Publications des unités MIA-Jouy, MIG, MaIAGE

Sélection : ($type:"article")and(author:"Bergou" or author:"Dinh" or author:"Fromion" or author:"Goelzer" or author:"Kieu" or author:"Liebermeister" or author:"Peres" or author:"Tournier" or author:"Trubuil");  Critères de tri / (Sorted on) : year, author, year;  (tri descendant/ reverse order); 


[1] M. T. Wortel, E. Noor, M. Ferris, Bruggeman, and W. Liebermeister. Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield. Plos Computational Biology, 14(2): 21 p., 2018.

[2] S. Peres, S. Schuster, and P. Dague. Thermodynamic constraints for identifying elementary flux modes. Biochemical Society Transactions, 46: 641-647, 2018.

[3] L. Noda-Garcia, W. Liebermeister, and D. Tawfik. Metabolite–enzyme coevolution: From single enzymes to metabolic pathways and networks. Annual Review of Biochemistry, 19(1): 187-216, 2018.

[4] B. Laflaquière, G. Leclercq, C. Choey, J. Chen, S. Peres, C. Ito, and M. Jolicoeur. Identifying Biomarkers of Wharton's Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect. Metabolites, 8(1): 18 p., 2018.

[5] M. Chaves and L. Tournier. Analysis tools for interconnected Boolean networks with biological applications. Frontiers Physiology, 9(586): 1-18, 2018.

[6] X. Zhao, M. Kasbi, J. Chen, S. Peres, and M. Jolicoeur. A dynamic metabolic flux analysis of ABE - acetone-butanol-ethanol - fermentation by clostridium acetobutylicum ATCC 824, with riboflavin as a by-product. Biotechnology and Bioengineering, 114(12): 2907-2919, 2017.
Keywords : ABE ; cell energetics ; Clostridium ; dynamic model ; metabolism ; riboflavin. [ DOI ]

[7] L. Tournier, A. Goelzer, and V. Fromion. Optimal resource allocation enables mathematical exploration of microbial metabolic configurations. Journal of Mathematical Biology, 76(4), 2017. DOI:10.1007/s00285-017-1118-5.

[8] S. Peres, M. Jolicoeur, C. Moulin, P. Dague, and S. Schuster. How important is thermodynamics for identifying elementary flux modes? PLOS One, 12(2): N° d'article: e0171440, 2017. DOI: 10.1371/journal.pone.0171440.

[9] K. Laib, A. Korniienko, M. Dinh, G. Scorletti, and F. Morel. Hierarchical robust performance analysis of uncertain large scale systems. IEEE Transactions on Automatic Control , online, 16 p., 2017.
Keywords : Uncertain large scale systems ; robustness analy- sis ; IQC analysis ; LMI optimization ; hierarchical approach ; IQC propagation. [ DOI ]

[10] A. Kalantari, T. Chen, B. Ji, I. A. Stancik, V. Ravikumar, D. Franjevic, C. Saulou-Berion, A. Goelzer, and I. Mijakovic. Conversion of glycerol to 3-hydroxypropanoic acid by genetically engineered bacillus subtilis. Frontiers in Microbiology, 8: 1-11, 2017. DOI: 10.3389/fmicb.2017.00638.

[11] V. Henry, A. Goelzer, A. Ferré, S. Fischer, M. Dinh, V. Loux, Froidevaux, and V. Fromion. The bacterial interlocked process ontology (bipon): a systemic multi-scale unified representation of biological processes in prokaryotes. Journal of Biomedical Semantics, 8(53): 16 P., 2017.
Keywords : Systems biology ; Multi-scale systemic description ; Prokaryotic biological processes ; Mathematical models ; Biological ontology.

[12] A. Goelzer and V. Fromion. Resource allocation in living organisms. Biochemical Society Transactions, 45(4), 2017. DOI:10.1042/BST20160436.

