Publications
  1. Otero JM, Nielsen J (2010) Industrial Systems Biology. Biotechnol. Bioeng. 105:439-460

  2. Kim I-K, Roldao A, Siewers V, Nielsen J (2012) A system-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res., 2012 Mar;12(2):228-48

  3. Tyo KE, Siewers V (2011) Meeting report: Gothenburg Life Science Conference XI: Industrial Systems Biology. Biotechnol. J. 6:259-261

  4. Nielsen J (2011) Editorial: Industrial Systems Biology. Biotechnol. J. 6:255

  5. Liu LM, Agren R, Bordel S, Nielsen J. (2010) Use of genome-scale metabolic models for understanding microbial physiology. FEBS Lett. 584:2556-2564.

  6. Österlund T, Nookaew I, Nielsen J (2012) Fifteen years of large scale metabolic modeling of yeast: Developments and impacts. Biotechnol. Adv., in press

  7. Cvijovic M, Bordel S, Nielsen J (2011) Mathematical models of cell factories: Moving towards the cores of industrial biotechnology. Microbiol. Biotechnol. 4:572-584

  8. Cvijovic M, Olivares-Hernandez R, Agren R, Vongsangnak W, Nookaew I, Patil KR, Nielsen J (2010) BioMet Toolbox: Genome-wide analysis of metabolism. Nuc. Acid Res. 38:W144-W149

  9. Wiechert W, Noack S (2011) Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile, Current Opinion Biotechnol. 22:604–610

  10. Kotte O, Heinemann M (2009) A divide–and–conquer approach to analyze underdetermined biochemical models. Bioinformatics 25:519-525

  11. Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol. Systems Biol. 6:355

  12. Rocha M, Maia P, Mendes R, Pinto JP, Ferreira EC, Nielsen J, Patil KR, Rocha I (2008) Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics 9:499

  13. Vilaça P, Maia P, Rocha I, Rocha M (2010) Metaheuristics for strain optimization using transcriptional information enriched metabolic models. Lecture Notes in Computer Science 6023:205-216

  14. Evangelista P, Rocha I, Ferreira EC, Rocha M (2009) Evolutionary approaches for strain optimization using dynamic models under a metabolic engineering perspective. Lecture Notes in Computer Science 5483:140-151

  15. Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M (2010) OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology 4:45

  16. Vilaça P, Rocha I, Rocha MA (2011) Computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information. BioSystems 103:435-441

  17. Bordel S, Nielsen J (2010) Identification of flux control in metabolic networks using non-equilibrium thermodynamics. Metab. Eng. 13:369-377

  18. Hadlich F, Nöh K, Wiechert W (2010) Determination of flux directions by thermodynamic network analysis: computing informative metabolite pools. Math. Comp. Sim. 10:1016

  19. Bordel S, Agren R, Nielsen J (2010) Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes. 2010. PLoS Comput. Biol. 6:e1000859.

  20. Droste P, Miebach S, Niedenführ S, Wiechert W, Nöh K (2011) Visualizing multi-omics data in metabolic networks with the software Omix - A case study. BioSystems 105:154-161

  21. Fendt SM, Oliveira AP, Christen S, Picotti P, Dechant RC, Sauer U (2010) Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol. Systems Biol. 6:432

  22. Fazio A, Jewett M, Daran-Lapujade P, Mustacchi R, Usaite R, Pronk JT, Workman C, Nielsen J (2008) Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design. BMC Genomics 9:341

  23. Usaite R, Jewett MC, Oliveira AP, Yates JR, Olsson L, Nielsen J (2009). Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol. Systems Biol. 5:319

  24. Vongsangnak W, Hansen K, Nielsen J (2011)Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae. Biotechnol. Bioeng. 108:1130-1139

  25. Canelas A.B., Burton N., Fazio A., Zhang J., Pitkänen J., van den Brink J.,  Bakker B., Bouwman J., Castrillo J.,  Cankorur A., Chumnanpuen P., Daran-Lapujade P., Dikicioglu D., van Eunen K., Ewald J.C., Heijnen J.J., Kirdar B., Niebel A., Penttilä M., Pronk J., Reuss M, Rintala E., Sauer U., Sherman D., Siemann-Hertzberg M., Westerhoff H., Petranovic D., Oliver S., Workman C., Zamboni N., Nielsen J. (2010) Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains. Nature Comm. 1:145

  26. Rantanen A, Rousu J, Jouhten P, Zamboni N, Maaheimo H, Ukkonen E (2008) An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments.  BMC Bioinformatics 9:266

  27. Zamboni N, Fendt SM, Rühl M, Sauer U (2009) (13)C-based metabolic flux analysis. Nat. Protoc. 4:878–92

  28. Wahl SA, Nöh K, Wiechert W (2008) 13C labeling experiments at metabolic nonstationary conditions: an exploratory study. BMC Bioinformatics 9:152

  29. Christen S, Sauer U (2011) Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics. FEMS Yeast Res 11:263-272

  30. Canelas AB, ten Pierick A, et al.  (2009) Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomics. Anal. Chem. 81:7379-7389

  31. Ewald JC, Heux S, Zamboni N (2009) High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal. Chem. 81:3623-3629.

  32. Vielhauer O, Zakhartsev M, Horn T, Takors R, Reuss M (2012) Simplified absolute metabolite quantification by gas-chromatography dilution mass spectrometry on the basis of commercial available source material. J. Chromatography B, 879:3859-70.

  33. Otero JM, Vongsangak W, Asadollahi MA, Olivares-Hernandes R, Maury J, Farinelli L, Barlocher L, Østerås M, Schalk M, Clark A, Nielsen J (2010) Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. BMC Genomics 11:723

  34. Hong K-K, Vongsangnak W, Vemuri GN, Nielsen J (2011) Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc. Nat. Acad. Sci. USA 108:12179-12184



 

The SYSINBIO project, Coordination and Support Action, contract no.: 212766, is funded by the European Commission within the seventh Framework Programme.