Publications
At the present time, a total of 79 scientific publications in peer-reviewed journals and conference proceedings have been produced by the consortium (see below). There are 18 joint publications involving different BaSysBio partners. Please note that only published and "in press" articles have been included in this list. Additional publications are currently under review or will be submitted imminently. Importantly, these include two major pan-consortium manuscripts that reflect the highlights of our multi-laboratory and inter-disciplinary approach to Systems Biology.Optimization in computational systems biology
Banga, J. R., (2008).
BMC Syst Biol 2: 47
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome
Becher, D., K. Hempel, S. Sievers, D. Zuhlke, J. Pane-Farre, A. Otto, S. Fuchs, D. Albrecht, J. Bernhardt, S. Engelmann, U. Volker, J. M. van Dijl & M. Hecker, (2009).
PLoS One 4: e8176
Suite of novel vectors for ectopic insertion of GFP, CFP and IYFP transcriptional fusions in single copy at the amyE and bglS loci in Bacillus subtilis
Bisicchia, P., E. Botella & K. M. Devine, (2010a).
Plasmid 64: 143-149
Peptidoglycan metabolism is controlled by the WalRK (YycFG) and PhoPR two-component systems in phosphate-limited Bacillus subtilis cells
Bisicchia, P., E. Lioliou, D. Noone, L. I. Salzberg, E. Botella, S. Hubner & K. M. Devine, (2010b).
Mol Microbiol 75: 972-989
Fragmentation-free LC-MS can identify hundreds of proteins
Bochet, P., F. Rugheimer, T. Guina, P. Brooks, D. Goodlett, P. Clote & B. Schwikowski, (2011).
Proteomics 11: 22-32
pBaSysBioII: an integrative plasmid generating gfp transcriptional fusions for high-throughput analysis of gene expression in Bacillus subtilis
Botella, E., M. Fogg, M. Jules, S. Piersma, G. Doherty, A. Hansen, E. L. Denham, L. Le Chat, P. Veiga, K. Bailey, P. J. Lewis, J. M. van Dijl, S. Aymerich, A. J. Wilkinson & K. M. Devine, (2010).
Microbiology 156: 1600-1608
Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis
Bruck, J., W. Liebermeister & E. Klipp, (2008).
Genome Inform 20: 1-14
Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
Buescher, J. M., D. Czernik, J. C. Ewald, U. Sauer & N. Zamboni, (2009).
Anal Chem 81: 2135-2143
Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites
Buescher, J. M., S. Moco, U. Sauer & N. Zamboni, (2010).
Anal Chem 82: 4403-4412
Recombination between ccrC genes in a type V (5C2&5) staphylococcal cassette chromosome mec (SCCmec) of Staphylococcus aureus ST398 leads to conversion from methicillin resistance to methicillin susceptibility in vivo
Chlebowicz, M. A., K. Nganou, S. Kozytska, J. P. Arends, S. Engelmann, H. Grundmann, K. Ohlsen, J. M. van Dijl & G. Buist, (2010).
Antimicrob Agents Chemother 54: 783-791
Considerations for the distinction of ccrC-containing staphylococcal cassette chromosome mec elements
Chlebowicz, M. A., J. M. van Dijl & G. Buist, (2011).
Antimicrob Agents Chemother 55: 1823-1824
Characterization of a serine/threonine kinase involved in virulence of Staphylococcus aureus
Debarbouille, M., S. Dramsi, O. Dussurget, M. A. Nahori, E. Vaganay, G. Jouvion, A. Cozzone, T. Msadek & B. Duclos, (2009).
J Bacteriol 191: 4070-4081
Peptidoglycan crosslinking relaxation plays an important role in Staphylococcus aureus WalKR-dependent cell viability
Delaune, A., O. Poupel, A. Mallet, Y. M. Coic, T. Msadek & S. Dubrac, (2011).
