David James Sherman

Publication Activity (10 Years)

Years Active: 1998-2015
Publications (10 Years): 0

Top Topics

Machine Learning Algorithms

Statistical Model

Computational Models

Metabolic Networks

Top Venues

BMC Syst. Biol.

J. Bioinform. Comput. Biol.

J. Comput. Biol.

Publications

Anna Zhukova, David James Sherman
Mimoza: web-based semantic zooming and navigation in metabolic networks. BMC Syst. Biol. 9 (2015)
Nicolás Loira, Anna Zhukova, David James Sherman
Pantograph: A template-based method for genome-scale metabolic model reconstruction. J. Bioinform. Comput. Biol. 13 (2) (2015)
Anna Zhukova, David James Sherman
Knowledge-based Generalization of Metabolic Models. J. Comput. Biol. 21 (7) (2014)
Anna Zhukova, David James Sherman
Knowledge-based generalization of metabolic networks: A practical study. J. Bioinform. Comput. Biol. 12 (2) (2014)
Nicolás Loira, Thierry Dulermo, Jean-Marc Nicaud, David James Sherman
A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst. Biol. 6 (2012)
Macha Nikolski, David James Sherman
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 25 (17) (2009)
Géraldine Jean, David James Sherman, Macha Nikolski
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. J. Comput. Biol. 16 (9) (2009)
Nikolay Vyahhi, Adrien Goëffon, Macha Nikolski, David James Sherman
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios. GECCO (2009)
David James Sherman, Tiphaine C. Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, Pascal Durrens
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Pascal Durrens, Macha Nikolski, David James Sherman
Fusion and Fission of Genes Define a Metric between Fungal Genomes. PLoS Comput. Biol. 4 (10) (2008)
Adrien Goëffon, Macha Nikolski, David James Sherman
An efficient probabilistic population-based descent for the median genome problem. GECCO (2008)
Macha Nikolski, David James Sherman
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 23 (2) (2007)
David James Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res. 34 (Database-Issue) (2006)
Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman
ProViz: protein interaction visualization and exploration. Bioinform. 21 (2) (2005)
Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler
IntAct: an open source molecular interaction database. Nucleic Acids Res. 32 (Database-Issue) (2004)
David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res. 32 (Database-Issue) (2004)
David James Sherman, Nicolas Magnier
Factotum: Automatic and Systematic Sharing Support for Systems Analyzers. TACAS (1998)
Macha Nikolskaïa, Antoine Rauzy, David James Sherman
Almana: A BDD Minimization Tool Integrating Heuristic and Rewriting Methods. FMCAD (1998)