David James Sherman

114
Documents

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

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Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling

Maxime Lecomte , Wenfan Cao , Julie Aubert , David James Sherman , Hélène Falentin et al.

Metabolic Engineering, 2024, 83, pp.24 - 38. ⟨10.1016/j.ymben.2024.02.014⟩

Article dans une revue hal-04509395v1
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Community-scale models of microbiomes: articulating metabolic modelling and metagenome sequencing

Klara Cerk , Pablo Ugalde-Salas , Chabname Ghassemi Nedjad , Maxime Lecomte , Coralie Muller et al.

Microbial Biotechnology, 2024, ⟨10.1111/1751-7915.14396⟩

Article dans une revue hal-04409251v1
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The functional microbiome of grapevine throughout plant evolutionary history and lifetime

Paola Fournier , Lucile Pellan , Didac Barroso-Bergadà , David Bohan , Thierry Candresse et 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
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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 Sherman et al.

Yeast, 2018, 35 (1), pp.141-156. ⟨10.1002/yea.3248⟩

Article dans une revue hal-01585808v1
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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 Dutilh et al.

OENO One, 2017, 51 (3), pp.309 - 322. ⟨10.20870/oeno-one.2017.51.4.1861⟩

Article dans une revue hal-01666981v1
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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
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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 Biasioli et 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

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
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The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Gotthard Kunze , Claude Gaillardin , Małgorzata Czernicka , Pascal Durrens , Tiphaine Martin et al.

Biotechnology for Biofuels, 2014, 7 (1), pp.66. ⟨10.1186/1754-6834-7-66⟩

Article dans une revue pasteur-00988609v1
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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 Sherman et al.

PLoS ONE, 2014, 9 (1), pp.e86298. ⟨10.1371/journal.pone.0086298⟩

Article dans une revue hal-00986680v1

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum.

Pedro Almeida , Carla Gonçalves , Sara Teixeira , Diego Libkind , Martin Bontrager et al.

Nature Communications, 2014, 5, pp.4044. ⟨10.1038/ncomms5044⟩

Article dans une revue hal-01002466v1
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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
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Diversity and variability of NOD-like receptors in fungi

Witold Dyrka , Marina Lamacchia , Pascal Durrens , Bostjan Kobe , Asen Daskalov et al.

Genome Biology and Evolution, 2014, in press. ⟨10.1093/gbe/evu251⟩

Article dans une revue hal-01083450v1
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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
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Draft genome sequence of <em>Rhodosporidium toruloides</em> CECT1137, an oleaginous yeast of biotechnological interest

Nicolas Morin , Xavier Calcas , Hugo Devillers , Pascal Durrens , David James Sherman et al.

Genome Announcements, 2014, 2 (4), ⟨10.1128/genomeA.00641-14⟩

Article dans une revue hal-02635833v1

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 Sherman et 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

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 Montecino et al.

BioSystems, 2012, 108 (1-3), pp.63-72. ⟨10.1016/j.biosystems.2012.01.008⟩

Article dans une revue hal-00681022v1
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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

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 Mei et al.

Chemical Geology, 2012, 334, pp.345-363. ⟨10.1016/j.chemgeo.2012.10.010⟩

Article dans une revue istex hal-00761072v1

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
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A community standard format for the representation of protein affinity reagents.

David E Gloriam , Sandra Orchard , Daniela Bertinetti , Erik Björling , Erik Bongcam-Rudloff et 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 Daruvar et al.

Nature Biotechnology, 2010, 28 (7), pp.650-3. ⟨10.1038/nbt0710-650⟩

Article dans une revue inria-00544750v1

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 Pitkänen et al.

Nature Communications, 2010, 1 (9), pp.145. ⟨10.1038/ncomms1150⟩

Article dans une revue inria-00562005v1

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
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Comparative genomics of protoploid Saccharomycetaceae

Jean-Luc Souciet , Bernard Dujon , Claude Gaillardin , Mark Johnston , Philippe V Baret et al.

Genome Research, 2009, 19, pp.1696-1709. ⟨10.1101/gr.091546.109⟩

Article dans une revue inria-00407511v1
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Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

David James Sherman , Tiphaine Martin , Macha Nikolski , Cyril Cayla , Jean-Luc Souciet et al.

Nucleic Acids Research, 2009, 37, pp.D550-D554. ⟨10.1093/nar/gkn859⟩

Article dans une revue hal-04943449v1

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
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Unusual composition of a yeast chromosome arm is associated with its delayed replication.

Célia Payen , Gilles Fischer , Christian Marck , Caroline Proux , David James Sherman et 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 Quinn et 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 Cahill et 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 Nikolski et 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 Casaregola et 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

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale

Roland Barriot , Jerome Poix , Alexis Groppi , Aurélien Barré , Nicolas Goffard et al.

Nucleic Acids Research, 2004, 32 (12), pp.3581-9. ⟨10.1093/nar/gkh681⟩

Article dans une revue inria-00202722v1

IntAct: an open source molecular interaction database

Henning Hermjakob , Luisa Montecchi-Palazzi , Sugath Mudali , Samuel Kerrien , Sandra Orchard et al.

Nucleic Acids Research, 2004, 32, pp.D452--5

Article dans une revue hal-00306577v1

Novel Transporters from Hemiascomycete Yeasts

Benoît de Hertogh , Emmanuel Talla , Fredj Tekaia , Emmanuelle Beyne , David James Sherman et 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
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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
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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 Maillard et al.

FOODMICRO 2022, Aug 2022, Athènes, Greece

Communication dans un congrès hal-03781287v1
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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.

Wenfan Cao , Maxime Lecomte , Solène Le Fur , Julie J. Aubert , Marie-Bernadette Maillard et 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
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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
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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
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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

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
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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

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

Knowledge-based zooming for metabolic models

Anna Zhukova , David James Sherman

JOBIM, Jul 2013, Toulouse, France

Communication dans un congrès hal-00859437v1

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 Sherman et 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

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
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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

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
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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

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

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

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

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
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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

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

The Génolevures website is designed around comparative genomic studies of hemiascomycetous yeasts

Tiphaine Martin , Pascal Durrens , Emmanuelle Beyne , Macha Nikolski , Florian Iragne et 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
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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

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

The Génolevures online database

Tiphaine Martin , Pascal Durrens , Emmanuelle Beyne , Macha Nikolski , Florian Iragne et al.

XXIIIrd International Conference on Yeast Genetics and Molecular Biology, Jul 2007, Melbourne, Australia. pp.S135

Communication dans un congrès inria-00401921v1

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

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

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

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 Goffard et 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
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Enhancing Microbial Genome Reconstruction in Complex Environments by combining Short-and Long-read Sequencing

Carole Belliardo , Arthur Péré , Alain Franc , Jean-Marc Frigerio , Nicolas Maurice et al.

2025 - Journées scientifiques Agroécologie et Numérique, Jan 2025, Dijon, France. , pp.1-1, 2025

Poster de conférence hal-04920790v1
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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 Vicedomini et al.

Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024

Poster de conférence hal-04423917v1
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Dynamic Flux Balance Analysis with Metamodels

Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou et al.

JOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France.

Poster de conférence hal-04236775v1
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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

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

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
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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

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 Bely et 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
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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
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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
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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