J. Faulon

J. Faulon, Zhaoduo Zhang, A. Martino, 2007, Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research.

Understanding and engineering enzymes for enhanced biofuel production.

J. Faulon, B. Simmons, R. Sapra, 2009 .

Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts

Peter L. Voyvodic, Chase L. Beisel, J. Faulon, 2021, bioRxiv.

Statistical models for bituminous coal: a three-dimensional evaluation of structural and physical properties based on computer-generated structures

J. Faulon, P. Hatcher, G. Carlson, 1993 .

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

Pablo Carbonell, J. Faulon, Neil Swainston, 2022, Nature Communications.

Molecular dynamics computer simulations of silica aerogels

J. Faulon, P. Pohl, Douglas M. Smith, 1995 .

Reaction Network Generation

Andreas Bender, Pablo Carbonell, Jean-Loup Faulon, 2010 .

PMG: Multi-core Metabolite Identiﬁcation 1

Julio E. Peironcely, S. Jongmans, J. Faulon, 2013 .

Stochastic Generator of Chemical Structure. 1. Application to the Structure Elucidation of Large Molecules

Jean-Loup Faulon, J. Faulon, 1994, Journal of chemical information and computer sciences.

Engineering Escherichia coli towards de novo production of gatekeeper (2S)-flavanones: naringenin, pinocembrin, eriodictyol and homoeriodictyol

Andrew Currin, Rainer Breitling, Pablo Carbonell, 2020, Synthetic biology.

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0

Pablo Carbonell, Mathilde Koch, Jean-Loup Faulon, 2017, bioRxiv.

Statistical ensemble analysis for simulating extrinsic noise-driven response in NF-κB signaling networks

Steven J. Plimpton, Jean-Loup Faulon, Jaewook Joo, 2010, BMC Systems Biology.

Systems chemical biology.

Tudor I. Oprea, Alexander Tropsha, Mark Daniel Rintoul, 2007 .

Pore structure of imogolite computer models

J. Faulon, P. Pohl, Douglas M. Smith, 1996 .

Reinforcement Learning for Bio-Retrosynthesis.

Mathilde Koch, Thomas Duigou, Jean-Loup Faulon, 2019, ACS synthetic biology.

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli.

Neil Swainston, Rainer Breitling, Pablo Carbonell, 2019, ACS synthetic biology.

Massively Parallel Simulations of Diffusion in Dense Polymeric Structures

Jean-Loup Faulon, J. David Hobbs, David M. Ford, 1997, ACM/IEEE SC 1997 Conference (SC'97).

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

Carole Goble, Neil Swainston, Rainer Breitling, 2018, Communications Biology.

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Pablo Carbonell, Jean-Loup Faulon, Alfred Fernández-Castané, 2014, Biotechnology journal.

Disparate data fusion for protein phosphorylation prediction

Jean-Loup Faulon, Genetha A. Gray, W. Michael Brown, 2010, Ann. Oper. Res..

Origins of Specificity and Promiscuity in Metabolic Networks

Pablo Carbonell, Jean-Loup Faulon, Guillaume Lecointre, 2011, The Journal of Biological Chemistry.

Noise-induced oscillatory shuttling of NF-kappaB in a two compartment IKK-NF-kappaB-IkappaB-A20 signaling model.

J. Faulon, S. Plimpton, Jaewook Joo, 2008, 1010.0888.

Reverse Engineering Biological Networks: Applications in Immune Responses to Bio-toxins Reverse Engineering Biological Networks: Applications in Immune Responses to Bio-toxins

E. V. Thomas, J. Faulon, D. Haaland, 2005 .

Correlation between Microporosity and Fractal Dimension of Bituminous Coal Based on Computer-Generated Models

J. Faulon, P. Hatcher, J. Mathews, 1994 .

SAND 2004-6383 Unlimited Release Model-Building Codes for Membrane Proteins

Malin M. Young, J. Faulon, W. M. Brown, 2005 .

Molecular signatures-based prediction of enzyme promiscuity

Pablo Carbonell, Jean-Loup Faulon, Pablo Carbonell, 2010, Bioinform..

Sensing new chemicals with bacterial transcription factors.

