Jens Nielsen

Summary

Affiliation: Technical University of Denmark
Country: Denmark

Publications

  1. pmc Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae
    Francisco J Pizarro
    Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Macul, Santiago, Chile
    Appl Environ Microbiol 74:6358-68. 2008
  2. pmc Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
    Birgitte Regenberg
    Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe Universitat, Max von Laue Str, 9, 60438 Frankfurt am Main, Germany
    Genome Biol 7:R107. 2006
  3. pmc Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans
    Helga David
    Fluxome Sciences A S, Diplomvej, DK 2800 Kgs, Lyngby, Denmark
    Genome Biol 7:R108. 2006
  4. pmc Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
    Tunahan Cakir
    Bogazici University, Department of Chemical Engineering, 34342, Bebek, Istanbul, Turkey
    BMC Syst Biol 1:18. 2007
  5. pmc It is all about metabolic fluxes
    Jens Nielsen
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    J Bacteriol 185:7031-5. 2003
  6. ncbi request reprint The next wave in metabolome analysis
    Jens Nielsen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Trends Biotechnol 23:544-6. 2005
  7. ncbi request reprint Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae
    Jens Nielsen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    FEMS Yeast Res 8:122-31. 2008
  8. pmc Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools
    Gianni Panagiotou
    Center for Microbial Biotechnology, Department of Systems Biology, Building 223, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark
    Appl Environ Microbiol 75:2212-20. 2009
  9. pmc Evolutionary programming as a platform for in silico metabolic engineering
    Kiran Raosaheb Patil
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    BMC Bioinformatics 6:308. 2005
  10. pmc Identification of in vivo enzyme activities in the cometabolism of glucose and acetate by Saccharomyces cerevisiae by using 13C-labeled substrates
    Margarida Moreira dos Santos
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800, Lyngby, Denmark
    Eukaryot Cell 2:599-608. 2003

Collaborators

Detail Information

Publications95

  1. pmc Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae
    Francisco J Pizarro
    Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Macul, Santiago, Chile
    Appl Environ Microbiol 74:6358-68. 2008
    ..Our study provides global insight into how growth temperature affects differential physiological and transcriptional responses in laboratory and wine strains of S. cerevisiae...
  2. pmc Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae
    Birgitte Regenberg
    Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe Universitat, Max von Laue Str, 9, 60438 Frankfurt am Main, Germany
    Genome Biol 7:R107. 2006
    ..We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying between 2 and 35 hours...
  3. pmc Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans
    Helga David
    Fluxome Sciences A S, Diplomvej, DK 2800 Kgs, Lyngby, Denmark
    Genome Biol 7:R108. 2006
    ..CONCLUSION: Our analysis indicates that some of the genes are regulated by common transcription factors, making it possible to establish new putative links between known transcription factors and genes through clustering...
  4. pmc Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
    Tunahan Cakir
    Bogazici University, Department of Chemical Engineering, 34342, Bebek, Istanbul, Turkey
    BMC Syst Biol 1:18. 2007
    ..The CEF analysis is based on a simple stoichiometric model that includes reactions of the central carbon metabolism and the amino acid metabolism...
  5. pmc It is all about metabolic fluxes
    Jens Nielsen
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    J Bacteriol 185:7031-5. 2003
  6. ncbi request reprint The next wave in metabolome analysis
    Jens Nielsen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Trends Biotechnol 23:544-6. 2005
    ....
  7. ncbi request reprint Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae
    Jens Nielsen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    FEMS Yeast Res 8:122-31. 2008
    ..Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given...
  8. pmc Studies of the production of fungal polyketides in Aspergillus nidulans by using systems biology tools
    Gianni Panagiotou
    Center for Microbial Biotechnology, Department of Systems Biology, Building 223, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark
    Appl Environ Microbiol 75:2212-20. 2009
    ....
  9. pmc Evolutionary programming as a platform for in silico metabolic engineering
    Kiran Raosaheb Patil
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    BMC Bioinformatics 6:308. 2005
    ....
