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Number of documents

101

Research

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.

Journal articles46 documents

  • Warren Albertin, Maria Chernova, Pascal Durrens, Erwan Guichoux, David James Sherman, et al.. Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human-related fermentations. Yeast, Wiley, 2018, 35 (1), pp.141-156. ⟨10.1002/yea.3248⟩. ⟨hal-01585808⟩
  • Constantina Badea, Kevin Binning, Jean-François Verlhiac, David Sherman. In the Aftermath of Terrorism: Effects of Self- versus Group-Affirmation on Support for Discriminatory Policies. Journal of Experimental Social Psychology, Elsevier, In press. ⟨hal-02916245⟩
  • Hugo Campbell-Sills, Mariette El Khoury, Marine Gammacurta, Cecile Miot-Sertier, Lucie Dutilh, et al.. Two different Oenococcus oeni lineages are associated to either red or white wines in Burgundy: genomics and metabolomics insights. OENO One, Institut des Sciences de la Vigne et du Vin (Université de Bordeaux), 2017, 51 (3), pp.309 - 322. ⟨10.20870/oeno-one.2017.51.4.1861⟩. ⟨hal-01666981⟩
  • Hugo Campbell-Sills, Mariette El Khoury, Marion Favier, Andrea Romano, Franco Biasioli, et al.. Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines.. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2015, 7 (6), pp.1506-18. ⟨10.1093/gbe/evv084⟩. ⟨hal-01202801⟩
  • Nicolás Loira, Anna Zhukova, David James Sherman. Pantograph: A template-based method for genome-scale metabolic model reconstruction. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2015, 10, pp.1550006. ⟨10.1142/S0219720015500067⟩. ⟨hal-01123733⟩
  • Anna Zhukova, David James Sherman. Mimoza: web-based semantic zooming and navigation in metabolic networks. BMC Systems Biology, BioMed Central, 2015, 9, pp.10. ⟨10.1186/s12918-015-0151-5⟩. ⟨hal-01123715⟩
  • Anna Zhukova, David James Sherman. Knowledge-based generalization of metabolic networks: a practical study. Journal of Bioinformatics and Computational Biology, World Scientific Publishing, 2014, 12(2) (1441001), ⟨10.1142/S0219720014410017⟩. ⟨hal-00906911⟩
  • Pedro Almeida, Carla Gonçalves, Sara Teixeira, Diego Libkind, Martin Bontrager, et al.. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.. Nature Communications, Nature Publishing Group, 2014, 5, pp.4044. ⟨10.1038/ncomms5044⟩. ⟨hal-01002466⟩
  • Adrien Zimmer, Cécile Durand, Nicolás Loira, Pascal Durrens, David James Sherman, et al.. QTL dissection of Lag phase in wine fermentation reveals a new translocation responsible for Saccharomyces cerevisiae adaptation to sulfite.. PLoS ONE, Public Library of Science, 2014, 9 (1), pp.e86298. ⟨10.1371/journal.pone.0086298⟩. ⟨hal-00986680⟩
  • Anna Zhukova, David James Sherman. Knowledge-based generalization of metabolic models. Journal of Computational Biology, Mary Ann Liebert, 2014, 21 (7), pp.534-47. ⟨10.1089/cmb.2013.0143⟩. ⟨hal-00925881⟩
  • Witold Dyrka, Marina Lamacchia, Pascal Durrens, Bostjan Kobe, Asen Daskalov, et al.. Diversity and variability of NOD-like receptors in fungi. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, in press. ⟨10.1093/gbe/evu251⟩. ⟨hal-01083450⟩
  • Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, et al.. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.. Biotechnology for Biofuels, BioMed Central, 2014, 7 (1), pp.66. ⟨10.1186/1754-6834-7-66⟩. ⟨pasteur-00988609⟩
  • Nicolas Morin, Xavier Calcas, Hugo Devillers, Pascal Durrens, David James Sherman, et al.. Draft genome sequence of Rhodosporidium toruloides CECT1137, an oleaginous yeast of biotechnological interest. Genome Announcements, American Society for Microbiology, 2014, 2 (4), ⟨10.1128/genomeA.00641-14⟩. ⟨hal-02635833⟩
  • Rodrigo Assar, Martín A Montecino, Alejandro Maass, David J Sherman. Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models.. BioSystems, Elsevier, 2014, 121, pp.43-53. ⟨10.1016/j.biosystems.2014.05.007⟩. ⟨hal-01002987⟩
