-66⟩ Article dans une revue pasteur-00988609v1
A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Pedro Almeida,Carla Gonçalves,Sara Teixeira,Diego Libkind,Martin Bontrageret al. Nature Communications, 2014, 5, pp.4044. ⟨10.1038/ncomms5044⟩ Article dans une revue hal-01002466v1
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
Diversity and variability of NOD-like receptors in fungi Witold Dyrka,Marina Lamacchia,Pascal Durrens,Bostjan Kobe,Asen Daskalovet al. Genome Biology and Evolution, 2014, in press. ⟨10.1093/gbe/evu251⟩ Article dans une revue 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⟩ Article dans une revue hal-00925881v1
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 Shermanet al. Genome Announcements, 2013, 1 (1), pp.e00097-12. ⟨10.1128/genomeA.00097-12⟩ Article dans une revue hal-00863284v1
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
Train in Vain: The role of the self in claimed self-handicapping strategies Lucie Finez,David Sherman Journal of Sport and Exercise Psychology, 2012, 34 (5), pp.600-620. ⟨10.1123/jsep.34.5.600⟩ Article dans une revue hal-01490625v1
Speciation of nickel (II) chloride complexes in hydrothermal fluids: In situ XAS study Yuan Tian,Barbara Etschmann,Weihua Liu,Stacey Borg,Yuan Meiet al. Chemical Geology, 2012, 334, pp.345-363. ⟨10.1016/j.chemgeo.2012.10.010⟩ Article dans une revue istex 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 Montecinoet al. 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 istex 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 Pitkänenet al. Nature Communications, 2010, 1 (9), pp.145. ⟨10.1038/ncomms1150⟩ Article dans une revue inria-00562005v1
A community standard format for the representation of protein affinity reagents. David E Gloriam,Sandra Orchard,Daniela Bertinetti,Erik Björling,Erik Bongcam-Rudloffet al. Molecular and Cellular Proteomics, 2010, 9 (1), pp.1-10. ⟨10.1074/mcp.M900185-MCP200⟩ Article dans une revue inria-00544751v1
Minimum information about a protein affinity reagent (MIAPAR). Julie Bourbeillon,Sandra Orchard,Itai Benhar,Carl Borrebaeck,Antoine de Daruvaret al. Nature Biotechnology, 2010, 28 (7), pp.650-3. ⟨10.1038/nbt0710-650⟩ Article dans une revue inria-00544750v1
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 istex 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 Soucietet al. Nucleic Acids Research, 2009, 37, pp.D550-D554. ⟨10.1093/nar/gkn859⟩ Article dans une revue hal-04943449v1
Comparative genomics of protoploid Saccharomycetaceae Jean-Luc Souciet,Bernard Dujon,Claude Gaillardin,Mark Johnston,Philippe V Baretet al. Genome Research, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩ Article dans une revue 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⟩ 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 Shermanet al. Genome Research, 2009, 19, pp.1710-1721. ⟨10.1101/gr.090605.108⟩ Article dans une revue inria-00407518v1
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
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
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
Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Samuel Kerrien,Sandra Orchard,Luisa Montecchi-Palazzi,Bruno Aranda,Af Quinnet al. BMC Biology, 2007, 5, pp.9;5(1):44. ⟨10.1186/1741-7007-5-44⟩ 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 Cahillet al. Nature Methods, 2007, 4, pp.13-17. ⟨10.1038/nmeth0107-13⟩ Article dans une revue 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⟩ Article dans une revue inria-00202434v1
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 Nikolskiet al. Nucleic Acids Research, 2006, 34 (Database issue), pp.D432-5. ⟨10.1093/nar/gkj160⟩ Article dans une revue hal-00118142v1
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
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
Genome evolution in yeasts. Bernard Dujon,David Sherman,Gilles Fischer,Pascal Durrens,Serge Casaregolaet al. Nature, 2004, 430 (6995), pp.35-44. ⟨10.1038/nature02579⟩ Article dans une revue istex 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⟩ Article dans une revue inria-00407519v1
IntAct: an open source molecular interaction database Henning Hermjakob,Luisa Montecchi-Palazzi,Sugath Mudali,Samuel Kerrien,Sandra Orchardet al. 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 Goffardet al. Nucleic Acids Research, 2004, 32 (12), pp.3581-9. ⟨10.1093/nar/gkh681⟩ Article dans une revue inria-00202722v1
Novel Transporters from Hemiascomycete Yeasts Benoît de Hertogh,Emmanuel Talla,Fredj Tekaia,Emmanuelle Beyne,David James Shermanet al. 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

Communication dans un congrès (45)

Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling 6 may 2025 / Modélisation du microbiome David James Sherman,Hélène Falentin,Clémence Frioux,Simon Labarthe,Maxime Lecomte NEM 2025 - Journées Nutrition & Ecologie Microbienne, workshop modélisation du microbiome, May 2025, Rennes (Distanciel), France Communication dans un congrès hal-05059688v1
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 Maillardet al. FOODMICRO 2022, Aug 2022, Athènes, Greece Communication dans un congrès hal-03781287v1
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 Maillardet al. 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
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
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
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
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
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
Knowledge-based zooming for metabolic models Anna Zhukova,David James Sherman JOBIM, Jul 2013, Toulouse, France Communication dans un congrès hal-00859437v1
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
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
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
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
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
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 Shermanet al. 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
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
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
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
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
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
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
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
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
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
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
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 Iragneet al. 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
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 Iragneet al. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135 Communication dans un congrès inria-00401921v1
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
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
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
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 Goffardet al. 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

Poster de conférence (13)

Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing Carole Belliardo,Arthur Péré,Alain Franc,Jean-Marc Frigerio,Nicolas Mauriceet al. 2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025 Poster de conférence hal-04920790v1
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 Vicedominiet al. Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024 Poster de conférence hal-04423917v1
Dynamic Flux Balance Analysis with Metamodels Clémence Frioux,Sylvie Huet,Simon Labarthe,Julien Martinelli,Thibault Malouet al. JOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. Poster de conférence 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 Poster de conférence hal-03839337v1
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 CMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France Poster de conférence hal-03533795v1
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
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 Belyet al. 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

Autre publication scientifique (2)

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

Pré-publication, Document de travail (3)

Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics Carole Belliardo,Nicolas Maurice,Arthur Pere,Samuel Mondy,Alain Francet al. 2025 Pré-publication, Document de travail hal-05340126v1
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 Falentinet al. 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

Rapport (1)

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

Logiciel (1)

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