[13] M. Dinh, L. Strafella, P. Flores, A. Chastanet, R. Carballido Y Lopez, and V. Fromion. Validation of the 3-under-2 principle of cell wall growth in gram-positive bacteria by simulation of a simple coarse-grained model. arXiv:1702.0274, 24 p., 2017. > physics > arXiv:1702.02747.

[14] R. Dessalles, V. Fromion, and P. Robert. A stochastic analysis of autoregulation of gene expression. Journal of Mathematical Biology, 75(5): 1253-1283, 2017.
Keywords : escherichia-coli ; cells ; model ; networks ; operon. [ DOI ]

[15] C. Billaudeau, A. Chastanet, Z. Yao, C. Cornilleau, N. Mirouze, V. Fromion, and R. Carballido Lopez. Contrasting mechanisms of growth in two model rod-shaped bacteria. Nature Communications, 8, 2017. article n° 15370. [ DOI ]

[16] E. H. Bergou, Y. Diouane, and S. Gratton. On the use of the energy norm in trust-region and adaptive cubic regularization subproblems. Computational Optimization and Applications, 68(3): 533-554, 2017.
Keywords : Nonlinear optimization ; Unconstrained optimization ; Trust-region algorithm ; Adaptive regularized framework using cubics ; Line search algorithm ; Energy nom. [ DOI ]

[17] J. Moreira da Veiga, M. Hamraz, M. Abolhassani, E. Bigan, S. Peres, L. Paulevé, M. L. Nogueira, J. M. Steyaert, and L. Schwartz. The redox status of cancer cells supports mechanisms behind the warburg effect. Metabolites, 6(4): 13 p. article n° 33, 2016. DOI:10.3390/metabo6040033.

[18] J. Mandel, E. H. Bergou, S. Gürol, S. Gratton, and I. Kasanický. Hybrid Levenberg–Marquardt and weak-constraint ensemble Kalman smoother method. Nonlinear Processes in Geophysics, 23(2): 59-73, 2016.

[19] J. P. Faria, R. Overbeek, R. C. Taylo, N. Conrad, V. Vonstein, A. Goelzer, V. Fromion, M. Rocha, I. Rocha, and C. S. Henry. Reconstruction of the regulatory network for bacillus subtilis and reconciliation with gene expression data. Frontiers in Microbiology, 7: 11 p., 2016.

[20] F. Deslandes, B. Laroche, and A. Trubuil. Fusion detection in time-lapse microscopy images : application to lipid droplets coalescence in plant seeds. IFAC-PapersOnLine, 49(26): 239-244, 2016.

[21] M. De Paepe, L. Tournier, E. Moncaut, O. Son, P. Langella, and M. A. Petit. Carriage of λ latent virus is costly for its bacterial host due to frequent reactivation in monoxenic mouse intestine. Plos Genetics, 12(2), 2016. article n° e1005861.

[22] O. Borkowski, A. Goelzer, M. Schaffer, M. Calabre, U. Mäder, S. Aymerich, M. Jules, and V. Fromion. Translation elicits a growth rate-dependent, genome-wide, differential protein production in Bacillus subtilis. Molecular Systems Biology, 12(5): 870, 2016.

[23] E. H. Bergou, S. Gratton, and L. N. Vicente. Levenberg-marquardt methodbbased on probabilistic gradient models and inexact subproblem solution, with application to data assimilation. SIAM/ASA Journal on Uncertainty Quantification, 4(1): 924-951, 2016.

[24] M. Miquel, G. Trigui, A. Trubuil, and B. Dubreucq. Imaging and quantitative analysis of size and distribution of sperical bodies, e.g. embryonic oil bodies. Bio-protocole, 5(1): 6 pages, 2015. article n° e1369 sur web. [ http ]

[25] A. Goelzer, J. Muntel, V. Chubukov, M. Jules, E. Prestel, R. Nölker, M. Mariadassou, S. Aymerich, M. Hecker, P. Noirot, D. Becher, and V. Fromion. Quantitative prediction of genome-wide resource allocation in bacteria. Metabolic Engineering, 32: 232-243, 2015. ident.Prodinra n° 334521.