  • Rodrigo Assar, David James Sherman. Implementing biological hybrid systems: Allowing composition and avoiding stiffness. Applied Mathematics and Computation, Elsevier, 2013. ⟨hal-00853997⟩
  • Andrea Romano, Hein Trip, Hugo Campbell-Sills, Olivier Bouchez, David Sherman, et al.. Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines.. Genome Announcements, American Society for Microbiology, 2013, 1 (1), pp.e00097-12. ⟨10.1128/genomeA.00097-12⟩. ⟨hal-00863284⟩
  • Rodrigo Assar, Andrea V Leisewitz, Alice Garcia, Nibaldo C Inestrosa, Martín A Montecino, et al.. Reusing and composing models of cell fate regulation of human bone precursor cells.. BioSystems, Elsevier, 2012, 108 (1-3), pp.63-72. ⟨10.1016/j.biosystems.2012.01.008⟩. ⟨hal-00681022⟩
  • Nicolás Loira, Thierry Dulermo, Jean-Marc Nicaud, David James Sherman. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Biology, BioMed Central, 2012, 6 (1), pp.35. ⟨10.1186/1752-0509-6-35⟩. ⟨hal-00784406⟩
  • yuan Tian, Barbara Etschmann, Weihua Liu, Stacey Borg, yuan Mei, et al.. Speciation of nickel (II) chloride complexes in hydrothermal fluids: In situ XAS study. Chemical Geology, Elsevier, 2012, 334, pp.345-363. ⟨10.1016/j.chemgeo.2012.10.010⟩. ⟨hal-00761072⟩
  • Pascal Durrens, Tiphaine Martin, David James Sherman. The Génolevures database. Comptes Rendus Biologies, Elsevier, 2011, 334 (8-9), pp.585-589. ⟨10.1016/j.crvi.2011.05.004⟩. ⟨inria-00539200⟩
  • David E Gloriam, Sandra Orchard, Daniela Bertinetti, Erik Björling, Erik Bongcam-Rudloff, et al.. A community standard format for the representation of protein affinity reagents.. Molecular and Cellular Proteomics, American Society for Biochemistry and Molecular Biology, 2010, 9 (1), pp.1-10. ⟨10.1074/mcp.M900185-MCP200⟩. ⟨inria-00544751⟩
  • Julie Bourbeillon, Sandra Orchard, Itai Benhar, Carl Borrebaeck, Antoine de Daruvar, et al.. Minimum information about a protein affinity reagent (MIAPAR).. Nature Biotechnology, Nature Publishing Group, 2010, 28 (7), pp.650-3. ⟨10.1038/nbt0710-650⟩. ⟨inria-00544750⟩
  • André B Canelas, Nicola Harrison, Alessandro Fazio, Jie Zhang, Juha-Pekka Pitkänen, et al.. Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains.. Nature Communications, Nature Publishing Group, 2010, 1 (9), pp.145. ⟨10.1038/ncomms1150⟩. ⟨inria-00562005⟩
  • Jean-Luc Souciet, Bernard Dujon, Claude Gaillardin, Mark Johnston, Philippe V Baret, et al.. Comparative genomics of protoploid Saccharomycetaceae. Genome Research, Cold Spring Harbor Laboratory Press, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩. ⟨inria-00407511⟩
  • Célia Payen, Gilles Fischer, Christian Marck, Caroline Proux, David James Sherman, et al.. Unusual composition of a yeast chromosome arm is associated with its delayed replication.. Genome Research, Cold Spring Harbor Laboratory Press, 2009, 19, pp.1710-1721. ⟨10.1101/gr.090605.108⟩. ⟨inria-00407518⟩
  • Géraldine Jean, David James Sherman, Macha Nikolski. Mining the semantics of genome super-blocks to infer ancestral architectures. Journal of Computational Biology, Mary Ann Liebert, 2009, 16 (9), pp.1267-1284. ⟨10.1089/cmb.2008.0046⟩. ⟨inria-00414692⟩
  • David James Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, et al.. Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.. Nucleic Acids Research, Oxford University Press, 2009, pp.D550-D554. ⟨10.1093/nar/gkn859⟩. ⟨inria-00341578⟩
  • David James Sherman. Minimum information requirements : neither bandits in the Attic nor bats in the belfry. New Biotechnology, Elsevier, 2009, 25 (4), pp.173-4. ⟨10.1016/j.nbt.2008.12.002⟩. ⟨inria-00407505⟩
  • Florian Iragne, Macha Nikolski, David James Sherman. Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts.. FEMS Yeast Research, Oxford University Press (OUP), 2008, 8 (1), pp.132-9. ⟨10.1111/j.1567-1364.2007.00290.x⟩. ⟨inria-00202723⟩