PLoS One 6: e17054
The dynamic protein partnership of RNA polymerase in Bacillus subtilis
Delumeau, O., F. Lecointe, J. Muntel, A. Guillot, E. Guédon, V. Monnet, M. Hecker, D. Becher, P. Polard & P. Noirot, (2011).
Proteomics: (in press).
Stage-specific fluorescence intensity of GFP and mCherry during sporulation In Bacillus Subtilis
Doherty, G. P., K. Bailey & P. J. Lewis, (2010a).
BMC Res Notes 3: 303
Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition
Doherty, G. P., M. J. Fogg, A. J. Wilkinson & P. J. Lewis, (2010b).
Microbiology 156: 3532-3543
Profiling the surfacome of Staphylococcus aureus
Dreisbach, A., K. Hempel, G. Buist, M. Hecker, D. Becher & J. M. van Dijl, (2010).
Proteomics 10: 3082-3096
The cell surface proteome of Staphylococcus aureus
Dreisbach, A., J. M. Van Dijl & G. Buist, (2011).
Proteomics (in press).
Immunity to the bacteriocin sublancin 168 Is determined by the SunI (YolF) protein of Bacillus subtilis
Dubois, J. Y., T. R. Kouwen, A. K. Schurich, C. R. Reis, H. T. Ensing, E. N. Trip, J. C. Zweers & J. M. van Dijl, (2009).
Antimicrob Agents Chemother 53: 651-661
A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway
Dubrac, S., P. Bisicchia, K. M. Devine & T. Msadek, (2008).
Mol Microbiol 70: 1307-1322
New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus
Dubrac, S., I. G. Boneca, O. Poupel & T. Msadek, (2007).
J Bacteriol 189: 8257-8269
Tearing down the wall: peptidoglycan metabolism and the WalK/WalR (YycG/YycF) essential two-component system
Dubrac, S. & T. Msadek, (2008).
Adv Exp Med Biol 631: 214-228
Life without the essential bacterial tRNA(Ile2) -lysidine synthetase TilS: a case of tRNA gene recruitment in Bacillus subtilis
Fabret, C., E. Dervyn, B. Dalmais, A. Guillot, C. Marck, H. Grosjean & P. Noirot, (2011).
Mol Microbiol 80: 1062-1074
Investigation of the Staphylococcus aureus GraS/GraR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways
Falord, M., U. Mader, A. Hiron, M. Debarbouille & T. Msadek, (2011).
PLoS One: (in press).
Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
Fendt, S. M., J. M. Buescher, F. Rudroff, P. Picotti, N. Zamboni & U. Sauer, (2010).
Mol Syst Biol 6: 356
Higher-throughput approaches to crystallization and crystal structure determination
Fogg, M. J. & A. J. Wilkinson, (2008).
Biochem Soc Trans 36: 771-775
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis
Goelzer, A., F. Bekkal Brikci, I. Martin-Verstraete, P. Noirot, P. Bessieres, S. Aymerich & V. Fromion, (2008).
BMC Syst Biol 2: 20
Cell design in bacteria as a convex optimization problem
Goelzer, A., V. Fromion & G. Scorletti, (2011).
Automatica 47: 1210–1218
Novel antibacterial compounds specifically targeting the essential WalR response regulator
Gotoh, Y., A. Doi, E. Furuta, S. Dubrac, Y. Ishizaki, M. Okada, M. Igarashi, N. Misawa, H. Yoshikawa, T. Okajima, T. Msadek & R. Utsumi, (2010).
J Antibiot (Tokyo) 63: 127-134
A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation
Hahne, H., U. Mader, A. Otto, F. Bonn, L. Steil, E. Bremer, M. Hecker & D. Becher, (2010).
J Bacteriol 192: 870-882
A proteomic view of cell physiology and virulence of Staphylococcus aureus
Hecker, M., D. Becher, S. Fuchs & S. Engelmann, (2010).