[26] V. Fromion, E. Leoncini, and P. Robert. A stochastic model of the production of multiple proteins in cells. Siam Journal on Applied Mathematics, 2015. ident. prodinra : 326349.

[27] J. Muntel, V. Fromion, S. Goelzer, A.and Maaß, U. Mäder, K. Büttner, M. Hecker, and D. Becher. Comprehensive absolute quantification of the cytosolic proteome of bacillus subtilis by data independent, parallel fragmentation in liquid chromatography/mass spectrometry (lc/mse). Molecular & Cellular Proteomics, 13(4): 1008-1019, 2014. [ DOI ]

[28] M. Miquel, G. Trigui, S. D'Andrea, Z. Kelemen, S. Baud, A. Berger, C. Deruyffelaere, A. Trubuil, L. Lepiniec, and B. Dubreucq. Specialization of oleosins in ob dynamics during seed development in arabidopsis thaliana seeds. Plant Physiology, 164(4): 1866-1878, 2014. online.
Keywords : arabidopsis; oil body; oleosin; seed development.

[29] S. Maai, G. Wachlin, J. Bernhardt, C. Eymann, V. FROMION, K. Riedel, D. Becher, and M. Hecker. Highly precise quantification of protein molecules per cell during stress and starvation responses in bacillus subtilis. Molecular & cellular proteomics : MCP, 13(9): 2260-76, 2014. [ DOI ]

[30] L. Tournier and M. Chaves. Interconnection of asynchronous boolean networks, asymptotic and transient dynamics. Automatica, 49(4): 884 - 893, 2013.

[31] S. Nikolaev, N. A. Kolchanov, S. K. Golushko, J.-C. Palauqui, A. Urban, E. Amelina, A. V. Yurchenko, K. S. Golushko, U. Zubairova, A. V. Penenko, and A. Trubuil. Modeling of plant embryo morphodynamics at early developmental stages. Russian Journal of Genetics: Applied Research, 3(3): 176-183, 2013.
Keywords : developmental biology ; embryogenesis ; morphodynamics ; morphogenesis ; plant embryo ; confocal microscopy ; image analysis ; cell lineage ; cell mechanics ; finite element method ; modeling.

[32] V. Fromion, E. Leoncini, and P. Robert. Stochastic gene expression in cells: a point process approach. SIAM J. on Applied Mathematics, 73: 195-211, 2013.

[33] V. Bidnenko, L. Shi, A. Kobir, M. Ventroux, N. Pigeonneau, C. Henry, A. Trubuil, M. Noirot-Gros, and I. Mijakovic. Bacillus subtilis serine/threonine protein kinase yabt is involved in spore development via phosphorylation of a bacterial recombinase. Molecular microbiology, 88(5): 921-935, 2013.
Keywords : Bacillus subtilis ; YabT.

[34] P. Nicolas, U. Mäder, E. Dervyn, T. Rochat, A. Leduc, N. Pigeonneau, E. Bidnenko, E. Marchadier, M. Hoebeke, S. Aymerich, D. Becher, P. Bisicchia, E. Botella, O. Delumeau, G. Doherty, E. L. Denham, M. J. Fogg, V. Fromion, A. Goelzer, A. Hansen, E. Härtig, C. R. Harwood, G. Homuth, H. Jarmer, M. Jules, E. Klipp, L. L. Chat, F. g ois Lecointe, P. Lewis, W. Liebermeister, A. March, R. A. T. Mars, P. Nannapaneni, D. Noone, S. Pohl, B. Rinn, F. Rügheimer, P. K. Sappa, F. Samson, M. Schaffer, B. Schwikowski, L. Steil, J. Stülke, T. Wiegert, K. M. Devine, A. J. Wilkinson, J. M. van Dijl, M. Hecker, U. Völker, P. Bessières, and P. Noirot. Condition-dependent transcriptome reveals high-level regulatory architecture in bacillus subtilis. Science, 335(6072): 1103-1106, 2012. [ DOI | http ]

[35] M. Celton, I. Sanchez, A. Goelzer, V. Fromion, C. Camarasa, and S. Dequin. A comparative transcriptomic, fluxomic and metabolomic analysis of the reponse of saccharomyces cerevisiae to increases in NADPH oxidation. Bioinformatics, 13(1): 317, 2012.

