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ORCIDDavid J. Sherman
Person information
- affiliation: University of Bordeaux 1, LABRI, France
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Journal Articles
- 2015
[j18]Anna Zhukova, David James Sherman
:
Mimoza: web-based semantic zooming and navigation in metabolic networks. BMC Syst. Biol. 9: 10 (2015)- [j17]Nicolás Loira, Anna Zhukova, David James Sherman:
Pantograph: A template-based method for genome-scale metabolic model reconstruction. J. Bioinform. Comput. Biol. 13(2): 1550006:1-1550006:19 (2015) - 2014
- [j16]Rodrigo Assar, Martín A. Montecino, Alejandro Maass, David J. Sherman:
Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models. Biosyst. 121: 43-53 (2014) - [j15]Anna Zhukova, David James Sherman:
Knowledge-based generalization of metabolic networks: A practical study. J. Bioinform. Comput. Biol. 12(2) (2014) - [j14]Anna Zhukova, David James Sherman:
Knowledge-based Generalization of Metabolic Models. J. Comput. Biol. 21(7): 534-547 (2014) - 2013
- [j13]Rodrigo Assar, David J. Sherman:
Implementing biological hybrid systems: Allowing composition and avoiding stiffness. Appl. Math. Comput. 223: 167-179 (2013) - 2012
- [j12]Rodrigo Assar, Andrea V. Leisewitz, Alice Garcia, Nibaldo C. Inestrosa, Martín A. Montecino, David J. Sherman:
Reusing and composing models of cell fate regulation of human bone precursor cells. Biosyst. 108(1-3): 63-72 (2012) - [j11]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: 35 (2012) - 2009
- [j10]Macha Nikolski, David James Sherman:
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 25(17): 2294 (2009) - [j9]Géraldine Jean, David James Sherman, Macha Nikolski:
Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. J. Comput. Biol. 16(9): 1267-1284 (2009) - [j8]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): 550-554 (2009) - 2008
- [j7]Pascal Durrens, Macha Nikolski, David James Sherman:
Fusion and Fission of Genes Define a Metric between Fungal Genomes. PLoS Comput. Biol. 4(10) (2008) - 2007
- [j6]Macha Nikolski, David James Sherman:
Family relationships: should consensus reign? - consensus clustering for protein families. Bioinform. 23(2): 71-76 (2007) - [j5]Roland Barriot, David J. Sherman, Isabelle Dutour:
How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. BMC Bioinform. 8 (2007) - 2006
- [j4]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): 432-435 (2006) - 2005
- [j3]Florian Iragne, Macha Nikolski, Bertrand Mathieu, David Auber, David James Sherman:
ProViz: protein interaction visualization and exploration. Bioinform. 21(2): 272-274 (2005) - 2004
- [j2]David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski:
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. Nucleic Acids Res. 32(Database-Issue): 315-318 (2004) - [j1]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): 452-455 (2004)
Conference and Workshop Papers
- 2010
- [c10]Rodrigo Assar, Felipe A. Vargas, David J. Sherman:
Reconciling Competing Models: A Case Study of Wine Fermentation Kinetics. ANB 2010: 98-116 - 2009
- [c9]Nikolay Vyahhi, Adrien Goëffon, Macha Nikolski, David James Sherman:
Swarming along the evolutionary branches sheds light on genome rearrangement scenarios. GECCO 2009: 241-246 - 2008
- [c8]Adrien Goëffon, Macha Nikolski, David James Sherman:
An efficient probabilistic population-based descent for the median genome problem. GECCO 2008: 315-322 - 1998
- [c7]Macha Nikolskaïa, Antoine Rauzy, David James Sherman:
Almana: A BDD Minimization Tool Integrating Heuristic and Rewriting Methods. FMCAD 1998: 100-114 - [c6]David James Sherman, Nicolas Magnier:
Factotum: Automatic and Systematic Sharing Support for Systems Analyzers. TACAS 1998: 249-262 - 1996
- [c5]Alain Miniussi, David J. Sherman:
Squeezing Intermediate Construction in Equational Programs. Dagstuhl Seminar on Partial Evaluation 1996: 284-302 - 1994
- [c4]Timo Metzemakers, Alain Miniussi, David J. Sherman, Robert Strandh:
Improving Arithmetic Performance using Fine-Grain Unfolding. PLILP 1994: 324-339 - 1992
- [c3]David J. Sherman, Robert Strandh:
Call Unfolding Strategies for Equational Logic Programs. PEPM 1992: 48-53 - 1991
- [c2]David J. Sherman, Robert Strandh, Irène Durand:
Optimization of Equational Programs Using Partial Evaluation. PEPM 1991: 72-82 - [c1]Irène Durand, David J. Sherman, Robert Strandh:
Partial Evaluation of an Intermediate Language for Equational Programs. JTASPEFT/WSA 1991: 98-106
Coauthor Index
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