METASYS Articles

2015

 

Smallbone K, Millard P: Multi-scale modelling of E. coli metabolism. PeerJ PrePrints, 3, e1128. DOI : 10.7287/peerj.preprints.914v1

Stanford NJ, Millard P, Swainston N: RobOKoD: microbial strain design for (over)production of target compounds. Frontiers in cell and developmental biology 2015, 3:17.

Sokol S, Portais JC: Theoretical Basis for Dynamic Label Propagation in Stationary Metabolic Networks under Step and Periodic Inputs. PloS one 2015, 10:e0144652.

Ryffel F, Helfrich EJ, Kiefer P, Peyriga L, Portais JC, Piel J, Vorholt JA: Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves. The ISME journal 2015.

Muller JE, Meyer F, Litsanov B, Kiefer P, Potthoff E, Heux S, Quax WJ, Wendisch VF, Brautaset T, Portais JC, Vorholt JA: Engineering Escherichia coli for methanol conversion. Metabolic engineering 2015, 28:190-201.

Millard P, Portais JC, Mendes P: Impact of kinetic isotope effects in isotopic studies of metabolic systems. BMC systems biology 2015, 9:64.

Lessmeier L, Pfeifenschneider J, Carnicer M, Heux S, Portais JC, Wendisch VF: Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Applied microbiology and biotechnology 2015.

Heux S, Meynial-Salles I, O'Donohue MJ, Dumon C: White biotechnology: state of the art strategies for the development of biocatalysts for biorefining. Biotechnology advances 2015.

Enjalbert B, Cocaign-Bousquet M, Portais JC, Letisse F: Acetate Exposure Determines the Diauxic Behavior of Escherichia coli during the Glucose-Acetate Transition. Journal of bacteriology 2015, 197:3173-3181.

 2014

 

 Walther T, Letisse F, Peyriga L, Alkim C, Liu Y, Lardenois A, Martin-Yken H, Portais JC, Primig M, Francois J: Developmental stage dependent metabolic regulation during meiotic differentiation in budding yeast. BMC biology 2014, 12:60.

Vieira G, Carnicer M, Portais JC, Heux S: FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. Bioinformatics 2014, 30:2986-2988.

Silva RR, Jourdan F, Salvanha DM, Letisse F, Jamin EL, Guidetti-Gonzalez S, Labate CA, Vencio RZ: ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. Bioinformatics 2014, 30:1336-1337.

Millard P, Sokol S, Letisse F, Portais JC: IsoDesign: a software for optimizing the design of 13C-metabolic flux analysis experiments. Biotechnology and bioengineering 2014, 111:202-208.

Millard P, Massou S, Wittmann C, Portais JC, Letisse F: Sampling of intracellular metabolites for stationary and non-stationary (13)C metabolic flux analysis in Escherichia coli. Analytical biochemistry 2014, 465:38-49.

Millard P, Massou S, Portais JC, Letisse F: Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns. Analytical chemistry 2014, 86:10288-10295.

Millard P, Letisse F, Sokol S, Portais JC: Correction of MS data for naturally occurring isotopes in isotope labelling experiments. Methods in molecular biology 2014, 1191:197-207.

Heux S, Poinot J, Massou S, Sokol S, Portais JC: A novel platform for automated high-throughput fluxome profiling of metabolic variants. Metabolic engineering 2014, 25:8-19.

Xu YF, Letisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD: Nucleotide degradation and ribose salvage in yeast. Molecular systems biology 2013, 9:665.

 2013

 

 Revelles O, Millard P, Nougayrede JP, Dobrindt U, Oswald E, Letisse F, Portais JC: The carbon storage regulator (Csr) system exerts a nutrient-specific control over central metabolism in Escherichia coli strain Nissle 1917. PloS one 2013, 8:e66386.

Enjalbert B, Letisse F, Portais JC: Physiological and Molecular Timing of the Glucose to Acetate Transition in Escherichia coli. Metabolites 2013, 3:820-837.

Boisseau R, Charrier B, Massou S, Portais JC, Akoka S, Giraudeau P: Fast spatially encoded 3D NMR strategies for (13)C-based metabolic flux analysis. Analytical chemistry 2013, 85:9751-9757.

2012

 

 Sokol S, Millard P, Portais JC: influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments. Bioinformatics 2012, 28:687-693.

Schneider K, Peyraud R, Kiefer P, Christen P, Delmotte N, Massou S, Portais JC, Vorholt JA: The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AM1 during growth on acetate. The Journal of biological chemistry 2012, 287:757-766.