[36] M. Celton, A. Goelzer, C. Camarasa, V. Fromion, and S. Dequin. A constraint based model analysis of the metabolic consequences of increased NADPH oxidation in saccharomyces cerevisiae. Metabolic Engineering, 14(4): 366-379, 2012.

[37] J. M. Buescher, W. Liebermeister, M. Jules, M. Uhr, J. Muntel, E. Botella, B. Hessling, R. J. Kleijn, L. Le Chat, F. Lecointe, U. Mäder, P. Nicolas, S. Piersma, F. Rügheimer, D. Becher, P. Bessières, E. Bidnenko, E. L. Denham, E. Dervyn, K. M. Devine, G. Doherty, S. Drulhe, L. Felicori, M. J. Fogg, A. Goelzer, A. Hansen, C. R. Harwood, M. Hecker, S. Hubner, C. Hultschig, H. Jarmer, E. Klipp, A. Leduc, P. Lewis, F. Molina, P. Noirot, S. Peres, N. Pigeonneau, S. Pohl, S. Rasmussen, B. Rinn, M. Schaffer, J. Schnidder, B. Schwikowski, J. M. V. Dijl, P. Veiga, S. Walsh, A. J. Wilkinson, J. Stelling, S. Aymerich, and U. Sauer. Global network reorganization during dynamic adaptations of bacillus subtilis metabolism. Science, 335(6072): 1099-1103, 2012. [ DOI | http ]

[38] L. Aichaoui, M. Jules, L. Le Chat, S. Aymerich, V. Fromion, and A. Goelzer. Basylica : a tool for automatic processing of a bacterial live cell array. Bioinformatics, 28(20): 2705-6, 2012.

[39] L. Aichaoui, M. Jules, L. Le Chat, S. Aymerich, V. Fromion, and A. Goelzer. Basylica : a tool for automatic processing of a bacterial live cell array. Bioinformatics, -, 2012.

[40] E. Marchadier, R. Carballido-López, S. Brinster, C. fabret, P. Mervelet, P. Bessières, M.-F. Noirot-Gros, V. Fromion, and P. Noirot. An expanded protein-protein interaction network in bacillus subtilis reveals a group of hubs: Exploration by an integrative approach. proteomics, 11(15): 2981-91, 2011.

[41] L. López-Kleine, A. Trubuil, and V. Monnet. Sensitivity analysis of protein role prediction methods: Which are the relevant data? The Open Genomics Journal, 4: 1-9, 2011.
Keywords : Protein prediction algorithms, data quality, sensitivity analysis. [ http | .pdf ]

[42] A. Goelzer and V. Fromion. Bacterial growth rate reflects a bottleneck in resource allocation. BBA general Subjects, 1810(10): 978-988, 2011. [ DOI ]

[43] A. Goelzer, V. Fromion, and G. Scorletti. Cell design in bacteria as a convex optimization problem. Automatica, 47(6): 1210-1218, 2011. [ DOI ]

[44] J. Dominguez-Escobar, A. Chastanet, A.-H. Crevenna, V. Fromion, R. Wedlich-Söldner, and R. Carballido-López. Processive movement of mreb-associated cell wall biosynthetic complexes in bacteria. Science, 333(6039: 225-8, 2011.

[45] M. Chaves, L. Tournier, and J.-L. Gouzé. Comparing Boolean and piecewise affine differential models for genetic networks. Acta Biotheor., 58: 217-232, 2010.

[46] X. Litrico and V. Fromion. Modal decomposition of linearized open channel flow. Networks and Heterogeneous Media, 4(2): 325-357, 2009.

[47] X. Litrico and V. Fromion. Boundary control of hyperbolic conservation laws using a frequency domain approach. Automatica, 45(3): 647-656, 2009.

