Optimization of Equational Programs Using Partial Evaluation. - David J. Sherman; Robert Strandh; Irène Durand (PEPM, 1991)

Partial Evaluation of an Intermediate Language for Equational Programs. - Irène Durand; David J. Sherman; Robert Strandh (JTASPEFT/WSA, 1991)

Call Unfolding Strategies for Equational Logic Programs. - David J. Sherman; Robert Strandh (PEPM, 1992)

Improving Arithmetic Performance using Fine-Grain Unfolding. - Timo Metzemakers; Alain Miniussi; David J. Sherman; Robert Strandh (PLILP, 1994)

Squeezing Intermediate Construction in Equational Programs. - Alain Miniussi; David J. Sherman (Dagstuhl Seminar on Partial Evaluation, 1996)

Almana: A BDD Minimization Tool Integrating Heuristic and Rewriting Methods. - Macha Nikolskaïa; Antoine Rauzy; David James Sherman (FMCAD, 1998)

Factotum: Automatic and Systematic Sharing Support for Systems Analyzers. - David James Sherman; Nicolas Magnier (TACAS, 1998)

IntAct: an open source molecular interaction database. - 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; et al. (Nucleic Acids Res., 2004)

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. - David James Sherman; Pascal Durrens; Emmanuelle Beyne; Macha Nikolski (Nucleic Acids Res., 2004)

ProViz: protein interaction visualization and exploration. - Florian Iragne; Macha Nikolski; Bertrand Mathieu; David Auber; David James Sherman (Bioinform., 2005)

Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. - David James Sherman; Pascal Durrens; Florian Iragne; Emmanuelle Beyne; Macha Nikolski; Jean-Luc Souciet (Nucleic Acids Res., 2006)

Family relationships: should consensus reign? - consensus clustering for protein families. - Macha Nikolski; David James Sherman (Bioinform., 2007)

How to decide which are the most pertinent overly-represented features during gene set enrichment analysis. - Roland Barriot; David J. Sherman; Isabelle Dutour (BMC Bioinform., 2007)

An efficient probabilistic population-based descent for the median genome problem. - Adrien Goëffon; Macha Nikolski; David James Sherman (GECCO, 2008)

Fusion and Fission of Genes Define a Metric between Fungal Genomes. - Pascal Durrens; Macha Nikolski; David James Sherman (PLoS Comput. Biol., 2008)

Swarming along the evolutionary branches sheds light on genome rearrangement scenarios. - Nikolay Vyahhi; Adrien Goëffon; Macha Nikolski; David James Sherman (GECCO, 2009)

Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures. - Géraldine Jean; David James Sherman; Macha Nikolski (J. Comput. Biol., 2009)

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. - David James Sherman; Tiphaine C. Martin; Macha Nikolski; Cyril Cayla; Jean-Luc Souciet; Pascal Durrens (Nucleic Acids Res., 2009)

Reconciling Competing Models: A Case Study of Wine Fermentation Kinetics. - Rodrigo Assar; Felipe A. Vargas; David J. Sherman (ANB, 2010)

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; David J. Sherman (Biosyst., 2012)

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. - Nicolás Loira; Thierry Dulermo; Jean-Marc Nicaud; David James Sherman (BMC Syst. Biol., 2012)

Implementing biological hybrid systems: Allowing composition and avoiding stiffness. - Rodrigo Assar; David J. Sherman (Appl. Math. Comput., 2013)

Modeling acclimatization by hybrid systems: Condition changes alter biological system behavior models. - Rodrigo Assar; Martín A. Montecino; Alejandro Maass; David J. Sherman (Biosyst., 2014)

Knowledge-based generalization of metabolic networks: A practical study. - Anna Zhukova; David James Sherman (J. Bioinform. Comput. Biol., 2014)

Knowledge-based Generalization of Metabolic Models. - Anna Zhukova; David James Sherman (J. Comput. Biol., 2014)

Mimoza: web-based semantic zooming and navigation in metabolic networks. - Anna Zhukova; David James Sherman (BMC Syst. Biol., 2015)

Pantograph: A template-based method for genome-scale metabolic model reconstruction. - Nicolás Loira; Anna Zhukova; David James Sherman (J. Bioinform. Comput. Biol., 2015)