Nombre de documents

89

CV de David James Sherman


Article dans une revue42 documents

  • 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>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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. <http://genomea.asm.org/content/1/1/e00097-12.long>. <10.1128/genomeA.00097-12>. <hal-00863284>
  • Rodrigo Assar, David James Sherman. Implementing biological hybrid systems: Allowing composition and avoiding stiffness. Applied Mathematics and Computation, Elsevier, 2013. <hal-00853997>
  • Nicolás Loira, Thierry Dulermo, Jean-Marc Nicaud, David Sherman. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Systems Biology, BioMed Central, 2012, 6 (1), pp.35. <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=22558935>. <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>
  • 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>
  • Pascal Durrens, Tiphaine Martin, David James Sherman. The Génolevures database. Comptes Rendus de l'Académie des Sciences, Série Biologies, Elsevier, 2011, 334 (8-9), pp.585-589. <10.1016/j.crvi.2011.05.004>. <inria-00539200>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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, epub ahead of print. <10.1101/gr.090605.108>. <inria-00407518>
  • 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>
  • 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 (OUP): Policy C - Option B, 2009, pp.D550-D554. <10.1093/nar/gkn859>. <inria-00341578>
  • Maria Cvijovic, Hayssam Soueidan, Edda Klipp, David James Sherman, Macha Nikolski. Exploratory Simulation of Cell Ageing Using Hierarchical Models. Genome Informatics, 2008, 21, pp.114--125. <hal-00407512>
  • 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>
  • 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>
  • 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>
  • 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>
  • 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 (OUP): Policy C - Option B, 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>
  • 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>
  • 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 (OUP): Policy C - Option B, 2004, 32 (Database issue), pp.D315-8. <10.1093/nar/gkh091>. <inria-00407519>
  • 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 (OUP): Policy C - Option B, 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 (OUP): Policy C - Option B, 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>