[48] A. Goelzer, B. Charnomordic, S. Colombie, V. Fromion, and J. Sablayrolles. Simulation and optimization software for alcoholic fermentation in winemaking conditions. Fodd Control, 20(7): 635-642, 2009.

[49] L. Lopez-Kleine, V. Monnet, C. Pechoux, and A. Trubuil. Role of bacterial peptidase F inferred by statistical analysis and further experimental validation. HFSP, 2(1): 29-41, 2008.
Keywords : Statistical inference, proteolysis in bacteria, protein secretion, Lactococcus lactis.

[50] A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete, P. Noirot, P. Bessi Nhres, S. Aymerich, and V. Fromion. Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of bacillus subtilis. BMC Systems Biology, 2:20, 2008. [ DOI | http ]

[51] V. Racine, M. Sachse, J. Salamero, V. Fraisier, A. Trubuil, and J.-B. Sibarita. Visualization and quantification of vesicle trafficking on a 3D cytoskeleton network in living cells. Journal of Microscopy, 225(3): 214-228, 2007.
Keywords : kymogram, membrane dynamics, object tracking, 3D+t visualization.
Mots-clés : dymogramme, dynamique membranaire, suivi d'objet, visualisation 3D+T.

[52] X. Litrico, V. Fromion, and G. Scorletti. Robust feedforward boundary control of hyperbolic conservation laws. Networks and Heterogeneous Media, 2(4): 717-731, 2007.

[53] X. Litrico and V. Fromion. Tuning of robust distant downstream pi controllers for an irrigation canal pool: (I)Theory. Journal of Irrigation and Drainage Engineering, 132(4): 369-379, 2006.

[54] X. Litrico and V. Fromion. H control of an irrigation canal pool with a mixed control politics. IEEE Transactions on Control Systems Technology, 14: 99-111, 2006.

[55] X. Litrico and V. Fromion. Boundary control of linearized Saint-Venant equations oscill ating modes. Automatica, 42 (6): 967-972, 2006.

[56] X. Litrico, V. Fromion, and J.-P. Baume. Tuning of robust distant downstream pi controllers for an irrigation canal pool: (II) Implementation issues. Journal of Irrigation and Drainage Engineering, 132(4): 359-368, 2006.

[57] J. Wang, C. Caron, X. He, A. Carpentier, M.-Y. Mistou, A. Trubuil, C. Gitton, C. Henry, and A. Guillot. A system for integrative and post-planned analysis of 2-DE/MS centered proteomics data. Journal of Integrative Bioinformatics, 2005. Online Journal.
Keywords : Electrophoresis, Mass Spectrometry, Proteomics, Data integration. Data Mining..
Mots-clés : Bioinformatique, 2DE, électrophorèse, MS, Fouille de données, Protéomique.

[58] L. Pardini, B. Kaeffer, A. Trubuil, A. Bourreille, and J.-P. Galmiche. Human intestinal circadian clock : expression of clock genes in colonocytes lining the crypt. Chronobiology International, 22(6): 951-961, 2005.
Keywords : Large intestine, colon, per-1, per-2, clock genes, circadian rhythm.

[59] O. Loudet, V. Gaudon, A. Trubuil, and F. Daniel-Vedele. Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family. Theoretical Applied Genetics, 110(4): 742-753, 2005.

[60] X. Litrico, V. Fromion, J.-P. Baume, and M. Rijo. Experimental validation of a methodology to control irrigation canals based on Saint-Venant equations. Journal of Control Engineering Practice, 13/11: 1425-1437, 2005.

[61] C. Gitton, M. Meyrand, J. Wang, C. Caron, A. Trubuil, A. Guillot, and M.-Y. Mistou. Proteomic signature of lactococcus lactis NCDO763 cultivated in milk. Appl Environ Microbiol, 71: 7152-7163, 2005.

