
David James Sherman
112
Documents
Presentation
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
Publications
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Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025
Conference poster
hal-04920790
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Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencingJournées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024
Conference poster
hal-04423917
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Dynamic Flux Balance Analysis with MetamodelsJOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France.
Conference poster
hal-04236775
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Characterising competition and cooperation potentials in microbial communities using discrete models of metabolism. An exploratory analysisJOBIM 2022 - JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES, Jul 2022, Rennes, France
Conference poster
hal-03839337
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Dynamic Flux Balance Analysis with MetamodelsMicrobial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom.
Conference poster
hal-04252041
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Modelling metabolic network dynamics in a cheese bacterial communityCMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France
Conference poster
hal-03533795
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Modelling metabolic network dynamics in a cheese bacterial communityMPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States
Conference poster
hal-03533786
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Modelling metabolic network dynamics in a cheese bacterial communityJOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Conference poster
hal-03533781
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Deciphering the language of fungal pathogen recognition receptorsEMBO Young Scientists Forum 2015, Jul 2015, Warsaw, Poland. , 2015
Conference poster
hal-01171745
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Identification by QTL mapping of new genes and their allelic forms conferring robustness to environmental variations in wine fermentation27. 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-02742176
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Three-level representation of metabolic networksJournées EDMI, Nov 2014, Bordeaux, France
Conference poster
hal-01081711
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Biological Knowledge, Problem Detecting, Model Refinement and DiagnosticsEMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology 2012, Apr 2012, Cambridge, United Kingdom. 2012
Conference poster
hal-00867375
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Mixed-formalism hierarchical modeling and simulation with BioRica11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446
Conference poster
inria-00529669
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Reconstruction and validation of the genome-scale metabolic model of Yarrowia lipolytica iNL750Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'10), Sep 2010, Montpellier, France. 2010
Conference poster
hal-00652929
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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling2023
Preprints, Working Papers, ...
hal-04088301
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Deciphering the language of fungal pathogen recognition receptors2014
Preprints, Working Papers, ...
hal-01083421
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Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese.FOODMICRO 2022, Aug 2022, Athènes, Greece
Conference papers
hal-03781287
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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
Conference papers
hal-03694338
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Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communitiesJournée GT Bioss 2022, Nov 2022, Nantes, France
Conference papers
hal-03857781
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Characterizing microbial interactions in controlled and natural microbial communitiesWorkshop SymBioDiversity, May 2022, Santiago, Chile
Conference papers
hal-03857848
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Metabolic modelling deciphers interactions in a cheese bacterial communityMetaboday 2021, Mar 2021, Bordeaux, France
Conference papers
hal-03531761
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Diversity and Domestication in Oenological YeastsMoscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia
Conference papers
hal-01212044
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Deciphering the language of fungal pathogen recognition receptors8th Symposium of the Polish Bioinformatics Society, Polish Bioinformatics Society, Sep 2015, Lublin, Poland
Conference papers
hal-01203357
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Knowledge-based generalization of metabolic networks: An applicational studyMoscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia
Conference papers
hal-00859440
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Taming the complexity of 'n-ary' relations in comparative genomics9th International Conference on Genome Biology and Bioinformatics, Georgia Tech and Emory University, Nov 2013, Atlanta, Georgia, United States
Conference papers
hal-00938262
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Knowledge-based zooming for metabolic modelsJOBIM, Jul 2013, Toulouse, France
Conference papers
hal-00859437
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What is the optimal representation of a generalized metabolic model using SBML and SBGN?COMBINE 2013, Sep 2013, Paris, France
Conference papers
hal-00867373
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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
Conference papers
hal-00646867
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Reconciling competing models: a case study of wine fermentation kineticsAlgebraic 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-00541215
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Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid SystemsXII Latin American Congress of Probability and Mathematical Statistics, Mar 2012, Viña del Mar, Chile
Conference papers
hal-00686072
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Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce styleSeqBio 2011, Dec 2011, Lille, France
Conference papers
hal-00654797
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Comparative annotation and scaling-out challenges for paraphyletic strategiesEMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Understanding the Complexity of Diversity, EMBO, Oct 2011, San Feliu de Guixols, Spain
Conference papers
hal-00652903