Communication dans un congrès39 documents

  • Witold Dyrka, Pascal Durrens, Mathieu Paoletti, Sven Saupe, David Sherman. Deciphering the language of fungal pathogen recognition receptors. 8th Symposium of the Polish Bioinformatics Society, Sep 2015, Lublin, Poland. <http://ptbi.org.pl/zjazd2015/>. <hal-01203357>
  • David James Sherman. Diversity and Domestication in Oenological Yeasts. Moscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia. 2015, Седьмая Московская международная конференция по вычислительной молекулярной биологии МССМВ'15. <http://mccmb.belozersky.msu.ru/2015/index.html>. <hal-01212044>
  • Anna Zhukova, David James Sherman. Knowledge-based zooming for metabolic models. JOBIM, Jul 2013, Toulouse, France. 2013. <hal-00859437>
  • Anna Zhukova, David James Sherman. Knowledge-based generalization of metabolic networks: An applicational study. Moscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia. 2013. <hal-00859440>
  • 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. 2013. <hal-00867373>
  • David James Sherman. Taming the complexity of 'n-ary' relations in comparative genomics. Mark Borodovsky. 9th International Conference on Genome Biology and Bioinformatics, Nov 2013, Atlanta, Georgia, United States. 2013. <hal-00938262>
  • 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. 2012. <hal-00686072>
  • 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. 2011. <hal-00653518>
  • 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.. Univ. Bordeaux Segalen (P. Darriet, L. Geny, P. Lucas, A. Lonvaud, G. de Revel, P.L. Teissedre). Oeno2011- 9e symposium international d'oenologie de Bordeaux: Actes de colloques du 9e symposium international d'oenologie de Bordeaux, Jun 2011, Bordeaux, France. Dunod, Paris, pp.358-363, 2012. <hal-00646867>
  • Natalia Golenetskaya, David James Sherman. Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style. SeqBio 2011, Dec 2011, Lille, France. 2011. <hal-00654797>
  • David James Sherman, Natalia Golenetskaya. Addressing scaling-out challenges for comparative genomics. Moscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia. 2011. <hal-00649189>
  • Rodrigo Assar, Alice Garcia, David James Sherman. Modeling Stochastic Switched Systems with BioRica. Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Jun 2011, Paris, France. pp.297--304, 2011, Actes Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011. <inria-00617419>
  • 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, Oct 2011, San Feliu de Guixols, Spain. 2011. <hal-00652903>
  • David James Sherman, Nicolás Loira, Natalia Golenetskaya. High-performance comparative annotation. Makeev, Vsevolod and Kucherov, Gregory. Bioinformatics after next-generation sequencing, Jun 2010, Zvenigorod, Russia. 2010, inria. <inria-00563533>
  • David James Sherman. Methods for understanding function and history in small eukaryote genomes. Mireille Régnier. Colloquium LIX, Nov 2010, Palaiseau, France. 2010, inria. <inria-00563529>
  • David James Sherman. Two examples of evolutionary algorithms in reconstructing genome evolution. Workshop on Evolutionary Algorithms - Challenges in Theory and Practice, Mar 2010, Bordeaux, France. 2010, inria. <inria-00563519>
  • 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. 2010. <inria-00524386>
  • Rodrigo Assar, Felipe Vargas, David James Sherman. Reconciling competing models: a case study of wine fermentation kinetics. Katsuhisa Horimoto and Masahiko Nakatsui and Nikolaj Popov. Algebraic and Numeric Biology 2010, Jul 2010, Hagenberg, Austria. Springer, 6479, pp.68--83, 2012, Lecture Notes in Computer Science; Algebraic and Numeric Biology. <http://www.springerlink.com/content/566804w0vg708g67/>. <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, Oct 2010, Edinburgh, United Kingdom. 2010. <hal-00652922>
  • Nikolay Vyahhi, Adrien Goëffon, David James Sherman, Macha Nikolski. Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios. Franz Rothlauf. ACM SIGEVO Conference on Genetic and evolutionary computation, 2009, Montréal, Canada. ACM, 2009. <inria-00407508>
  • Rodrigo Assar, Hayssam Soueidan, David James Sherman. Hierarchical study of Guyton Circulatory Model. Eric Rivals, Irena Rusu. Les Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2009, Jun 2009, Nantes, France. Eric Rivals, Irena Rusu, 2009. <inria-00404135>
  • 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. 2009. <inria-00409534>
  • 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, Oct 2009, San Feliu de Guixols, Spain. 2009. <inria-00524390>
  • Tiphaine Martin, David James Sherman, Macha Nikolski, Jean-Luc Souciet, Pascal Durrens. Base de données Génolevures : génomique comparative des Hemiascomycetes. Eric Rivals and Irena Rusu. Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182, 2009. <inria-00401915>
  • 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. 2008. <inria-00407631>
  • David James Sherman. Genomic Exploration of the Hemiascomycetous Yeasts. 3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia. 2008. <inria-00350570>
  • 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. ACM, pp.315-322, 2008. <hal-00341672>
  • Hayssam Soueidan, David James Sherman, Macha Nikolski. BioRica: A multi model description and simulation system. F0SBE, 2007, Germany. pp.279-287, 2007. <hal-00306550>
  • 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, 2007. <inria-00350567>
  • 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, 2007. <inria-00352592>
  • 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. Wiley, 24-S1, pp.S132, 2007, Yeast. <inria-00402220>
  • Tiphaine Martin, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, Florian Iragne, et al.. The Génolevures online database. J.Micheal Cherry and Ian G. Macreadie. XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. 24, pp.S135, 2007, Number S1; Yeast. <inria-00401921>
  • David James Sherman. Bases de données et fouille de données chez les levures hémiascomycètes. Conférence FungEffector, May 2007, Bordeaux, France. 2007. <inria-00352600>
  • David James Sherman. The Génolevures database. Yeast Genome 10th Anniversary, Sep 2006, Brussels, Belgium. 2006. <inria-00407495>
  • David James Sherman. Mining the Hemiascomycete Yeasts. Yeast Systems Biology 1st Workshop, Nov 2006, Vienna, Austria. 2006. <inria-00407492>
  • Emmanuelle Beyne, Jean-Paul Lasserre, Stéphane Claverol, David James Sherman, Marc Bonneu. A whole-cell proteomics approach for comparing hemiascomycete yeast genomes. Jean-Luc Souciet and Teun Boekhout. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain. 2005. <inria-00407503>
  • David James Sherman. Génolevures complete genomes provide data and tools for com- parative genomics of hemiascomycetous yeasts. Jean-Luc Souciet and Teun Boekhout. ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain. 2005. <inria-00407502>
  • 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, 2004. <hal-00307645>
  • David James Sherman, Nicolas Magnier. Factotum: Automatic and systematic sharing support for systems analyzers. Springer-Verlag. Tools and Algorithms for the Construction and Analysis of Systems (TACAS'98), Mar 1998, Lisbon, Portugal. 1384, 1998, LNCS. <inria-00334475>

Pré-publication, Document de travail1 document

  • Witold Dyrka, Pascal Durrens, Mathieu Paoletti, Sven J Saupe, David J Sherman. Deciphering the language of fungal pathogen recognition receptors. 2014. <hal-01083421>

Poster5 documents

  • 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, <http://troll.cent.uw.edu.pl/embo_ysf2015/index.html>. <hal-01171745>
  • Anna Zhukova, David James Sherman. Three-level representation of metabolic networks. Journées EDMI, Nov 2014, LaBRI, 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, European Bioinformatics Institute, Cambridge, United Kingdom. 2012. <hal-00867375>
  • 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>
  • 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>

Autre publication2 documents

  • David James Sherman, Natalia Golenetskaya. Databases and Ontologies for Affinity Binders. Overview of advances in defining ontologies and building knowledge bases for affinity binders, ov.. 2010. <inria-00563531>
  • David James Sherman. Protein Families in Yeasts. Invited seminar at Georgetown University. 2006. <inria-00407493>