  • Maria Cvijovic, Hayssam Soueidan, Edda Klipp, David James Sherman, Macha Nikolski. Exploratory Simulation of Cell Ageing Using Hierarchical Models. Genome Informatics Series, Universal Academy Press Inc., 2008, 21, pp.114--125. ⟨hal-00407512⟩
  • Pascal Durrens, Macha Nikolski, David James Sherman. Fusion and fission of genes define a metric between fungal genomes.. PLoS Computational Biology, Public Library of Science, 2008, 4 (10), pp.e1000200. ⟨10.1371/journal.pcbi.1000200⟩. ⟨inria-00341569⟩
  • Florian Iragne, Macha Nikolski, David Sherman. Extrapolation of metabolic pathways as an aid to modelling completely sequenced. FEMS Yeast Research, Oxford University Press (OUP), 2007, pp.132-139. ⟨hal-00306592⟩
  • Macha Nikolski, David James Sherman. Family relationships: should consensus reign?- consensus clustering for protein families. Bioinformatics, Oxford University Press (OUP), 2007, 23, pp.e71--e76. ⟨10.1093/bioinformatics/btl314⟩. ⟨inria-00202434⟩
  • Roland Barriot, David James Sherman, Isabelle Dutour. How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. BMC Bioinformatics, BioMed Central, 2007, 8 (1), ⟨10.1186/1471-2105-8-332⟩. ⟨inria-00202721⟩
  • Samuel Kerrien, Sandra Orchard, Luisa Montecchi-Palazzi, Bruno Aranda, Af Quinn, et al.. Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular. BMC Biology, BioMed Central, 2007, 5, pp.9;5(1):44. ⟨hal-00306554⟩
  • Michael J. Taussing, Oda Stoevesandt, Carl a K Borrebaeck, Andrew R Bradbury, Dolores Cahill, et al.. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nature Methods, Nature Publishing Group, 2007, 4, pp.13-17. ⟨10.1038/nmeth0107-13⟩. ⟨hal-00306585⟩
  • David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, et al.. Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.. Nucleic Acids Research, Oxford University Press, 2006, 34 (Database issue), pp.D432-5. ⟨10.1093/nar/gkj160⟩. ⟨hal-00118142⟩
  • Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman. ProViz: protein interaction visualization and exploration. Bioinformatics, Oxford University Press (OUP), 2005, 21 (2), pp.272-274. ⟨10.1093/bioinformatics/bth494⟩. ⟨inria-00202436⟩
  • Pascal Durrens, David James Sherman. A systematic nomenclature of chromosomal elements for hemiascomycete yeasts. Yeast, Wiley, 2005, 22 (5), pp.337-342. ⟨10.1002/yea.1214⟩. ⟨inria-00202435⟩
  • David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet. Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.. Nucleic Acids Research, Oxford University Press, 2004, 32 (Database issue), pp.D315-8. ⟨10.1093/nar/gkh091⟩. ⟨inria-00407519⟩
  • Bernard Dujon, David Sherman, Gilles Fischer, Pascal Durrens, Serge Casaregola, et al.. Genome evolution in yeasts.. Nature, Nature Publishing Group, 2004, 430 (6995), pp.35-44. ⟨10.1038/nature02579⟩. ⟨hal-00104411⟩
  • Henning Hermjakob, Luisa Montecchi-Palazzi, Sugath Mudali, Samuel Kerrien, Sandra Orchard, et al.. IntAct: an open source molecular interaction database. Nucleic Acids Research, Oxford University Press, 2004, 32, pp.D452--5. ⟨hal-00306577⟩
  • Roland Barriot, Jerome Poix, Alexis Groppi, Aurélien Barré, Nicolas Goffard, et al.. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Research, Oxford University Press, 2004, 32 (12), pp.3581-9. ⟨10.1093/nar/gkh681⟩. ⟨inria-00202722⟩
  • Benoît de Hertogh, Emmanuel Talla, Fredj Tekaia, Emmanuelle Beyne, David James Sherman, et al.. Novel Transporters from Hemiascomycete Yeasts. Journal of Molecular Microbiology and Biotechnology, Karger, 2003, 6 (1), pp.19-28. ⟨10.1159/000073405⟩. ⟨inria-00202437⟩
  • Alain Miniussi, David James Sherman. Squeezing Intermediate Construction in Equational Programs. Lecture Notes in Computer Science, Springer, 1996, 1110, pp.284 -302. ⟨hal-00389564⟩
  • Timo Metzemakers, Alain Miniussi, David James Sherman, Robert Strandh. Improving Arithmetic Performance using Fine-Grain Unfolding. Lecture Notes in Computer Science, Springer, 1994, pp.324 - 339. ⟨hal-00389567⟩