  10. pmc Identification of in vivo enzyme activities in the cometabolism of glucose and acetate by Saccharomyces cerevisiae by using 13C-labeled substrates
    Margarida Moreira dos Santos
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800, Lyngby, Denmark
    Eukaryot Cell 2:599-608. 2003
    ..Cytoplasmic alanine aminotransferase activity was detected, and evidence was found that alpha-isopropylmalate synthase has two active forms in vivo, one mitochondrial and the other a short cytoplasmic form...
  11. pmc Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: a three factor design
    Alessandro Fazio
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK 2800, Kgs, Lyngby, Denmark
    BMC Genomics 9:341. 2008
    ..The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability...
  12. doi request reprint Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply
    Songsak Wattanachaisaereekul
    Center for Microbial Biotechnology, Technical University of Denmark, Department of Systems Biology, Denmark
    Metab Eng 10:246-54. 2008
    ..The production of 6-MSA was scaled up by the cultivation in minimal media containing 50 g/L of glucose, and hereby a final titer of 554+/-26 mg/L of 6-MSA was obtained...
  13. ncbi request reprint Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae
    Vijayendran Raghevendran
    Center for Microbial Biotechnology, Building 223, BioCentrum DTU, Technical University of Denmark, DK 2800, Kongens Lyngby, Denmark
    J Biol Chem 281:12308-14. 2006
    ....
  14. pmc Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
    Renata Usaite
    Department of Systems Biology, Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    Mol Syst Biol 5:319. 2009
    ....
  15. ncbi request reprint Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains
    Thomas Grotkjaer
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Metab Eng 7:437-44. 2005
    ..CR4. Furthermore, the analysis indicated that the glyoxylate cycle was activated in CPB.CR4...
  16. ncbi request reprint Phenotypic characterization of glucose repression mutants of Saccharomyces cerevisiae using experiments with 13C-labelled glucose
    Vijayendran Raghevendran
    Centre for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, Lyngby DK 2800, Denmark
    Yeast 21:769-79. 2004
    ..Furthermore, deletion of the genes MIG1, MIG1/MIG2 and REG1 did not result in a significant change in the phenotype at the fluxome level...
  17. ncbi request reprint Elucidation of the role of Grr1p in glucose sensing by Saccharomyces cerevisiae through genome-wide transcription analysis
    Steen L Westergaard
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    FEMS Yeast Res 5:193-204. 2004
    ....
  18. ncbi request reprint Manipulation of malic enzyme in Saccharomyces cerevisiae for increasing NADPH production capacity aerobically in different cellular compartments
    Margarida Moreira dos Santos
    Center for Process Biotechnology, Technical University of Denmark, BioCentrum DTU, Building 223, DK 2800 Lyngby, Denmark
    Metab Eng 6:352-63. 2004
    ..This may find application in redirecting fluxes for improving specific biotechnological applications...
  19. ncbi request reprint Altering the expression of two chitin synthase genes differentially affects the growth and morphology of Aspergillus oryzae
    Christian Muller
    Center for Process Biotechnology, BioCentrum DTU building, 223, Søltofts Plads, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Microbiology 148:4025-33. 2002
    ..Northern analysis indicated no change in the transcription of the chitin synthase genes csmA and chsC when chsB expression was altered, and there was no change in the transcription of chsB and chsC when csmA was disrupted...
  20. ncbi request reprint Grr1p is required for transcriptional induction of amino acid permease genes and proper transcriptional regulation of genes in carbon metabolism of Saccharomyces cerevisiae
    Nadine Eckert-Boulet
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, BioCentrum DTU, 2800 Lyngby, Denmark
    Curr Genet 47:139-49. 2005
    ....
  21. ncbi request reprint Control of fluxes towards antibiotics and the role of primary metabolism in production of antibiotics
    Nina Gunnarsson
    BioCentrum DTU, Center for Microbial Biotechnology, Building 223, Søltofts Plads, 2800 Lyngby, Denmark
    Adv Biochem Eng Biotechnol 88:137-78. 2004
    ....
  22. ncbi request reprint In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
    Christoffer Bro
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Metab Eng 8:102-11. 2006
    ..Similarly, expression of GAPN in a strain harbouring xylose reductase and xylitol dehydrogenase led to an improvement in ethanol yield by up to 25% on xylose/glucose mixtures...
