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 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
Conference poster hal-04920790 v1
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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
Conference poster hal-04423917 v1
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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.
Conference poster hal-04236775 v1
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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
Conference poster hal-03839337 v1
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Dynamic Flux Balance Analysis with Metamodels

Clémence Frioux , Sylvie Huet , Simon Labarthe , Julien Martinelli , Thibault Malou et al.
Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom.
Conference poster hal-04252041 v1

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
Conference poster hal-03533795 v1

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
Conference poster hal-03533786 v1

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
Conference poster hal-03533781 v1
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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
Conference poster hal-01171745 v1

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⟩
Conference poster hal-02742176 v1
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Three-level representation of metabolic networks

Anna Zhukova , David James Sherman
Journées EDMI, Nov 2014, Bordeaux, France
Conference poster hal-01081711 v1

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
Conference poster hal-00867375 v1
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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
Conference poster inria-00529669 v1

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
Conference poster hal-00652929 v1
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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⟩
Journal articles hal-04509395 v1
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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⟩
Journal articles hal-04409251 v1
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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⟩
Journal articles (Review article) hal-03858395 v1
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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⟩
Journal articles hal-01585808 v1
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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⟩
Journal articles hal-01666981 v1
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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⟩
Journal articles hal-01123715 v1
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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⟩
Journal articles hal-01202801 v1

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⟩
Journal articles hal-01123733 v1

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⟩
Journal articles hal-01002987 v1
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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⟩
Journal articles hal-00986680 v1
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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⟩
Journal articles pasteur-00988609 v1

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⟩
Journal articles hal-01002466 v1
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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⟩
Journal articles hal-00906911 v1
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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⟩
Journal articles hal-01083450 v1
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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⟩
Journal articles hal-00925881 v1
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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⟩
Journal articles hal-02635833 v1

Implementing biological hybrid systems: Allowing composition and avoiding stiffness

Rodrigo Assar , David James Sherman
Applied Mathematics and Computation, 2013
Journal articles hal-00853997 v1

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⟩
Journal articles hal-00863284 v1

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⟩
Journal articles istex hal-00681022 v1
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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⟩
Journal articles hal-00784406 v1

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⟩
Journal articles istex hal-00761072 v1

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⟩
Journal articles inria-00539200 v1

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⟩
Journal articles inria-00544750 v1
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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⟩
Journal articles inria-00544751 v1

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⟩
Journal articles inria-00562005 v1

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⟩
Journal articles istex inria-00407505 v1
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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⟩
Journal articles inria-00407511 v1
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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⟩
Journal articles hal-04943449 v1

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⟩
Journal articles inria-00414692 v1
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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⟩
Journal articles inria-00407518 v1

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⟩
Journal articles inria-00202723 v1

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
Journal articles hal-00407512 v1

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⟩
Journal articles inria-00341569 v1

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
Journal articles hal-00306554 v1

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⟩
Journal articles hal-00306585 v1

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⟩
Journal articles inria-00202434 v1

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⟩
Journal articles inria-00202721 v1

Extrapolation of metabolic pathways as an aid to modelling completely sequenced

Florian Iragne , Macha Nikolski , David Sherman
FEMS Yeast Research, 2007, pp.132-139
Journal articles hal-00306592 v1

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⟩
Journal articles hal-00118142 v1

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⟩
Journal articles inria-00202436 v1

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⟩
Journal articles inria-00202435 v1

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⟩
Journal articles istex hal-00104411 v1

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⟩
Journal articles inria-00407519 v1

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
Journal articles hal-00306577 v1

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⟩
Journal articles inria-00202722 v1

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⟩
Journal articles inria-00202437 v1

Squeezing Intermediate Construction in Equational Programs

Alain Miniussi , David James Sherman
Lecture Notes in Computer Science, 1996, 1110, pp.284 -302
Journal articles hal-00389564 v1

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
Journal articles hal-00389567 v1
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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
Conference papers hal-03781287 v1
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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
Conference papers hal-03694338 v1
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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
Conference papers hal-03857781 v1
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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
Conference papers hal-03857848 v2

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
Conference papers hal-03531761 v1

Diversity and Domestication in Oenological Yeasts

David James Sherman
Moscow Conference on Computational and Molecular Biology (MCCMB'15), Jul 2015, Moscow, Russia
Conference papers hal-01212044 v1
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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
Conference papers hal-01203357 v1
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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
Conference papers hal-00859440 v1

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
Conference papers hal-00938262 v1

Knowledge-based zooming for metabolic models

Anna Zhukova , David James Sherman
JOBIM, Jul 2013, Toulouse, France
Conference papers hal-00859437 v1

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
Conference papers hal-00867373 v1

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
Conference papers hal-00646867 v1
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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⟩
Conference papers inria-00541215 v1

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
Conference papers hal-00686072 v1

Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style

Natalia Golenetskaya , David James Sherman
SeqBio 2011, Dec 2011, Lille, France
Conference papers hal-00654797 v1

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
Conference papers hal-00652903 v1

Addressing scaling-out challenges for comparative genomics

David James Sherman , Natalia Golenetskaya
Moscow Conference on Computational Molecular Biology, Jul 2011, Moscow, Russia
Conference papers hal-00649189 v1
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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
Conference papers inria-00617419 v1

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
Conference papers hal-00653518 v1

High-performance comparative annotation

David James Sherman , Nicolás Loira , Natalia Golenetskaya
Bioinformatics after next-generation sequencing, Russian Academy of Sciences, Jun 2010, Zvenigorod, Russia
Conference papers inria-00563533 v1

Methods for understanding function and history in small eukaryote genomes

David James Sherman
Colloquium LIX, École Polytechnique, Nov 2010, Palaiseau, France
Conference papers inria-00563529 v1

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
Conference papers inria-00563519 v1

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
Conference papers inria-00524386 v1

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
Conference papers hal-00652922 v1

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
Conference papers inria-00407508 v1

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
Conference papers inria-00401915 v1
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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
Conference papers inria-00404135 v1

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
Conference papers inria-00409534 v1

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
Conference papers inria-00524390 v1

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
Conference papers inria-00407631 v1

Genomic Exploration of the Hemiascomycetous Yeasts

David James Sherman
3rd Workshop on Algorithms in bioinformatics, Oct 2008, Moscow, Russia
Conference papers inria-00350570 v1
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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
Conference papers hal-00341672 v1

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
Conference papers inria-00401921 v1

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
Conference papers inria-00352592 v1

BioRica: A multi model description and simulation system

Hayssam Soueidan , David James Sherman , Macha Nikolski
F0SBE, 2007, Germany. pp.279-287
Conference papers hal-00306550 v1

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
Conference papers inria-00350567 v1

Bases de données et fouille de données chez les levures hémiascomycètes

David James Sherman
Conférence FungEffector, May 2007, Bordeaux, France
Conference papers inria-00352600 v1

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
Conference papers inria-00402220 v1

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
Conference papers inria-00407495 v1

Mining the Hemiascomycete Yeasts

David James Sherman
Yeast Systems Biology 1st Workshop, Karl Küchler, Nov 2006, Vienna, Austria
Conference papers inria-00407492 v1

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
Conference papers inria-00407502 v1

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
Conference papers inria-00407503 v1

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
Conference papers hal-00307645 v1

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
Conference papers inria-00334475 v1
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Deriving Gene Associations for Metabolic Models

Razanne Issa , David James Sherman
[Research Report] RR-9246, Inria Bordeaux Sud-Ouest. 2018
Reports (Research report) hal-01976744 v1