Peyraud R, Kiefer P, Christen P, Portais JC, Vorholt JA: Co-consumption of methanol and succinate by Methylobacterium extorquens AM1. PloS one 2012, 7:e48271.

Millard P, Letisse F, Sokol S, Portais JC: IsoCor: correcting MS data in isotope labeling experiments. Bioinformatics 2012, 28:1294-1296.

Giraudeau P, Cahoreau E, Massou S, Pathan M, Portais JC, Akoka S: UFJCOSY: a fast 3D NMR method for measuring isotopic enrichments in complex samples. Chemphyschem : a European journal of chemical physics and physical chemistry 2012, 13:3098-3101.

Cahoreau E, Peyriga L, Hubert J, Bringaud F, Massou S, Portais JC: Isotopic profiling of (1)(3)C-labeled biological samples by two-dimensional heteronuclear J-resolved nuclear magnetic resonance spectroscopy. Analytical biochemistry 2012, 427:158-163.

 2011

 

 Peyraud R, Schneider K, Kiefer P, Massou S, Vorholt JA, Portais JC: Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. BMC systems biology 2011, 5:189.

Heux S, Philippe B, Portais JC: High-throughput workflow for monitoring and mining bioprocess data and its application to inferring the physiological response of Escherichia coli to perturbations. Applied and environmental microbiology 2011, 77:7040-7049.

Giraudeau P, Massou S, Robin Y, Cahoreau E, Portais JC, Akoka S: Ultrafast quantitative 2D NMR: an efficient tool for the measurement of specific isotopic enrichments in complex biological mixtures. Analytical chemistry 2011, 83:3112-3119.

Enjalbert B, Jourdan F, Portais JC: Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism. PloS one 2011, 6:e21318.

 2010

 

 Walther T, Novo M, Rossger K, Letisse F, Loret MO, Portais JC, Francois JM: Control of ATP homeostasis during the respiro-fermentative transition in yeast. Molecular systems biology 2010, 6:344.

 2009

 

 Rodriguez-Prados JC, de Atauri P, Maury J, Ortega F, Portais JC, Chassagnole C, Acerenza L, Lindley ND, Cascante M: In silico strategy to rationally engineer metabolite production: A case study for threonine in Escherichia coli. Biotechnology and bioengineering 2009, 103:609-620.

Peyraud R, Kiefer P, Christen P, Massou S, Portais JC, Vorholt JA: Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:4846-4851.

 2008

 

 Kiefer P, Portais JC, Vorholt JA: Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry. Analytical biochemistry 2008, 382:94-100.

 2007

 

 van der Werf MJ, Takors R, Smedsgaard J, Nielsen J, Ferenci T, Portais JC, Wittmann C, Hooks M, Tomassini A, Oldiges M, et al: Standard reporting requirements for biological samples in metabolomics experiments: microbial and in vitro biology experiments. Metabolomics : Official journal of the Metabolomic Society 2007, 3:189-194.

Troufflard S, Roscher A, Thomasset B, Barbotin JN, Rawsthorne S, Portais JC: In vivo 13C NMR determines metabolic fluxes and steady state in linseed embryos. Phytochemistry 2007, 68:2341-2350.

Nicolas C, Kiefer P, Letisse F, Kromer J, Massou S, Soucaille P, Wittmann C, Lindley ND, Portais JC: Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS letters 2007, 581:3771-3776.

Massou S, Nicolas C, Letisse F, Portais JC: NMR-based fluxomics: quantitative 2D NMR methods for isotopomers analysis. Phytochemistry 2007, 68:2330-2340.

Massou S, Nicolas C, Letisse F, Portais JC: Application of 2D-TOCSY NMR to the measurement of specific(13C-enrichments in complex mixtures of 13C-labeled metabolites. Metabolic engineering 2007, 9:252-257.

Kiefer P, Nicolas C, Letisse F, Portais JC: Determination of carbon labeling distribution of intracellular metabolites from single fragment ions by ion chromatography tandem mass spectrometry. Analytical biochemistry 2007, 360:182-188.

Chistoserdova L, Crowther GJ, Vorholt JA, Skovran E, Portais JC, Lidstrom ME: Identification of a fourth formate dehydrogenase in Methylobacterium extorquens AM1 and confirmation of the essential role of formate oxidation in methylotrophy. Journal of bacteriology 2007, 189:9076-9081.

Bolten CJ, Kiefer P, Letisse F, Portais JC, Wittmann C: Sampling for metabolome analysis of microorganisms. Analytical chemistry 2007, 79:3843-3849.