  23. doi request reprint The roles of galactitol, galactose-1-phosphate, and phosphoglucomutase in galactose-induced toxicity in Saccharomyces cerevisiae
    Willem A de Jongh
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, Søltofts Plads, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 101:317-26. 2008
    ....
  24. ncbi request reprint Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol
    Gianni Panagiotou
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Soltofts Plads, Building 223, 2800 Lyngby, Denmark
    J Biotechnol 115:425-34. 2005
    ..On the other hand, the presence of high levels of gamma-amino-n-butyric acid (GABA) under anaerobic conditions suggests a functional GABA bypass and a possible block in the TCA cycle at these conditions...
  25. ncbi request reprint Glucose metabolism in the antibiotic producing actinomycete Nonomuraea sp. ATCC 39727
    Nina Gunnarsson
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, Søltofts Plads, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 88:652-63. 2004
    ..In contrast, expression levels of genes encoding enzymes in the ED and EMP pathways were not affected by phosphate limitation...
  26. ncbi request reprint Steady-state and transient-state analyses of aerobic fermentation in Saccharomyces kluyveri
    Kasper Møller
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, 2800 Lyngby, Denmark
    FEMS Yeast Res 2:233-44. 2002
    ..kluyveri led to ethanol formation after a delay of 20-50 min (depending on culture conditions prior to the pulse), which is in contrast to S. cerevisiae that ferments immediately after glucose addition...
  27. ncbi request reprint Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm
    Thomas Grotkjaer
    Center for Microbial Biotechnology BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Bioinformatics 22:58-67. 2006
    ..The algorithm preserves valuable properties of hierarchical clustering, which is useful for visualization and interpretation of the results...
  28. ncbi request reprint Use of genome-scale microbial models for metabolic engineering
    Kiran Raosaheb Patil
    Center for Process Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Curr Opin Biotechnol 15:64-9. 2004
    ..Genome-scale stoichiometric models of microorganisms represent a first step in this direction...
  29. ncbi request reprint Lipase production by recombinant strains of Aspergillus niger expressing a lipase-encoding gene from Thermomyces lanuginosus
    Wai Prathumpai
    BioCentrum DTU, Center for Microbial Biotechnology, Technical University of Denmark, Building 223, 2800 Lyngby, Denmark
    Appl Microbiol Biotechnol 65:714-9. 2004
    ..niger. However, SDS-PAGE analysis showed that most of the produced lipase was bound to the cell wall...
  30. doi request reprint Enhancement of farnesyl diphosphate pool as direct precursor of sesquiterpenes through metabolic engineering of the mevalonate pathway in Saccharomyces cerevisiae
    Mohammad A Asadollahi
    Department of Systems Biology, Center for Microbial Biotechnology, Building 223, Technical University of Denmark DTU, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 106:86-96. 2010
    ..This could be explained by a toxicity effect of cubebol, possibly resulting in higher transcription levels for the genes under control of MET3 promoter, which could lead to accumulation of squalene and ergosterol...
  31. pmc Metabolic network analysis of Streptomyces tenebrarius, a Streptomyces species with an active entner-doudoroff pathway
    Irina Borodina
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 71:2294-302. 2005
    ..Higher specific NADH and NADPH production rates were calculated in the cultivation on glucose-glycerol, which was associated with a lower percentage of nonreduced antibiotic kanamycin B carbamate...
  32. doi request reprint Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
    Mohammad A Asadollahi
    Center for Microbial Biotechnology CMB, Department of Systems Biology, Building 223, Technical University of Denmark DTU, DK 2800 Kgs Lyngby, Denmark
    Metab Eng 11:328-34. 2009
    ..Over-expression of GDH2 did not show a further effect on the final cubebol titer but this alteration significantly improved the growth rate compared to the GDH1 deleted strain...
  33. ncbi request reprint Genome-wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism
    Christoffer Bro
    Center for Process Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 85:269-76. 2004
    ..Furthermore, we showed that it might be necessary to analyze the expression of a subset of genes to extract all available information from global transcription analysis...