Jean-Loup Faulon, Baudoin Delépine, Vincent Libis, 2016, Current opinion in microbiology.

Is there any order in the structure of lignin

J. Faulon, P. Hatcher, 1994 .

A versatile active learning workflow for optimization of genetic and metabolic networks

J. Faulon, T. Erb, N. Cortina, 2021, bioRxiv.

Building a minimal and generalizable model of transcription factor–based biosensors: Showcasing flavonoids

Mathilde Koch, Jean-Loup Faulon, Heykel Trabelsi, 2018, Biotechnology and bioengineering.

Large scale active-learning-guided exploration for in vitro protein production optimization

J. Faulon, Paul Soudier, A. Pandi, 2020, Nature Communications.

A three-dimensional model for lignocellulose from gymnospermous wood

J. Faulon, P. Hatcher, G. Carlson, 1994 .

Engineering antibiotic production and overcoming bacterial resistance

Pablo Carbonell, Jean-Loup Faulon, Anne-Gaëlle Planson, 2011, Biotechnology journal.

Metabolic perceptrons for neural computing in biological systems

Peter L. Voyvodic, Mathilde Koch, Jean-Loup Faulon, 2019, Nature Communications.

Predicting protein-protein interactions using signature products

Jean-Loup Faulon, Diana C. Roe, Shawn Martin, 2005, Bioinform..

Stochastic generator of chemical structure. 4. Building polymeric systems with specified properties

Jean-Loup Faulon, J. Faulon, 2001, J. Comput. Chem..

In silico, in vitro, and in vivo machine learning in synthetic biology and metabolic engineering.

J. Faulon, Léon Faure, L. Faure, 2021, Current opinion in chemical biology.

Reverse engineering chemical structures from molecular descriptors: how many solutions?

Jean-Loup Faulon, Shawn Martin, W. Michael Brown, 2005, J. Comput. Aided Mol. Des..

Computer-aided design for metabolic engineering.

Pablo Carbonell, Jean-Loup Faulon, Cyrille Pauthenier, 2014, Journal of biotechnology.

Development of a Biosensor for Detection of Benzoic Acid Derivatives in Saccharomyces cerevisiae

J. Faulon, Sara Castaño-Cerezo, P. Urban, 2020, Frontiers in Bioengineering and Biotechnology.

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

Pablo Carbonell, Jean-Loup Faulon, Anne-Gaëlle Planson, 2011, BMC Systems Biology.

Genome scale enzyme–metabolite and drug–target interaction predictions using the signature molecular descriptor

Jean-Loup Faulon, Shawn Martin, Milind Misra, 2008 .

Custom-made transcriptional biosensors for metabolic engineering.

Mathilde Koch, Jean-Loup Faulon, Olivier Borkowski, 2019, Current opinion in biotechnology.

A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli

Pablo Carbonell, Jean-Loup Faulon, Vincent Libis, 2015, Front. Bioeng. Biotechnol..

A dataset of small molecules triggering transcriptional and translational cellular responses

Mathilde Koch, Jean-Loup Faulon, Baudoin Delépine, 2018, Data in brief.

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter L. Voyvodic, Mathilde Koch, Jean-Loup Faulon, 2018, Nature Communications.

OMG: Open Molecule Generator

Jean-Loup Faulon, Theo H. Reijmers, Julio E. Peironcely, 2012, Journal of Cheminformatics.

Constrained Walks and Self-Avoiding Walks: Implications for Protein Structure Determination

Mark Daniel Rintoul, Jean-Loup Faulon, Malin M. Young, 2000 .

A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

J. Faulon, Wolfram Liebermeister, Bastien Mollet, 2022, bioRxiv.

An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals

D. Kell, R. Goodacre, J. Micklefield, 2018, Communications Biology.

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

Jean-Loup Faulon, Cyrille Pauthenier, J. Faulon, 2014, Nucleic Acids Res..

Thermodynamic Properties of Asphaltenes Through Computer Assisted Structure Elucidation and Atomistic Simulations. 1. Bulk Arabian Light Asphaltenes

W. Goddard, J. Faulon, A. Strachan, 2004 .

Reinforcement Learning for Bio-Retrosynthesis

Mathilde Koch, Jean-Loup Faulon, Thomas Duigou, 2019 .