Conference papers41 documents

  • Wenfan Cao, Maxime Lecomte, Solène Le Fur, Julie J. Aubert, Marie-Bernadette Maillard, et al.. Métatranscriptomique et modèle métabolique pour identifier la succession des métabolismes bactériens en interaction lors de la fabrication d’un fromage modèle à pâte pressée.. 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. ⟨hal-03694338⟩
  • Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe. Metabolic modelling deciphers interactions in a cheese bacterial community. Metaboday 2021, Mar 2021, Bordeaux, France. ⟨hal-03531761⟩
  • Witold Dyrka, Pascal Durrens, Mathieu Paoletti, Sven J Saupe, David James Sherman. Deciphering the language of fungal pathogen recognition receptors. 8th Symposium of the Polish Bioinformatics Society, Polish Bioinformatics Society, Sep 2015, Lublin, Poland. ⟨hal-01203357⟩
  • David James Sherman. Diversity and Domestication in Oenological Yeasts. Moscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia. ⟨hal-01212044⟩
  • Anna Zhukova, David James Sherman. Knowledge-based generalization of metabolic networks: An applicational study. Moscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia. ⟨hal-00859440⟩
  • David James Sherman. Taming the complexity of 'n-ary' relations in comparative genomics. 9th International Conference on Genome Biology and Bioinformatics, Georgia Tech and Emory University, Nov 2013, Atlanta, Georgia, United States. ⟨hal-00938262⟩
  • Anna Zhukova, David James Sherman. Knowledge-based zooming for metabolic models. JOBIM, Jul 2013, Toulouse, France. ⟨hal-00859437⟩
  • Anna Zhukova, David James Sherman. What is the optimal representation of a generalized metabolic model using SBML and SBGN?. COMBINE 2013, Sep 2013, Paris, France. ⟨hal-00867373⟩
  • Rodrigo Assar, Martín A Montecino, David James Sherman. Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid Systems. XII Latin American Congress of Probability and Mathematical Statistics, Mar 2012, Viña del Mar, Chile. ⟨hal-00686072⟩
  • Rodrigo Assar, Alice Garcia, David James Sherman. Modeling Stochastic Switched Systems with BioRica. Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Institut Pasteur, Jun 2011, Paris, France. pp.297--304. ⟨inria-00617419⟩
  • David James Sherman, Natalia Golenetskaya. Addressing scaling-out challenges for comparative genomics. Moscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia. ⟨hal-00649189⟩
  • Aurélie Goulielmakis, Julen Bridier, Aurélien Barré, Olivier Claisse, David Sherman, et al.. How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock.. 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. ⟨hal-00646867⟩
  • David James Sherman, Natalia Golenetskaya, Tiphaine Martin, Pascal Durrens. Comparative annotation and scaling-out challenges for paraphyletic strategies. EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Understanding the Complexity of Diversity, EMBO, Oct 2011, San Feliu de Guixols, Spain. ⟨hal-00652903⟩
  • Natalia Golenetskaya, David James Sherman. Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style. SeqBio 2011, Dec 2011, Lille, France. ⟨hal-00654797⟩
  • Natalia Golenetskaya, David James Sherman. Assessing ''last mile'' tools for affinity binder databases. 5th ESF Workshop on Affinity Proteomics: Ligand Binders against the Human Proteome, Mar 2011, Alpbach, Austria. ⟨hal-00653518⟩
  • David James Sherman. Methods for understanding function and history in small eukaryote genomes. Colloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France. ⟨inria-00563529⟩
  • David James Sherman. Two examples of evolutionary algorithms in reconstructing genome evolution. Workshop on Evolutionary Algorithms - Challenges in Theory and Practice, INRIA Bordeaux Sud-Ouest, Mar 2010, Bordeaux, France. ⟨inria-00563519⟩
  • David James Sherman, Nicolás Loira, Natalia Golenetskaya. High-performance comparative annotation. Bioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia. ⟨inria-00563533⟩
  • Tiphaine Martin, David James Sherman, Pascal Durrens. Génolevures, knowledge base and annotation of hemiascomycete yeast genomes. Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, Sep 2010, Montpellier, France. ⟨inria-00524386⟩
  • Rodrigo Assar, Felipe A. Vargas, David James Sherman. Reconciling competing models: a case study of wine fermentation kinetics. 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⟩. ⟨inria-00541215⟩