Int J Med Microbiol 300: 76-87
Bacitracin and nisin resistance in Staphylococcus aureus : a novel pathway involving the BraS/BraR two-component system and both the BraD/BraE and VraD/VraE ABC transporters
Hiron, A., M. Falord, J. Valle, M. Débarbouillé & T. Msadek, (2011).
Mol Microbiol: (in press).
Comparative study of two plasticins: specificity, interfacial behavior, and bactericidal activity
Joanne, P., M. Falord, O. Chesneau, C. Lacombe, S. Castano, B. Desbat, C. Auvynet, P. Nicolas, T. Msadek & C. El Amri, (2009).
Biochemistry 48: 9372-9383
The Bacillus subtilis ywjI (glpX) gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the class III Fbp enzyme
Jules, M., L. Le Chat, S. Aymerich & D. Le Coq, (2009).
J Bacteriol 191: 3168-3171
Metabolic fluxes during strong carbon catabolite repression by malate in Bacillus subtilis
Kleijn, R. J., J. M. Buescher, L. Le Chat, M. Jules, S. Aymerich & U. Sauer, (2010).
J Biol Chem 285: 1587-1596
Thioredoxin A active-site mutants form mixed disulfide dimers that resemble enzyme-substrate reaction intermediates
Kouwen, T. R., J. Andrell, R. Schrijver, J. Y. Dubois, M. J. Maher, S. Iwata, E. P. Carpenter & J. M. van Dijl, (2008).
J Mol Biol 379: 520-534
MscL of Bacillus subtilis prevents selective release of cytoplasmic proteins in a hypotonic environment
Kouwen, T. R., H. Antelmann, R. van der Ploeg, E. L. Denham, M. Hecker & J. M. van Dijl, (2009a).
Proteomics 9: 1033-1043
Contributions of the pre- and pro-regions of a Staphylococcus hyicus lipase to secretion of a heterologous protein by Bacillus subtilis
Kouwen, T. R., A. K. Nielsen, E. L. Denham, J. Y. Dubois, R. Dorenbos, M. D. Rasmussen, W. J. Quax, R. Freudl & J. M. van Dijl, (2010).
Appl Environ Microbiol 76: 659-669
The large mechanosensitive channel MscL determines bacterial susceptibility to the bacteriocin sublancin 168
Kouwen, T. R., E. N. Trip, E. L. Denham, M. J. Sibbald, J. Y. Dubois & J. M. van Dijl, (2009b).
Antimicrob Agents Chemother 53: 4702-4711
Thiol-disulphide oxidoreductase modules in the low-GC Gram-positive bacteria
Kouwen, T. R., A. van der Goot, R. Dorenbos, T. Winter, H. Antelmann, M. C. Plaisier, W. J. Quax, J. M. van Dijl & J. Y. Dubois, (2007).
Mol Microbiol 64: 984-999
Overflow of a hyper-produced secretory protein from the Bacillus Sec pathway into the Tat pathway for protein secretion as revealed by proteogenomics
Kouwen, T. R., R. van der Ploeg, H. Antelmann, M. Hecker, G. Homuth, U. Mader & J. M. van Dijl, (2009c).
Proteomics 9: 1018-1032
Applications of thiol-disulfide oxidoreductases for optimized in vivo production of functionally active proteins in Bacillus
Kouwen, T. R. & J. M. van Dijl, (2009a).
Appl Microbiol Biotechnol 85: 45-52
Interchangeable modules in bacterial thiol-disulfide exchange pathways
Kouwen, T. R. & J. M. van Dijl, (2009b).
Trends Microbiol 17: 6-12
Annotation and merging of SBML models with semanticSBML
Krause, F., J. Uhlendorf, T. Lubitz, M. Schulz, E. Klipp & W. Liebermeister, (2010).
Bioinformatics 26: 421-422
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Liebermeister, W., J. Uhlendorf & E. Klipp, (2010).
Bioinformatics 26: 1528-1534
Parameter balancing in kinetic models of cell metabolism
Lubitz, T., M. Schulz, E. Klipp & W. Liebermeister, (2010).