Semisupervised Gaussian Process for Automated Enzyme Search.

Pablo Carbonell, Joseph Mellor, Jean-Loup Faulon, 2016, ACS synthetic biology.

Retropath: automated pipeline for embedded metabolic circuits.

Pablo Carbonell, Jean-Loup Faulon, Christophe Junot, 2014, ACS synthetic biology.

Large scale active-learning-guided exploration to maximize cell-free production

Mathilde Koch, Olivier Borkowski, Amir Pandi, 2019, bioRxiv.

Optimizing Cell-Free Biosensors to Monitor Enzymatic Production.

Jean-Loup Faulon, Olivier Borkowski, Amir Pandi, 2019, ACS synthetic biology.

Models for Cell-Free Synthetic Biology: Make Prototyping Easier, Better, and Faster

Mathilde Koch, Jean-Loup Faulon, Olivier Borkowski, 2018, Front. Bioeng. Biotechnol..

Random removal of edges from scale free graphs

Shawn Martin, R. Carr, J. Faulon, 2006 .

SensiPath: computer-aided design of sensing-enabling metabolic pathways

Pablo Carbonell, Jean-Loup Faulon, Baudoin Delépine, 2016, Nucleic Acids Res..

Isomorphism, Automorphism Partitioning, and Canonical Labeling Can Be Solved in Polynomial-Time for Molecular Graphs

Jean-Loup Faulon, J. Faulon, 1998, J. Chem. Inf. Comput. Sci..

Selenzyme: enzyme selection tool for pathway design

Neil Swainston, Rainer Breitling, Douglas B. Kell, 2017, bioRxiv.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

Sophia Ananiadou, Pablo Carbonell, Alan R. Williams, 2017, PloS one.

Applications of molecular modeling in coal research

J. Faulon, G. Carlson, 1994 .

A computer-aided molecular model for high volatile bituminous coal☆

Jean-Loup Faulon, G. A. Carlson, J. Faulon, 1993 .

A deterministic algorithm for constrained enumeration of transmembrane protein folds

W. Michael Brown, Jean-Loup Faulon, Kenneth L. Sale, 2005, Comput. Biol. Chem..

Boolean dynamics of genetic regulatory networks inferred from microarray time series data

Jean-Loup Faulon, Shawn Martin, Anthony Martino, 2007, Bioinform..

A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

J. Faulon, Wolfram Liebermeister, Bastien Mollet, 2023, bioRxiv.

Graphs: Flexible Representations of Molecular Structures and Biological Networks

Jean-Loup Faulon, Shawn Martin, Milind Misra, 2012 .

Inferring genetic networks from microarray data

J. Faulon, M. Werner-Washburne, G. Davidson, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems?

Jean-Loup Faulon, Dimitrios Vavylonis, Polly M. Fordyce, 2017, Cell systems.

Optimal bundling of transmembrane helices using sparse distance constraints

Malin M. Young, J. Faulon, G. A. Gray, 2004, Protein science : a publication of the Protein Society.

Plug-and-play metabolic transducers expand the chemical detection space of cell-free biosensors

Peter L. Voyvodic, J. Faulon, J. Bonnet, 2018, bioRxiv.

Galaxy-SynBioCAD: Automated Pipeline for Synthetic Biology Design and Engineering

Pablo Carbonell, J. Faulon, Neil Swainston, 2022, bioRxiv.

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

Pablo Carbonell, Jean-Loup Faulon, Joan Hérisson, 2020, bioRxiv.

XTMS: pathway design in an eXTended metabolic space

Pablo Carbonell, Jean-Loup Faulon, Joan Hérisson, 2014, Nucleic Acids Res..

Extended Metabolic Space Modeling.

Pablo Carbonell, Jean-Loup Faulon, Baudoin Delépine, 2018, Methods in molecular biology.

Enzyme Discovery: Enzyme Selection and Pathway Design.

Pablo Carbonell, Mathilde Koch, Jean-Loup Faulon, 2018, Methods in enzymology.

Data mining PubChem using a support vector machine with the Signature molecular descriptor: classification of factor XIa inhibitors.