  34. pmc Versatile enzyme expression and characterization system for Aspergillus nidulans, with the Penicillium brevicompactum polyketide synthase gene from the mycophenolic acid gene cluster as a test case
    Bjarne G Hansen
    Technical University of Denmark, Department of Systems Biology, Center for Microbial Biotechnology, Building 223, 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 77:3044-51. 2011
    ....
  35. ncbi request reprint Integration of gene expression data into genome-scale metabolic models
    Mats Akesson
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Metab Eng 6:285-93. 2004
    ..A critical discussion of correlation between gene expression and metabolic fluxes is given...
  36. pmc Modeling Lactococcus lactis using a genome-scale flux model
    Ana Paula Oliveira
    Fluxome Sciences A S, Søltofts Plads, Building 223, DK 2800 Kgs Lyngby, Denmark
    BMC Microbiol 5:39. 2005
    ..Flux balance analysis (FBA) and minimization of metabolic adjustment (MOMA) were used as modeling frameworks...
  37. ncbi request reprint Fungal genomics beyond Saccharomyces cerevisiae?
    Gerald Hofmann
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800, Lyngby, Denmark
    Curr Opin Biotechnol 14:226-31. 2003
    ..The developments in the past year demonstrate that we have only just started to exploit this potential...
  38. ncbi request reprint Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted
    Renata Usaite
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    J Biotechnol 133:73-81. 2008
    ..13 h(-1)) and were found to be 0.07, 0.08 and 0.04 h(-1) for the Deltasnf1, Deltasnf4 and Deltasnf1Deltasnf4 strains, respectively. The study showed that Snf1 kinase was not solely responsible for the derepression of galactose metabolism...
  39. pmc Improvement of galactose uptake in Saccharomyces cerevisiae through overexpression of phosphoglucomutase: example of transcript analysis as a tool in inverse metabolic engineering
    Christoffer Bro
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 71:6465-72. 2005
    ..This conclusion was supported by measurements of sugar phosphates, which showed that there were increased concentrations of glucose-6-phosphate, galactose-6-phosphate, and fructose-6-phosphate in the strain construct overexpressing PGM2...
  40. doi request reprint Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae
    Jerome Maury
    Center for Microbial Biotechnology, DTU BioSys, Building 223, 2800 Kgs Lyngby, Denmark
    FEBS Lett 582:4032-8. 2008
    ..cerevisiae. mRNA from the seven genes was detected, and the pathway was shown able to sustain growth of yeast in conditions of inhibition of its constitutive isoprenoid biosynthetic pathway...
  41. ncbi request reprint A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae
    Steen Lund Westergaard
    Center for Microbial Biotechnology, BioCentrum, Technical University of Denmark, Building 223, DK 2800 Kgs, Lyngby, Denmark
    Biotechnol Bioeng 96:134-45. 2007
    ....
  42. ncbi request reprint Transcription analysis using high-density micro-arrays of Aspergillus nidulans wild-type and creA mutant during growth on glucose or ethanol
    Jesper Mogensen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Fungal Genet Biol 43:593-603. 2006
    ....
  43. pmc Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
    Wanwipa Vongsangnak
    Department of Systems Biology, Technical University of Denmark, DK 2800 Lyngby, Denmark
    BMC Genomics 9:245. 2008
    ..We enhanced the function assignment by our developed annotation strategy. The resulting better annotation was used to reconstruct the metabolic network leading to a genome scale metabolic model of A. oryzae...
  44. ncbi request reprint A functional genomics approach using metabolomics and in silico pathway analysis
    Jochen Forster
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Biotechnol Bioeng 79:703-12. 2002
    ..The concept is illustrated using a simplified model for growth of Saccharomyces cerevisiae...
  45. ncbi request reprint Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
    Jochen Forster
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, Lyngby, Denmark
    OMICS 7:193-202. 2003
    ..A genome-scale in silico model can thus be used to systematically reconcile existing data and fill in our knowledge gaps about an organism...
  46. ncbi request reprint Effect of deletion of chitin synthase genes on mycelial morphology and culture viscosity in Aspergillus oryzae
    Christian Muller
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 81:525-34. 2003
    ..The chsB disruption strain had lower consistency index K values for all biomass concentrations investigated, which is a desirable trait for industrial Aspergillus fermentations...
