A scale-independent signal processing method for sequence analysis. - Alain Viari; Henry Soldano; E. Ollivier (Comput. Appl. Biosci., 1990)

'Multifrequency' location and clustering of sequence patterns from proteins. - E. Ollivier; Henry Soldano; Alain Viari (Comput. Appl. Biosci., 1991)

Cooperative Computer System For Genome Sequence Analysis. - Claudine Médigue; Thierry Vermat; Gilles Bisson; Alain Viari; Antoine Danchin (ISMB, 1995)

A Distance-Based Block Searching Algorithm. - Marie-France Sagot; Alain Viari; Henry Soldano (ISMB, 1995)

Finding flexible patterns in a text: an application to three-dimensional molecular matching. - Marie-France Sagot; Alain Viari; Joël Pothier; Henry Soldano (Comput. Appl. Biosci., 1995)

Searching for flexible repeated patterns using a non-transitive similarity relation. - Henry Soldano; Alain Viari; Marc Champesme (Pattern Recognit. Lett., 1995)

A Double Combinatorial Approach to Discovering Patterns in Biological Sequences. - Marie-France Sagot; Alain Viari (CPM, 1996)

Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices. - Marie-France Sagot; Alain Viari (CPM, 1997)

Multiple Sequence Comparison - A Peptide Matching Approach. - Marie-France Sagot; Alain Viari; Henry Soldano (Theor. Comput. Sci., 1997)

Pairwide and Multiple Identification of Three-Dimensional Common Substructures in Proteins. - V. Escalier; Joël Pothier; Henry Soldano; Alain Viari (J. Comput. Biol., 1998)

Imagene: an integrated computer environment for sequence annotation and analysis. - Claudine Médigue; François Rechenmann; Antoine Danchin; Alain Viari (Bioinform., 1999)

Ab initio reconstruction of metabolic pathways. - Frédéric Boyer; Alain Viari (ECCB, 2003)

How Does Computer Science Change Molecular Biology? - Alain Viari (STACS, 2003)

Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data. - Frédéric Boyer; Anne Morgat; Laurent Labarre; Joël Pothier; Alain Viari (Bioinform., 2005)

Reconstruction of Switching Thresholds in Piecewise-Affine Models of Genetic Regulatory Networks. - Samuel Drulhe; Giancarlo Ferrari-Trecate; Hidde de Jong; Alain Viari (HSCC, 2006)

Genepi: a blackboard framework for genome annotation. - Stéphane Descorps-Declère; Danielle Ziébelin; François Rechenmann; Alain Viari (BMC Bioinform., 2006)

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins. - Patrick Durand; Laurent Labarre; Alain Meil; Jean-Louis Divol; Yves Vandenbrouck; Alain Viari; Jérôme Wojcik (BMC Bioinform., 2006)

Repseek, a tool to retrieve approximate repeats from large DNA sequences. - Guillaume Achaz; Frédéric Boyer; Eduardo P. C. Rocha; Alain Viari; Eric Coissac (Bioinform., 2007)

Multiple Alignment of Biological Networks: A Flexible Approach. - Yves-Pol Deniélou; Frédéric Boyer; Alain Viari; Marie-France Sagot (CPM, 2009)

Bacterial syntenies: an exact approach with gene quorum. - Yves-Pol Deniélou; Marie-France Sagot; Frédéric Boyer; Alain Viari (BMC Bioinform., 2011)

UniPathway: a resource for the exploration and annotation of metabolic pathways. - Anne Morgat; Eric Coissac; Elisabeth Coudert; Kristian B. Axelsen; Guillaume Keller; Amos Bairoch; Alan J. Bridge; Lydie Bougueleret; Ioannis Xenarios; Alain Viari (Nucleic Acids Res., 2012)

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes. - Adam Alexander Thil Smith; Eugeni Belda; Alain Viari; Claudine Médigue; David Vallenet (PLoS Comput. Biol., 2012)