Jean-Loup Faulon, Derick C. Weis, Donald P Visco, 2008, Journal of molecular graphics & modelling.

RetroPath2.0: a retrosynthesis workflow for metabolic engineers

Pablo Carbonell, Jean-Loup Faulon, Baudoin Delépine, 2017, bioRxiv.

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways.

Jean-Loup Faulon, Baudoin Delépine, Vincent Libis, 2016, ACS synthetic biology.

Shotgun Protein Sequencing: LDRD Project 93501 Close-Out Report

J. Faulon, S. Report, G. Heffelfinger, 2009 .

Using product kernels to predict protein interactions.

Jean-Loup Faulon, Shawn Martin, W Michael Brown, 2008, Advances in biochemical engineering/biotechnology.

Stochastic Generator of Chemical Structure, 2. Using Simulated Annealing To Search the Space of Constitutional Isomers

Jean-Loup Faulon, J. Faulon, 1996, J. Chem. Inf. Comput. Sci..

Cell-Free Biosensors and AI Integration.

J. Faulon, Paul Soudier, L. Faure, 2022, Methods in molecular biology.

Reverse Engineering Biological Networks: Applications in Immune Responses to Bio-Toxins

E. V. Thomas, J. Faulon, D. Haaland, 2005 .

Artificial Metabolic Networks: enabling neural computation with metabolic networks

J. Faulon, Wolfram Liebermeister, Bastien Mollet, 2022 .

Compound toxicity screening and structure-activity relationship modeling in Escherichia coli.

Pablo Carbonell, Jean-Loup Faulon, Anne-Gaëlle Planson, 2012, Biotechnology and bioengineering.

The signature molecular descriptor. 3. Inverse-quantitative structure-activity relationship of ICAM-1 inhibitory peptides.

Jean-Loup Faulon, Shawn Martin, Mark D Rintoul, 2003, Journal of molecular graphics & modelling.

Developing a methodology for an inverse quantitative structure-activity relationship using the signature molecular descriptor.

Jean-Loup Faulon, Donald P Visco, Ramdas S Pophale, 2002, Journal of molecular graphics & modelling.

The Signature Molecular Descriptor. 4. Canonizing Molecules Using Extended Valence Sequences

Robert D. Carr, Jean-Loup Faulon, M. J. Collins, 2004, J. Chem. Inf. Model..

Cheminformatics

Egon L. Willighagen, Rajarshi Guha, John P. Overington, 2012, CACM.

Handbook of Chemoinformatics Algorithms

Andreas Bender, Jean-Loup Faulon, J. Faulon, 2010 .

Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor

J. Faulon, R. Sapra, M. Misra, 2008, Bioinform..

Reverse Engineering Biological Networks: Applications in Immune Responses to Bio-Toxins

E. V. Thomas, J. Faulon, D. Haaland, 2005 .

Retrosynthetic design of heterologous pathways.

Pablo Carbonell, Jean-Loup Faulon, Anne-Gaëlle Planson, 2013, Methods in molecular biology.

Prediction of β-strand packing interactions using the signature product

Jean-Loup Faulon, Shawn Martin, W Michael Brown, 2006, Journal of molecular modeling.

Molecular signatures-based prediction of enzyme promiscuity

Pablo Carbonell, J. Faulon, 2010, Bioinform..

Large scale active-learning-guided exploration for in vitro protein production optimization

Mathilde Koch, Jean-Loup Faulon, Olivier Borkowski, 2020, Nature Communications.

neo4jsbml: import systems biology markup language data into the graph database Neo4j

J. Faulon, Sandra Dérozier, T. Duigou, 2024, PeerJ.

Molecular modelling of polymers 17. Simulation and QSPR analyses of transport behavior in amorphous polymeric materials

Anton J. Hopfinger, Jean-Loup Faulon, J. S. Tokarski, 1997 .

A versatile active learning workflow for optimization of genetic and metabolic networks

J. Faulon, T. Erb, N. Cortina, 2022, Nature Communications.

Reservoir Computing with Bacteria

J. Faulon, Paul Ahavi, Thi-Ngoc-An Hoang, 2024, bioRxiv.