  47. ncbi request reprint Production of plant sesquiterpenes in Saccharomyces cerevisiae: effect of ERG9 repression on sesquiterpene biosynthesis
    Mohammad A Asadollahi
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 99:666-77. 2008
    ..9 and 20.2 mg/L, respectively. The results obtained in this study revealed the great potential of yeast as a cell factory for production of sesquiterpenes...
  48. doi request reprint Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity
    Lasse Pedersen
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 223, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 109:116-24. 2012
    ....
  49. pmc Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation
    Renata Usaite
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 72:6194-203. 2006
    ..In conclusion, our results reveal that the nitrogen source has substantial influence on the transcriptome of yeasts and that transcriptional changes may be correlated to physiology via a metabolic model...
  50. ncbi request reprint Metabolic network analysis of Bacillus clausii on minimal and semirich medium using (13)C-labeled glucose
    Torben Christiansen
    Center for Process Biotechnology, BioCentrum DTU, 2800 Lyngby, Denmark
    Metab Eng 4:159-69. 2002
    ..The metabolic network analysis was extended to include analysis of growth on the semirich medium containing amino acids, and the metabolic flux distribution on this medium was estimated and compared with growth on minimal medium...
  51. ncbi request reprint Aerobic physiology of redox-engineered Saccharomyces cerevisiae strains modified in the ammonium assimilation for increased NADPH availability
    Margarida Moreira dos Santos
    Center for Process Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Lyngby, Denmark
    FEMS Yeast Res 4:59-68. 2003
    ..No redox effect was observed in a strain containing a deletion of GLR1, encoding glutathione reductase, an enzyme that is NADPH-consuming...
  52. pmc A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species
    Mikael R Andersen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Proc Natl Acad Sci U S A 105:4387-92. 2008
    ..With this case example, we present a validated tool for transcriptome analysis of three Aspergillus species and a methodology for conducting cross-species evolutionary studies within a genus using comparative transcriptomics...
  53. doi request reprint Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae
    Dongmei Bai Flagfeldt
    Centre for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Yeast 26:545-51. 2009
    ..An up to 8.7-fold difference was detected between the sites conferring lowest and highest expression, respectively. This opens the opportunity for modulating gene expression levels while retaining promoter and culture conditions...
  54. doi request reprint Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger
    Susan Meijer
    Department for Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Building 223, 2800 Lyngby, Denmark
    J Ind Microbiol Biotechnol 36:1275-80. 2009
    ..Genome-scale stoichiometric metabolic model predictions can be used for identifying gene targets. Deletion of the acl led to increased succinic acid production by A. niger...
  55. ncbi request reprint CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose
    Helga David
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs, Lyngby, Denmark
    Microbiology 151:2209-21. 2005
    ..The derepression of key pathways leads to alterations in the demands for cofactors, thereby imposing changes in the central metabolism due to the coupling of the many different reactions via the redox and energy metabolism of the cells...
  56. pmc Systems analysis unfolds the relationship between the phosphoketolase pathway and growth in Aspergillus nidulans
    Gianni Panagiotou
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    PLoS ONE 3:e3847. 2008
    ..niger and A. oryzae. Here we identified the gene coding for a novel metabolic pathway in A. nidulans, namely the phosphoketolase pathway, and investigated the role of an increased phosphoketolase activity...
  57. pmc Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
    Ana Paula Oliveira
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK 2800 Kgs, Lyngby, Denmark
    BMC Syst Biol 2:17. 2008
    ..Such approaches systematically integrate the existing biological knowledge with the 'omics' data...
  58. pmc Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
    Mikael R Andersen
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark
    Genome Res 21:885-97. 2011
    ..88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi...
  59. pmc High-throughput metabolic state analysis: the missing link in integrated functional genomics of yeasts
    Silas G Villas-Bôas
    Centre for Microbial Biotechnology, Technical University of Denmark, BioCentrum DTU, Building 223, DK 2800 Kongens Lyngby, Denmark
    Biochem J 388:669-77. 2005
    ..More importantly, we demonstrate that this differential metabolite level data provides insight into specific metabolic pathways and lays the groundwork for integrated transcription-metabolism studies of yeasts...