[62] C. Gitton, M. Meyrand, J. Wang, C. Caron, A. Trubuil, A. Guillot, and M.-Y. Mistou. Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk. Appl. Envir. Microbiol., 71(11): 7152-7163, 2005.
Keywords : Lactic acid bacteria, Lactococcus lactis, Peptide mass fingerprinting, Two-dimensional gel electrophoresis.
Mots-clés : 2DE, Lactococus lactis, MS identification, Protéomique.

[63] M. Dinh, G. Scorletti, V. Fromion, and E. Magaroto. Parameter dependent H control by finite dimensional LMI optimization: application to trade-off dependent control. Int. J. Robust and Nonlinear Control, 15: 383-406, 2005.

[64] J. Wang, C. Caron, M.-Y. Mistou, C. Gitton, and A. Trubuil. Paris: a proteomic analysis and resources indexation system. Bioinformatics, 20: 133-5, 2004.

[65] J. Wang, C. Caron, M. Y. Mistou, C. Gitton, and A. Trubuil. PARIS: a Proteomic Analysis and Resources Indexation System. Bioinformatics, 20(1): 133-135, 2004.
Keywords : Electrophoresis, Image Analysis, Proteomics, Database. Data Mining..
Mots-clés : Bioinformatique, 2DE, électrophorèse, analyse d'image, Protéomique.

[66] H. Cardot, J.-Y. Koo, H. J. Park, and A. Trubuil. Boosting Diracs for electrophoresis. J. of Comput. and Graph. Statist., 13(3): 659-673, 2004.
Keywords : Backfitting, deconvolution, GCV, merging, positivity, selection of Diracs, spatial inhomogeneity, variables selection.

[67] J. Wang, A. Trubuil, C. Graffigne, and B. Kaeffer. 3-D aggregated object detection and labeling from multivariate confocal microscopy images : a model validation approach. IEEE Transactions on Systems, Man and Cybernetics, Part B, 33(4): 572-581, 2003.
Keywords : Image analysis, cytometry, intestinal crypts, confocal microscopy, multivariate statistics, model validation..
Mots-clés : Cytometrie, microscopie confocale, analyse d'image, crypte colique, statistique, validation, de modèle.

[68] C. Kervrann and A. Trubuil. Optimal level curves and minimizers of cost functionals in image segmentation. Journal of Mathematical Imaging and Vision, 17(2): 153-174, 2002.
Keywords : Image segmentation, energy minimization, level sets, level lines connected components.. [ .pdf ]

[69] C. Kervrann, M. Hoebeke, and A. Trubuil. Isophotes selection and reaction-diffusion model for object boundaries estimation. Int. Journal on Computer Vision, 50(1): 63-94, 2002.
Keywords : Grouping and segmentation, energy minimization, level sets, level lines, isophotes, connected components, anisotropic diffusion. [ .pdf ]

[70] B. Kaeffer, A. Trubuil, C. Kervrann, L. Pardini, and C. Cherbut. Three-dimensional binding of epidermal growth factor peptides in colonic tissues produced from rotating bioreactor. In Vitro Cellular and Developmental Biology - Animal, 38(8): 436-439, 2002.
Keywords : colon, primary culture, multidimensional microscopy, EGF, rotating wall vessel.

[71] B. Combal, F. Baret, M. Weiss, A. Trubuil, D. Macé, A. Pragnère, R. Myneni, Y. Knyazikhin, and L. Wang. Retrieval of canopy biophysical variables from bidirectional reflectance unsing prior information to solve the ill-posed inverse problem. Remote Sensing of Environment, (84): 1-15, 2002.
Keywords : Inverse problem, prior information, lookup table, quasi-newton, neural network..

[72] A. Trubuil. Discussion on the paper by Glasbey and Mardia “A penalized likelihood approach to image warping” (pp.465-492). J. R. Statist. Soc. B, 63(3): 507-508, 2001.

[73] A. Trubuil. Analysis of one-dimensional electrophoregrams. Computer Applications in the Biosciences, 9(4): 451-458, 1993.
Keywords : Electropheresis, image analysis, distortion, DNA, protein.


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