  • Nicolás Loira, David James Sherman. Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica. 11th International Conference on Systems Biology, ICSB, Oct 2010, Edinburgh, United Kingdom. ⟨hal-00652922⟩
  • Nikolay Vyahhi, Adrien Goëffon, David James Sherman, Macha Nikolski. Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios. ACM SIGEVO Conference on Genetic and evolutionary computation, ACM SIGEVO, 2009, Montréal, Canada. ⟨inria-00407508⟩
  • Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens. Base de données Génolevures : génomique comparative des Hemiascomycetes. Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182. ⟨inria-00401915⟩
  • Rodrigo Assar, Hayssam Soueidan, David James Sherman. Hierarchical study of Guyton Circulatory Model. JOBIM 2009 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France. ⟨inria-00404135⟩
  • Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens. The Génolevures website comparative genomic studies on hemiascomycetous yeasts. Comparative Genomics of Eukaryotic Microorganisms 2009, EMBL-EMBO, Oct 2009, San Feliu de Guixols, Spain. ⟨inria-00524390⟩
  • Tiphaine Martin, Macha Nikolski, David James Sherman, Jean-Luc Souciet, Pascal Durrens. The Génolevures online database. Second German/ French/European/ Meeting Yeast and Filamentous Fungi, May 2009, Strasbourg, France. ⟨inria-00409534⟩
  • David James Sherman. Genomic Exploration of the Hemiascomycetous Yeasts. 3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia. ⟨inria-00350570⟩
  • Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, et al.. The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeasts. First German/French/European/ Meeting Yeast and Filamentous Fungi, May 2008, Strasbourg, France. ⟨inria-00407631⟩
  • Adrien Goëffon, Macha Nikolski, David James Sherman. An Efficient Probabilistic Population-Based Descent for the Median Genome Problem. GECCO: Genetic And Evolutionary Computation Conference, Aug 2008, Atlanta, United States. pp.315-322. ⟨hal-00341672⟩
  • Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, et al.. The Génolevures online database. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135. ⟨inria-00401921⟩
  • Géraldine Jean, David James Sherman, Macha Nikolski. Reconstruction and visualization of genome rearrangements within the Kuyveromyces. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Oct 2007, San Feliu de Guixols, Spain. pp.44. ⟨inria-00350567⟩
  • David James Sherman. Bases de données et fouille de données chez les levures hémiascomycètes. Conférence FungEffector, May 2007, Bordeaux, France. ⟨inria-00352600⟩
  • Pascal Durrens, Macha Nikolski, David James Sherman. Gene Fusion and Fission Events in Fungal Genomes. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S132. ⟨inria-00352592⟩
  • Hayssam Soueidan, David James Sherman, Macha Nikolski. BioRica: A multi model description and simulation system. F0SBE, 2007, Germany. pp.279-287. ⟨hal-00306550⟩
  • Pascal Durrens, Macha Nikolski, David James Sherman. Gene fusion and fission events in fungus genomes. 23rd international conference on yeast genetics and molecular biology, Jul 2007, Melbourne, Australia. pp.S132. ⟨inria-00402220⟩
  • David James Sherman. The Génolevures database. Yeast Genome 10th Anniversary, Académie Royale des Sciences, des Letters et des Beaux-Arts de Belgique, Sep 2006, Brussels, Belgium. ⟨inria-00407495⟩
  • David James Sherman. Mining the Hemiascomycete Yeasts. Yeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria. ⟨inria-00407492⟩
  • David James Sherman. Génolevures complete genomes provide data and tools for com- parative genomics of hemiascomycetous yeasts. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain. ⟨inria-00407502⟩
  • Emmanuelle Beyne, Jean-Paul Lasserre, Stéphane Claverol, David James Sherman, Marc Bonneu. A whole-cell proteomics approach for comparing hemiascomycete yeast genomes. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain. ⟨inria-00407503⟩
  • Roland Barriot, Jérôme Poix, Alexis Groppi, Aurélien Barré, Nicolas Goffard, et al.. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Actes des 5ème Journées Ouvertes Biologie Informatique Mathématiques à Montréal (Canada), 2004, Canada. pp.3581-3589. ⟨hal-00307645⟩
  • David James Sherman, Nicolas Magnier. Factotum: Automatic and systematic sharing support for systems analyzers. Tools and Algorithms for the Construction and Analysis of Systems (TACAS'98), Mar 1998, Lisbon, Portugal. ⟨inria-00334475⟩

