Dynamic Programming for LR-PCR Segmention of Bacterium Genomes. - Rumen Andonov; Dominique Lavenier; Philippe Veber; Nicola Yanev (IPDPS, 2004)

Optimal Protein Threading by Cost-Splitting. - Philippe Veber; Nicola Yanev; Rumen Andonov; Vincent Poirriez (WABI, 2005)

Dynamic programming for LR-PCR segmentation of bacterium genomes. - Rumen Andonov; Dominique Lavenier; Philippe Veber; Nicola Yanev (Concurr. Comput. Pract. Exp., 2005)

Path-Equivalent Removals of epsilon-transitions in a Genomic Weighted Finite Automaton. - Mathieu Giraud; Philippe Veber; Dominique Lavenier (CIAA, 2006)

Path-Equivalent Developments in Acyclic Weighted Automata. - Mathieu Giraud; Philippe Veber; Dominique Lavenier (Int. J. Found. Comput. Sci., 2007)

Modélisation grande échelle de réseaux biologiques :vérification par contraintes booléennes de la cohérence des données. (Large-scale modeling of biological networks: checking data consistency using boolean constraints). - Philippe Veber (2007)

Detecting Inconsistencies in Large Biological Networks with Answer Set Programming. - Martin Gebser; Torsten Schaub; Sven Thiele; Björn Usadel; Philippe Veber (ICLP, 2008)

The System BioC for Reasoning about Biological Models in Action Language C. - Steve Dworschak; Torsten Grote; Arne König; Torsten Schaub; Philippe Veber (ICTAI (1), 2008)

Inferring the role of transcription factors in regulatory networks. - Philippe Veber; Carito Guziolowski; Michel Le Borgne; Ovidiu Radulescu; Anne Siegel (BMC Bioinform., 2008)

Lagrangian approaches for a class of matching problems in computational biology. - Nicola Yanev; Rumen Andonov; Philippe Veber; Stefan Balev (Comput. Math. Appl., 2008)

The BioASP Library: ASP Solutions for Systems Biology. - Martin Gebser; Arne König; Torsten Schaub; Sven Thiele; Philippe Veber (ICTAI (1), 2010)

Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming. - Martin Gebser; Carito Guziolowski; Mihail Ivanchev; Torsten Schaub; Anne Siegel; Sven Thiele; Philippe Veber (KR, 2010)

BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming. - Julien Jourde; Alain-Pierre Manine; Philippe Veber; Karën Fort; Robert Bossy; Érick Alphonse; Philippe Bessières (BioNLP@ACL (Shared Task), 2011)

BioNLP 2011 Task Bacteria Biotope - The Alvis system. - Zorana Ratkovic; Wiktoria Golik; Pierre Warnier; Philippe Veber; Claire Nédellec (BioNLP@ACL (Shared Task), 2011)

Detecting inconsistencies in large biological networks with answer set programming. - Martin Gebser; Torsten Schaub; Sven Thiele; Philippe Veber (Theory Pract. Log. Program., 2011)

BioNLP Shared Task - The Bacteria Track. - Robert Bossy; Julien Jourde; Alain-Pierre Manine; Philippe Veber; Érick Alphonse; Maarten van de Guchte; Philippe Bessières; Claire Nedellec (BMC Bioinform., 2012)

CAARS: comparative assembly and annotation of RNA-Seq data. - Carine Rey; Philippe Veber; Bastien Boussau; Marie Sémon (Bioinform., 2019)

Neural Networks beyond explainability: Selective inference for sequence motifs. - Antoine Villié; Philippe Veber; Yohann de Castro; Laurent Jacob (Trans. Mach. Learn. Res., 2023)