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
Publications
|
|
Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling 6 may 2025 / Modélisation du microbiomeNEM 2025 - Journées Nutrition & Ecologie Microbienne, workshop modélisation du microbiome, May 2025, Rennes (Distanciel), France |
|
|
Metatranscriptomics and metabolic modeling to identify bacterial metabolic interactions during the manufacture of a model pressed cheese.FOODMICRO 2022, Aug 2022, Athènes, Greece |
|
|
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 |
|
|
Characterizing microbial interactions in controlled and natural microbial communitiesWorkshop SymBioDiversity, May 2022, Santiago, Chile |
|
|
Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communitiesJournée GT Bioss 2022, Nov 2022, Nantes, France |
Metabolic modelling deciphers interactions in a cheese bacterial communityMetaboday 2021, Mar 2021, Bordeaux, France |
|
Diversity and Domestication in Oenological YeastsMoscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia |
|
|
|
Deciphering the language of fungal pathogen recognition receptors8th Symposium of the Polish Bioinformatics Society, Polish Bioinformatics Society, Sep 2015, Lublin, Poland |
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 |
|
|
|
Knowledge-based generalization of metabolic networks: An applicational studyMoscow Conference on Computational Molecular Biology, Jul 2013, Moscow, Russia |
What is the optimal representation of a generalized metabolic model using SBML and SBGN?COMBINE 2013, Sep 2013, Paris, France |
|
Knowledge-based zooming for metabolic modelsJOBIM, Jul 2013, Toulouse, France |
|
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 |
|
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 |
|
|
|
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⟩ |
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 |
|
Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce styleSeqBio 2011, Dec 2011, Lille, France |
|
Addressing scaling-out challenges for comparative genomicsMoscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia |
|
|
|
Modeling Stochastic Switched Systems with BioRicaJournées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Institut Pasteur, Jun 2011, Paris, France. pp.297--304 |
Assessing ''last mile'' tools for affinity binder databases5th ESF Workshop on Affinity Proteomics: Ligand Binders against the Human Proteome, Mar 2011, Alpbach, Austria |
|
High-performance comparative annotationBioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia |
|
Methods for understanding function and history in small eukaryote genomesColloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France |
|
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 |
|
Génolevures, knowledge base and annotation of hemiascomycete yeast genomesJournée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, Sep 2010, Montpellier, France |
|
Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica11th International Conference on Systems Biology, ICSB, Oct 2010, Edinburgh, United Kingdom |
|
Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement ScenariosACM SIGEVO Conference on Genetic and evolutionary computation, ACM SIGEVO, 2009, Montréal, Canada |
|
Base de données Génolevures : génomique comparative des HemiascomycetesJournée Ouvertes Biologie Informatique Mathématiques, JOBIM 2009, Jun 2009, Nantes, France. pp.181-182 |
|
|
|
Hierarchical study of Guyton Circulatory ModelJOBIM 2009 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2009, Nantes, France |
The Génolevures website comparative genomic studies on hemiascomycetous yeastsComparative Genomics of Eukaryotic Microorganisms 2009, EMBL-EMBO, Oct 2009, San Feliu de Guixols, Spain |
|
The Génolevures online databaseSecond German/ French/European/ Meeting Yeast and Filamentous Fungi, May 2009, Strasbourg, France |
|
The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeastsFirst German/French/European/ Meeting Yeast and Filamentous Fungi, May 2008, Strasbourg, France |
|
Genomic Exploration of the Hemiascomycetous Yeasts3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia |
|
|
|
An Efficient Probabilistic Population-Based Descent for the Median Genome ProblemGECCO: Genetic And Evolutionary Computation Conference, Aug 2008, Atlanta, United States. pp.315-322 |
BioRica: A multi model description and simulation systemF0SBE, 2007, Germany. pp.279-287 |
|
Gene Fusion and Fission Events in Fungal GenomesXXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S132 |
|
The Génolevures online databaseXXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135 |
|
Bases de données et fouille de données chez les levures hémiascomycètesConférence FungEffector, May 2007, Bordeaux, France |
|
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 |
|
Gene fusion and fission events in fungus genomes23rd international conference on yeast genetics and molecular biology, Jul 2007, Melbourne, Australia. pp.S132 |
|
Mining the Hemiascomycete YeastsYeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria |
|
The Génolevures databaseYeast Genome 10th Anniversary, Académie Royale des Sciences, des Letters et des Beaux-Arts de Belgique, Sep 2006, Brussels, Belgium |
|
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 |
|
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 |
|
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 |
|
Factotum: Automatic and systematic sharing support for systems analyzersTools and Algorithms for the Construction and Analysis of Systems (TACAS'98), Mar 1998, Lisbon, Portugal |
|
|
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 |
|
|
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 |
|
|
Dynamic Flux Balance Analysis with MetamodelsJOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. |
|
|
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 |
Modelling metabolic network dynamics in a cheese bacterial communityCMSB, The 19th conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France |
|
Modelling metabolic network dynamics in a cheese bacterial communityMPA, Metabolic Pathway Analysis, Aug 2021, Knoxville, United States |
|
Modelling metabolic network dynamics in a cheese bacterial communityJOBIM,Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France |
|
|
|
Deciphering the language of fungal pathogen recognition receptorsEMBO Young Scientists Forum 2015, Jul 2015, Warsaw, Poland. , 2015 |
|
|
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⟩ |
|
|
Three-level representation of metabolic networksJournées EDMI, Nov 2014, Bordeaux, France |
Biological Knowledge, Problem Detecting, Model Refinement and DiagnosticsEMBL-EBI-Wellcome Trust workshop on In Silico Systems Biology 2012, Apr 2012, Cambridge, United Kingdom. 2012 |
|
|
|
Mixed-formalism hierarchical modeling and simulation with BioRica11th International Conference on Systems Biology, Oct 2010, Edimbourg, United Kingdom. pp.P02.446 |
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 |
Databases and Ontologies for Affinity Binders2010 |
|
Protein Families in Yeasts2006 |
|
|
Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics2025 |
|
|
Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling2023 |
|
|
Deciphering the language of fungal pathogen recognition receptors2014 |
|
|
Deriving Gene Associations for Metabolic Models[Research Report] RR-9246, Inria Bordeaux Sud-Ouest. 2018 |