J Phys Chem B 114: 16298-16303
Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods
Mader, U., P. Nicolas, H. Richard, P. Bessieres & S. Aymerich, (2011).
Curr Opin Biotechnol 22: 32-41
Learning ontological rules to extract multiple relations of genic interactions from text
Manine, A. P., E. Alphonse & P. Bessieres, (2009).
Int J Med Inform 78: e31-38
An expanded protein–protein interaction network in Bacillus subtilis reveals a group of hubs: Exploration by an integrative approach
Marchadier, E., R. Carballido Lopez, S. Brinster, C. Fabret, P. Mervelet, P. Bessieres, M.-F. Noirot-Gros, V. Fromion & P. Noirot, (2011).
Proteomics: (in press).
Phylogenetic distances are encoded in networks of interacting pathways
Mazurie, A., D. Bonchev, B. Schwikowski & G. A. Buck, (2008).
Bioinformatics 24: 2579-2585
Staphylococcal PknB as the first prokaryotic representative of the proline-directed kinases
Miller, M., S. Donat, S. Rakette, T. Stehle, T. R. Kouwen, S. H. Diks, A. Dreisbach, E. Reilman, K. Gronau, D. Becher, M. P. Peppelenbosch, J. M. van Dijl & K. Ohlsen, (2010).
PLoS One 5: e9057
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
Nicolas, P., A. Leduc, S. Robin, S. Rasmussen, H. Jarmer & P. Bessieres, (2009).
Bioinformatics 25: 2341-2347
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis
Otto, A., J. Bernhardt, H. Meyer, M. Schaffer, F. A. Herbst, J. Siebourg, U. Mader, M. Lalk, M. Hecker & D. Becher, (2010).
Nat Commun 1: 137
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions
Peres, S., L. Felicori, S. Rialle, E. Jobard & F. Molina, (2010).
Bioinformatics 26: 1542-1547
A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
Peres, S., L. Molina, N. Salvetat, C. Granier & F. Molina, (2008).
BMC Bioinformatics 9: 460
Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress
Pohl, S., W. T. Tu, P. D. Aldridge, G. C., H. Hahn, U. Mäder, G. Homuth, T. D. Read & C. R. Harwood, (2011).
Proteomics (in press).
Transcriptional activator YesS is stimulated by histidine-phosphorylated HPr of the Bacillus subtilis phosphotransferase system
Poncet, S., M. Soret, P. Mervelet, J. Deutscher & P. Noirot, (2009).
J Biol Chem 284: 28188-28197
The transcriptionally active regions in the genome of Bacillus subtilis
Rasmussen, S., H. B. Nielsen & H. Jarmer, (2009).
Mol Microbiol 73: 1043-1057
Expression of soluble, active fragments of the morphogenetic protein SpoIIE from Bacillus subtilis using a library-based construct screen
Rawlings, A. E., V. M. Levdikov, E. Blagova, V. L. Colledge, P. J. Mas, J. Tunaley, L. Vavrova, K. S. Wilson, I. Barak, D. J. Hart & A. J. Wilkinson, (2010).
Protein Eng Des Sel 23: 817-825
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
Rialle, S., L. Felicori, C. Dias-Lopes, S. Peres, S. El Atia, A. R. Thierry, P. Amar & F. Molina, (2010).
Bioinformatics 26: 2298-2304
A generalized Fisher equation and its utility in chemical kinetics
Ross, J., A. Fernandez Villaverde, J. R. Banga, S. Vazquez & F. Moran, (2010).
Proc Natl Acad Sci U S A 107: 12777-12781
Subpopulation-specific metabolic pathway usage in mixed cultures as revealed by reporter protein-based 13C analysis
Ruhl, M., W. D. Hardt & U. Sauer, (2011).
Appl Environ Microbiol 77: 1816-1821
Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture
Ruhl, M., N. Zamboni & U. Sauer, (2010).
Biotechnol Bioeng 105: 795-804
Nested uncertainties in biochemical models
Schaber, J., W. Liebermeister & E. Klipp, (2009).