  60. pmc Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    Jochen Forster
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Genome Res 13:244-53. 2003
    ..The reconstructed metabolic network is the first comprehensive network for a eukaryotic organism, and it may be used as the basis for in silico analysis of phenotypic functions...
  61. doi request reprint NADPH-dependent glutamate dehydrogenase in Penicillium chrysogenum is involved in regulation of beta-lactam production
    Jette Thykaer
    Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark
    Microbiology 154:1242-50. 2008
    ..The results indicate that the NADPH-dependent glutamate dehydrogenase may be directly or indirectly involved in the regulation of beta-lactam production in industrial strains of P. chrysogenum...
  62. ncbi request reprint Metabolic network analysis of an adipoyl-7-ADCA-producing strain of Penicillium chrysogenum: elucidation of adipate degradation
    Jette Thykaer
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Metab Eng 4:151-8. 2002
    ..Thus, with a combination of labeling experiments and enzyme assays, the pathway of adipate degradation was elucidated, and the effect of adipate degradation on the primary metabolism was quantified...
  63. pmc Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods
    Renata Usaite
    BioCentrum DTU, Technical University of Denmark, Kgs Lyngby, Denmark
    J Proteome Res 7:266-75. 2008
    ..The functional categorization of the relative protein expression differences that occur in Snf1-deficient strains uncovers a wide range of biological processes regulated by this important cellular kinase...
  64. ncbi request reprint Impact of 'ome' analyses on inverse metabolic engineering
    Christoffer Bro
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs, Lyngby
    Metab Eng 6:204-11. 2004
    ..Here, we review the use of functional genomics methods in inverse metabolic engineering, examples are presented, and we discuss the identification of targets for metabolic engineering with low fold changes using these techniques...
  65. ncbi request reprint Optimization of heterologous production of the polyketide 6-MSA in Saccharomyces cerevisiae
    Songsak Wattanachaisaereekul
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Kgs Lyngby 2800, Denmark
    Biotechnol Bioeng 97:893-900. 2007
    ..Growth and product concentration were measured and kinetic parameters were calculated. It was shown that both PPTases could be efficiently used for activation of PKS's in yeast as good yields of 6-MSA were obtained with both enzymes...
  66. pmc Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques
    Maya P Piddocke
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark
    Microb Cell Fact 10:27. 2011
    ....
  67. ncbi request reprint A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants
    Sandrine Mas
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Biotechnol Bioeng 96:1014-22. 2007
    ..Based on the data, we identified metabolites that are primarily involved in discrimination of the different mutants, and hereby providing a link between high-throughput metabolome analysis, strain classification, and physiology...
  68. pmc Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger
    Mikael Rørdam Andersen
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    Mol Syst Biol 4:178. 2008
    ..The presented metabolic network and map are useful tools for examining systemwide data in a metabolic context. Results from the validated model show a great potential for expanding the use of A. niger as a high-yield production platform...
  69. pmc Diversion of flux toward sesquiterpene production in Saccharomyces cerevisiae by fusion of host and heterologous enzymes
    Line Albertsen
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Appl Environ Microbiol 77:1033-40. 2011
    ..This simple test case of synthetic biology demonstrates that engineering the spatial organization of metabolic enzymes around a branch point has great potential for diverting flux toward a desired product...
  70. doi request reprint Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger
    Gerald Hofmann
    Center for Microbial Biotechnology, BioCentrum, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Metab Eng 11:8-12. 2009
    ..Our findings therefore point to an interesting strategy to attenuate unwanted side effects resulting from oxygen limitation during industrial fermentations with A. niger...
  71. doi request reprint Antibiotic overproduction in Streptomyces coelicolor A3 2 mediated by phosphofructokinase deletion
    Irina Borodina
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
    J Biol Chem 283:25186-99. 2008
    ....