Poster communications9 documents

  • Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe. Modelling metabolic network dynamics in a cheese bacterial community. MPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States. ⟨hal-03533786⟩
  • Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe. Modelling metabolic network dynamics in a cheese bacterial community. CMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. ⟨hal-03533795⟩
  • Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux, Simon Labarthe. Modelling metabolic network dynamics in a cheese bacterial community. JOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. ⟨hal-03533781⟩
  • Witold Dyrka, Pascal Durrens, Sven J Saupe, Mathieu Paoletti, David James Sherman. Deciphering the language of fungal pathogen recognition receptors. EMBO Young Scientists Forum 2015, Jul 2015, Warsaw, Poland. 2015. ⟨hal-01171745⟩
  • Philippe Marullo, Maria Marti Raga, Adrien Zimmer, Emilien Peltier, Marina Bely, et al.. Identification by QTL mapping of new genes and their allelic forms conferring robustness to environmental variations in wine fermentation. 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⟩. ⟨hal-02742176⟩
  • Anna Zhukova, David James Sherman. Three-level representation of metabolic networks. Journées EDMI, Nov 2014, Bordeaux, France. ⟨hal-01081711⟩
  • Anna Zhukova, David James Sherman. Biological Knowledge, Problem Detecting, Model Refinement and Diagnostics. EMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology 2012, Apr 2012, Cambridge, United Kingdom. 2012. ⟨hal-00867375⟩
  • David James Sherman, Nicolás Loira. Reconstruction and validation of the genome-scale metabolic model of Yarrowia lipolytica iNL750. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), Sep 2010, Montpellier, France. 2010. ⟨hal-00652929⟩
  • Alice Garcia, David James Sherman. Mixed-formalism hierarchical modeling and simulation with BioRica. 11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446. ⟨inria-00529669⟩

Other publications2 documents

Preprints, Working Papers, ...2 documents

  • Clémence Frioux, Sylvie Huet, Simon Labarthe, Julien Martinelli, Thibault Malou, et al.. Accelerating metabolic models evaluation with statistical metamodels: application to Salmonella infection models. 2022. ⟨hal-03635862⟩
  • Witold Dyrka, Pascal Durrens, Mathieu Paoletti, Sven J Saupe, David J Sherman. Deciphering the language of fungal pathogen recognition receptors. 2014. ⟨hal-01083421⟩

Reports1 document

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