On using graph-equivalent classes for the structure elucidation of large molecules. - Jean-Loup Faulon (J. Chem. Inf. Comput. Sci., 1992)

Stochastic Generator of Chemical Structure. 1. Application to the Structure Elucidation of Large Molecules. - Jean-Loup Faulon (J. Chem. Inf. Comput. Sci., 1994)

Stochastic Generator of Chemical Structure, 2. Using Simulated Annealing To Search the Space of Constitutional Isomers. - Jean-Loup Faulon (J. Chem. Inf. Comput. Sci., 1996)

Massively Parallel Simulations of Diffusion in Dense Polymeric Structures. - Jean-Loup Faulon; J. David Hobbs; David M. Ford; Robert T. Wilcox (SC, 1997)

Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs. - Jean-Loup Faulon (J. Chem. Inf. Comput. Sci., 1998)

Stochastic generator of chemical structure. 4. Building polymeric systems with specified properties. - Jean-Loup Faulon (J. Comput. Chem., 2001)

Stochastic Generator of Chemical Structure. 3. Reaction Network Generation. - Jean-Loup Faulon; Allen G. Sault (J. Chem. Inf. Comput. Sci., 2001)

The Signature Molecular Descriptor. 2. Enumerating Molecules from Their Extended Valence Sequences. - Jean-Loup Faulon; Carla J. Churchwell; Donald P. Visco Jr. (J. Chem. Inf. Comput. Sci., 2003)

The Signature Molecular Descriptor. 1. Using Extended Valence Sequences in QSAR and QSPR Studies. - Jean-Loup Faulon; Donald P. Visco Jr.; Ramdas S. Pophale (J. Chem. Inf. Comput. Sci., 2003)

Dynamical Robustness in Gene Regulatory Networks. - Jean-Loup Faulon; Shawn Martin; Robert D. Carr (CSB, 2004)

Inferring Genetic Networks from Microarray Data. - Shawn Martin; George Davidson; Elebeoba E. May; Jean-Loup Faulon; Margaret Werner-Washburne (CSB, 2004)

The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences. - Jean-Loup Faulon; Michael J. Collins 003; Robert D. Carr (J. Chem. Inf. Model., 2004)

Inverse Design of Large Molecules using Linear Diophantine Equations. - Shawn Martin; W. Michael Brown; Jean-Loup Faulon; Derick C. Weis; Donald P. Visco (CSB Workshops, 2005)

Predicting protein-protein interactions using signature products. - Shawn Martin; Diana C. Roe; Jean-Loup Faulon (Bioinform., 2005)

A deterministic algorithm for constrained enumeration of transmembrane protein folds. - W. Michael Brown; Jean-Loup Faulon; Ken Sale (Comput. Biol. Chem., 2005)

Reverse engineering chemical structures from molecular descriptors: how many solutions? - Jean-Loup Faulon; W. Michael Brown; Shawn Martin (J. Comput. Aided Mol. Des., 2005)

Designing Novel Polymers with Targeted Properties Using the Signature Molecular Descriptor. - W. Michael Brown; Shawn Martin; Mark D. Rintoul; Jean-Loup Faulon (J. Chem. Inf. Model., 2006)

Boolean dynamics of genetic regulatory networks inferred from microarray time series data. - Shawn Martin; Zhaoduo Zhang; Anthony Martino; Jean-Loup Faulon (Bioinform., 2007)

Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor. - Jean-Loup Faulon; Milind Misra; Shawn Martin; Ken Sale; Rajat Sapra (Bioinform., 2008)

Disparate data fusion for protein phosphorylation prediction. - Genetha A. Gray; Pamela J. Williams; W. Michael Brown; Jean-Loup Faulon; Kenneth L. Sale (Ann. Oper. Res., 2010)

Molecular signatures-based prediction of enzyme promiscuity. - Pablo Carbonell; Jean-Loup Faulon (Bioinform., 2010)

A retrosynthetic biology approach to metabolic pathway design for therapeutic production. - Pablo Carbonell; Anne-Gaëlle Planson; Davide Fichera; Jean-Loup Faulon (BMC Syst. Biol., 2011)

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. - Pablo Carbonell; Davide Fichera; Shashi Bhushan Pandit; Jean-Loup Faulon (BMC Syst. Biol., 2012)

Cheminformatics. - Jörg K. Wegner; Aaron D. Sterling; Rajarshi Guha; Andreas Bender 002; Jean-Loup Faulon; Janna Hastings; Noel M. O'Boyle; John P. Overington; Herman van Vlijmen; Egon L. Willighagen (Commun. ACM, 2012)

OMG: open molecule generator. - Julio E. Peironcely; Miguel Rojas-Chertó; Davide Fichera; Theo H. Reijmers; Leon Coulier; Jean-Loup Faulon; Thomas Hankemeier (J. Cheminformatics, 2012)

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κ. - Jaewook Joo; Steven J. Plimpton; Jean-Loup Faulon (BMC Syst. Biol., 2013)

PMG: Multi-core Metabolite Identification. - Mohammad Mahdi Jaghoori; Sung-Shik T. Q. Jongmans; Frank S. de Boer; Julio E. Peironcely; Jean-Loup Faulon; Theo H. Reijmers; Thomas Hankemeier (CS2Bio, 2013)

Stereo Signature Molecular Descriptor. - Pablo Carbonell; Lars Carlsson; Jean-Loup Faulon (J. Chem. Inf. Model., 2013)

XTMS in Action: Retrosynthetic Design in the Extended Metabolic Space of Heterologous Pathways for High-Value Compounds. - Baudoin Delépine; Pablo Carbonell; Jean-Loup Faulon (CMSB, 2014)

XTMS: pathway design in an eXTended metabolic space. - Pablo Carbonell; Pierre Parutto; Joan Hérisson; Shashi Bhushan Pandit; Jean-Loup Faulon (Nucleic Acids Res., 2014)

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling. - Cyrille Pauthenier; Jean-Loup Faulon (Nucleic Acids Res., 2014)

SensiPath: computer-aided design of sensing-enabling metabolic pathways. - Baudoin Delépine; Vincent Libis; Pablo Carbonell; Jean-Loup Faulon (Nucleic Acids Res., 2016)

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. - Mathilde Koch; Thomas Duigou; Pablo Carbonell; Jean-Loup Faulon (J. Cheminformatics, 2017)

Selenzyme: enzyme selection tool for pathway design. - Pablo Carbonell; Jerry Wong; Neil Swainston; Eriko Takano; Nicholas J. Turner; Nigel S. Scrutton; Douglas B. Kell; Rainer Breitling; Jean-Loup Faulon (Bioinform., 2018)

PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts. - Neil Swainston; Mark Dunstan; Adrian J. Jervis; Christopher J. Robinson; Pablo Carbonell; Alan R. Williams; Jean-Loup Faulon; Nigel S. Scrutton; Douglas B. Kell (Bioinform., 2018)

RetroRules: a database of reaction rules for engineering biology. - Thomas Duigou; Melchior du Lac; Pablo Carbonell; Jean-Loup Faulon (Nucleic Acids Res., 2019)

Estimating the Learning Capacity of Bacterial Metabolic Networks. - Bastien Mollet; Paul Ahavi; Antoine Cornuéjols; Jean-Loup Faulon; Evelyne Lutton; Alberto Tonda (IDA, 2025)

Reverse engineering molecules from fingerprints through deterministic enumeration and generative models. - Philippe Meyer; Thomas Duigou; Guillaume Gricourt; Jean-Loup Faulon (J. Cheminformatics, 2025)