  72. ncbi request reprint Identification of the Entner-Doudoroff pathway in an antibiotic-producing actinomycete species
    Nina Gunnarsson
    Center for Process Biotechnology, BioCentrum DTU, Søltofts Plads, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Mol Microbiol 52:895-902. 2004
    ..The Nonomuraea genes encoding the key enzymes of the ED pathway were subsequently identified, sequenced and functionally described...
  73. ncbi request reprint Transcriptional profiling of extracellular amino acid sensing in Saccharomyces cerevisiae and the role of Stp1p and Stp2p
    Nadine Eckert-Boulet
    Centre for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Yeast 21:635-48. 2004
    ..Also, most of the structural genes involved in trehalose and glycogen synthesis and a few genes in the glyoxylate cycle and the pentose phosphate pathway are derepressed in the ssy1 and stp1 stp2 strains...
  74. ncbi request reprint Yeast systems biology to unravel the network of life
    Roberta Mustacchi
    Centre for Microbial Biotechnology CMB, Building 223, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Yeast 23:227-38. 2006
    ..This paper discusses the impacts of systems biology and how YSBN may play a role in the future development of the field...
  75. ncbi request reprint Metabolite profiling of fungi and yeast: from phenotype to metabolome by MS and informatics
    Jørn Smedsgaard
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Søltofs Plads Building 221, DK 2800 Kgs Lyngby, Denmark
    J Exp Bot 56:273-86. 2005
    ..One very efficient approach is direct infusion Mass Spectrometry (diMS) integrated with automated data handling, but a full metabolic picture requires the combination of several different analytical techniques...
  76. ncbi request reprint Use of laminar flow patterning for miniaturised biochemical assays
    Birgitte Regenberg
    Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark
    Lab Chip 4:654-7. 2004
    ..The system is simple, fast, reproducible, flexible, and has small sample requirements...
  77. ncbi request reprint An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology
    Jens Nielsen
    Center for Process Biotechnology, Building 223, BioCentrum DTU, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    FEMS Yeast Res 2:175-81. 2002
    ..Clearly this will have a significant impact on microbial physiology as well as on metabolic engineering...
  78. ncbi request reprint From genomes to in silico cells via metabolic networks
    Irina Borodina
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, DK 2800 Kgs Lyngby, Denmark
    Curr Opin Biotechnol 16:350-5. 2005
    ..Thus, genome-scale metabolic modeling currently stands out as one of the most promising approaches to obtain an in silico prediction of cellular function based on the interaction of all of the cellular components...
  79. ncbi request reprint Fungal metabolite analysis in genomics and phenomics
    Michael C Jewett
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Curr Opin Biotechnol 17:191-7. 2006
    ..Metabolomics has played a key role in functional genomics and strain classification...
  80. ncbi request reprint Transcriptional, proteomic, and metabolic responses to lithium in galactose-grown yeast cells
    Christoffer Bro
    Center for Process Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    J Biol Chem 278:32141-9. 2003
    ....
  81. pmc Transient marker system for iterative gene targeting of a prototrophic fungus
    Michael L Nielsen
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kongens Lyngby, Denmark
    Appl Environ Microbiol 73:7240-5. 2007
    ..Once the desired genome engineering is completed, pyrG function can be rapidly returned to wild type by a simple selection scheme...
  82. ncbi request reprint Mass spectrometry in metabolome analysis
    Silas G Villas-Bôas
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Mass Spectrom Rev 24:613-46. 2005
    ....
  83. pmc Metabolic engineering of the morphology of Aspergillus oryzae by altering chitin synthesis
    Christian Muller
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, 2800 Kgs Lyngby
    Appl Environ Microbiol 68:1827-36. 2002
    ..alpha-Amylase residing in the cell wall was stained by immunofluorescence, and the relationship between tip number and enzyme secretion is discussed...
  84. pmc Uncovering transcriptional regulation of metabolism by using metabolic network topology
    Kiran Raosaheb Patil
    Center for Microbial Biotechnology, BioCentrum DTU, Technical University of Denmark, Building 223, DK 2800 Kgs Lyngby, Denmark
    Proc Natl Acad Sci U S A 102:2685-9. 2005
    ..These changes then are propagated through the metabolic network because of the highly connected nature of metabolism...