IET Syst Biol 3: 1-9
Multi-objective optimization of biological networks for prediction of intracellular fluxes
Sendin, J. O., A. A. Alonso & J. R. Banga, (2009).
Advances in Soft Computing 49: 197-205
Multi-objective mixed integer strategy for the optimisation of biological networks
Sendin, J. O., O. Exler & J. R. Banga, (2010).
IET Syst Biol 4: 236-248
Synthetic effects of secG and secY2 mutations on exoproteome biogenesis in Staphylococcus aureus
Sibbald, M. J., T. Winter, M. M. van der Kooi-Pol, G. Buist, E. Tsompanidou, T. Bosma, T. Schafer, K. Ohlsen, M. Hecker, H. Antelmann, S. Engelmann & J. M. van Dijl, (2010).
J Bacteriol 192: 3788-3800
The pleiotropic CymR regulator of Staphylococcus aureus plays an important role in virulence and stress response
Soutourina, O., S. Dubrac, O. Poupel, T. Msadek & I. Martin-Verstraete, (2010).
PLoS Pathog 6: e1000894
CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation
Soutourina, O., O. Poupel, J. Y. Coppee, A. Danchin, T. Msadek & I. Martin-Verstraete, (2009).
Mol Microbiol 73: 194-211
Requirement of the agr locus for colony spreading of Staphylococcus aureus
Tsompanidou, E., M. J. Sibbald, M. A. Chlebowicz, A. Dreisbach, J. W. Back, J. M. van Dijl, G. Buist & E. L. Denham, (2011).
J Bacteriol 193: 1267-1272
Analysis of Degenerate Chemical Reaction Networks
Uhr, M., H. M. Kaltenbach, C. Conradi & J. Stelling, (2009).
In: Lecture Notes in Control and Information Sciences - Proceedings of Positive Systems: Theory and Applications. Berlin / Heidelberg: Springer, pp. 163-171
Structural sensitivity analysis of metabolic networks
Uhr, M. & J. Stelling, (2008).
In: Proc. IFAC World Congress 2008
Inference of transcriptional control design of metabolic networks
Uhr, M., A. F. Villaverde, J. A. Egea, J. R. Banga & J. Stelling, (2011).
In: Proc. IFAC World Congress 2011
Environmental salinity determines the specificity and need for Tat-dependent secretion of the YwbN protein in Bacillus subtilis
van der Ploeg, R., U. Mader, G. Homuth, M. Schaffer, E. L. Denham, C. G. Monteferrante, M. Miethke, M. A. Marahiel, C. R. Harwood, T. Winter, M. Hecker, H. Antelmann & J. M. van Dijl, (2011).
PLoS One 6: e18140
Genetic or chemical protease inhibition causes significant changes in the Bacillus subtilis exoproteome
Westers, L., H. Westers, G. Zanen, H. Antelmann, M. Hecker, D. Noone, K. M. Devine, J. M. van Dijl & W. J. Quax, (2008).
Proteomics 8: 2704-2713
Tandem affinity purification vectors for use in gram positive bacteria
Yang, X., G. P. Doherty & P. J. Lewis, (2008).
Plasmid 59: 54-62
Proteomics uncovers extreme heterogeneity in the Staphylococcus aureus exoproteome due to genomic plasticity and variant gene regulation
Ziebandt, A. K., H. Kusch, M. Degner, S. Jaglitz, M. J. Sibbald, J. P. Arends, M. A. Chlebowicz, D. Albrecht, R. Pantucek, J. Doskar, W. Ziebuhr, B. M. Broker, M. Hecker, J. M. van Dijl & S. Engelmann, (2010).
Proteomics 10: 1634-1644
Stress-responsive systems set specific limits to the overproduction of membrane proteins in Bacillus subtilis
Zweers, J. C., T. Wiegert & J. M. van Dijl, (2009).
Appl Environ Microbiol 75: 7356-7364