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Addressing scaling-out challenges for comparative genomicsMoscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia
Conference papers
hal-00649189
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Modeling Stochastic Switched Systems with BioRicaJournées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Institut Pasteur, Jun 2011, Paris, France. pp.297--304
Conference papers
inria-00617419
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Assessing ''last mile'' tools for affinity binder databases5th ESF Workshop on Affinity Proteomics: Ligand Binders against the Human Proteome, Mar 2011, Alpbach, Austria
Conference papers
hal-00653518
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High-performance comparative annotationBioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia
Conference papers
inria-00563533
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Methods for understanding function and history in small eukaryote genomesColloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France
Conference papers
inria-00563529
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Two examples of evolutionary algorithms in reconstructing genome evolutionWorkshop on Evolutionary Algorithms - Challenges in Theory and Practice, INRIA Bordeaux Sud-Ouest, Mar 2010, Bordeaux, France
Conference papers
inria-00563519
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Génolevures, knowledge base and annotation of hemiascomycete yeast genomesJournée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, Sep 2010, Montpellier, France
Conference papers
inria-00524386
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Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica11th International Conference on Systems Biology, ICSB, Oct 2010, Edinburgh, United Kingdom
Conference papers
hal-00652922
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Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement ScenariosACM SIGEVO Conference on Genetic and evolutionary computation, ACM SIGEVO, 2009, Montréal, Canada
Conference papers
inria-00407508
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Base de données Génolevures : génomique comparative des HemiascomycetesJournée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182
Conference papers
inria-00401915
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Hierarchical study of Guyton Circulatory ModelJOBIM 2009 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France
Conference papers
inria-00404135
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The Génolevures online databaseSecond German/ French/European/ Meeting Yeast and Filamentous Fungi, May 2009, Strasbourg, France
Conference papers
inria-00409534
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The Génolevures website comparative genomic studies on hemiascomycetous yeastsComparative Genomics of Eukaryotic Microorganisms 2009, EMBL-EMBO, Oct 2009, San Feliu de Guixols, Spain
Conference papers
inria-00524390
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The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeastsFirst German/French/European/ Meeting Yeast and Filamentous Fungi, May 2008, Strasbourg, France
Conference papers
inria-00407631
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Genomic Exploration of the Hemiascomycetous Yeasts3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia
Conference papers
inria-00350570
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An Efficient Probabilistic Population-Based Descent for the Median Genome ProblemGECCO: Genetic And Evolutionary Computation Conference, Aug 2008, Atlanta, United States. pp.315-322
Conference papers
hal-00341672
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The Génolevures online databaseXXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135
Conference papers
inria-00401921
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Gene Fusion and Fission Events in Fungal GenomesXXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S132
Conference papers
inria-00352592
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BioRica: A multi model description and simulation systemF0SBE, 2007, Germany. pp.279-287
Conference papers
hal-00306550
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Reconstruction and visualization of genome rearrangements within the KuyveromycesESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Oct 2007, San Feliu de Guixols, Spain. pp.44
Conference papers
inria-00350567
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Bases de données et fouille de données chez les levures hémiascomycètesConférence FungEffector, May 2007, Bordeaux, France
Conference papers
inria-00352600
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Gene fusion and fission events in fungus genomes23rd international conference on yeast genetics and molecular biology, Jul 2007, Melbourne, Australia. pp.S132
Conference papers
inria-00402220
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The Génolevures databaseYeast Genome 10th Anniversary, Académie Royale des Sciences, des Letters et des Beaux-Arts de Belgique, Sep 2006, Brussels, Belgium
Conference papers
inria-00407495
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Mining the Hemiascomycete YeastsYeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria
Conference papers
inria-00407492
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Génolevures complete genomes provide data and tools for com- parative genomics of hemiascomycetous yeastsESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain
Conference papers
inria-00407502
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A whole-cell proteomics approach for comparing hemiascomycete yeast genomesESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms, Nov 2005, Sant Feliu de Guixols, Spain
Conference papers
inria-00407503
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New strategy for the representation and the integration of biomolecular knowledge at a cellular scaleActes des 5ème Journées Ouvertes Biologie Informatique Mathématiques à Montréal (Canada), 2004, Canada. pp.3581-3589
Conference papers
hal-00307645
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Factotum: Automatic and systematic sharing support for systems analyzersTools and Algorithms for the Construction and Analysis of Systems (TACAS'98), Mar 1998, Lisbon, Portugal
Conference papers
inria-00334475
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Deriving Gene Associations for Metabolic Models[Research Report] RR-9246, Inria Bordeaux Sud-Ouest. 2018
Reports
(Research report)
hal-01976744
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Databases and Ontologies for Affinity Binders2010
Other publications
inria-00563531
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Protein Families in Yeasts2006
Other publications
inria-00407493
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