  85. doi request reprint In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network
    Kjeld Raunkjaer Kjeldsen
    Center for Microbial Biotechnology, DTU BioSys, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Biotechnol Bioeng 102:583-97. 2009
    ..Comparable flux values between in silico model and experimental values were seen, although some differences in the phenotypic behavior between the model and the experimental data were observed...
  86. ncbi request reprint Metabolic engineering of beta-lactam production
    Jette Thykaer
    Center for Process Biotechnology, BioCentrum, Technical University of Denmark, Building 223, DK 2800, Lyngby, Denmark
    Metab Eng 5:56-69. 2003
    ..This minireview discusses the recent developments in metabolic engineering and the applications of this approach for improving beta-lactam production...
  87. ncbi request reprint Physiological characterisation of recombinant Aspergillus nidulans strains with different creA genotypes expressing A. oryzae alpha-amylase
    Teit Agger
    Center for Process Biotechnology, BioCentrum DTU, Technical University of Denmark, DK 2800 Lyngby, Denmark
    J Biotechnol 92:279-85. 2002
    ..High-density batch cultivation was performed with the creA deletion strain and a final titre of 6.0 g l(-1) of alpha-amylase was reached after 162 h of cultivation...
  88. ncbi request reprint The simultaneous biosynthesis and uptake of amino acids by Lactococcus lactis studied by (13)C-labeling experiments
    Niels Bang Siemsen Jensen
    Center for Process Biotechnology, Department of Biotechnology, Building 223, Technical University of Denmark, DK 2800 Lyngby, Denmark
    Biotechnol Bioeng 78:11-6. 2002
    ..Phenylalanine, alanine, and threonine were also synthesized de novo in spite of their presence in the growth medium...
  89. pmc Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    Iman Famili
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0412, USA
    Proc Natl Acad Sci U S A 100:13134-9. 2003
    ..cerevisiae allows for computation of its integrated functions, producing in silico results that were consistent with observed phenotypic functions for approximately 70-80% of the conditions considered...
  90. pmc The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
    Intawat Nookaew
    Department of Chemical Engineering, Faculty of Engineering, King Mongkut s University of Technology Thonburi, Bangkok 10140, Thailand
    BMC Syst Biol 2:71. 2008
    ..g. genome-wide mRNA levels). To overcome this limitation, we reconstructed a new version of the Saccharomyces cerevisiae genome-scale model, iIN800 that includes a more rigorous and detailed description of lipid metabolism...
  91. ncbi request reprint Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks
    Intawat Nookaew
    Department of Chemical Engineering, King Mongkut s University of Technology Thonburi, Bangkok 10140, Thailand
    Biotechnol Bioeng 97:1535-49. 2007
    ..We demonstrate how FRCs can be used to map the operation of the metabolic network of the yeast Saccharomyces sp. under different growth conditions...
  92. pmc Deletion of RTS1, encoding a regulatory subunit of protein phosphatase 2A, results in constitutive amino acid signaling via increased Stp1p processing
    Nadine Eckert-Boulet
    Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK 2500 Copenhagen Valby, Denmark
    Eukaryot Cell 5:174-9. 2006
    ..Based on our findings we propose that the phosphatase complex containing Rts1p keeps the SPS-mediated pathway down-regulated in the absence of extracellular amino acids by dephosphorylating a component of the pathway...
  93. pmc Integration of metabolome data with metabolic networks reveals reporter reactions
    Tunahan Cakir
    Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
    Mol Syst Biol 2:50. 2006
    ..Hereby, the reported approach represents an attempt to map different layers of regulation within metabolic networks through combination of metabolome and transcriptome data...
  94. ncbi request reprint Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae
    Matthew D W Piper
    Kluyver Laboratory of Biotechnology, Technical University of Delft, Julianalaan 26, Delft 2628BC, The Netherlands
    J Biol Chem 277:37001-8. 2002
    ....
  95. doi request reprint Design and application of genome-scale reconstructed metabolic models
    Isabel Rocha
    Centro de Engenharia Biólogica, Universidade do Minho, Campus de Gualtar, Braga, Portugal
    Methods Mol Biol 416:409-31. 2008
    ....