Jens Nielsen

Summary

Affiliation: Chalmers University of Technology
Country: Sweden

Publications

  1. pmc Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae
    Lifang Liu
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biologicl Engineering, Chalmers University of Technology, SE 41296 Goteborg, Sweden
    BMC Syst Biol 8:73. 2014
  2. pmc The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    Rasmus Agren
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 9:e1002980. 2013
  3. pmc Integration of clinical data with a genome-scale metabolic model of the human adipocyte
    Adil Mardinoglu
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Mol Syst Biol 9:649. 2013
  4. pmc Understanding the interactions between bacteria in the human gut through metabolic modeling
    Saeed Shoaie
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
    Sci Rep 3:2532. 2013
  5. pmc Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    Rasmus Agren
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 8:e1002518. 2012
  6. pmc Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory
    Jose Manuel Otero
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS ONE 8:e54144. 2013
  7. 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
  8. pmc BioMet Toolbox: genome-wide analysis of metabolism
    Marija Cvijovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Nucleic Acids Res 38:W144-9. 2010
  9. pmc Mathematical models of cell factories: moving towards the core of industrial biotechnology
    Marija Cvijovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Microb Biotechnol 4:572-84. 2011
  10. pmc Reconstruction and evaluation of the synthetic bacterial MEP pathway in Saccharomyces cerevisiae
    Siavash Partow
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    PLoS ONE 7:e52498. 2012

Collaborators

Detail Information

Publications147 found, 100 shown here

  1. pmc Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae
    Lifang Liu
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biologicl Engineering, Chalmers University of Technology, SE 41296 Goteborg, Sweden
    BMC Syst Biol 8:73. 2014
    ..However, systemic analysis of its secretion system is lacking, generally due to the poorly annotated proteome...
  2. pmc The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    Rasmus Agren
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 9:e1002980. 2013
    ..It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production...
  3. pmc Integration of clinical data with a genome-scale metabolic model of the human adipocyte
    Adil Mardinoglu
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Mol Syst Biol 9:649. 2013
    ..Our study hereby shows a path to identify new therapeutic targets for treating obesity through combination of high throughput patient data and metabolic modeling...
  4. pmc Understanding the interactions between bacteria in the human gut through metabolic modeling
    Saeed Shoaie
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
    Sci Rep 3:2532. 2013
    ....
  5. pmc Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
    Rasmus Agren
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 8:e1002518. 2012
    ..A comparative analysis between the active metabolic networks of cancer types and healthy cell types allowed for identification of cancer-specific metabolic features that constitute generic potential drug targets for cancer treatment...
  6. pmc Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory
    Jose Manuel Otero
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS ONE 8:e54144. 2013
    ..cerevisiae, and hence show proof of concept that this is a potentially attractive cell factory for over-producing different platform chemicals...
  7. 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
    ....
  8. pmc BioMet Toolbox: genome-wide analysis of metabolism
    Marija Cvijovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Nucleic Acids Res 38:W144-9. 2010
    ..Overall, the BioMet Toolbox serves as a valuable resource for exploring the capabilities of these metabolic networks. BioMet Toolbox is freely available at www.sysbio.se/BioMet/...
  9. pmc Mathematical models of cell factories: moving towards the core of industrial biotechnology
    Marija Cvijovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Microb Biotechnol 4:572-84. 2011
    ..In this review we aim to summarize the main modelling approaches of biological processes and illustrate the particular applications that they have found in the field of industrial microbiology...
  10. pmc Reconstruction and evaluation of the synthetic bacterial MEP pathway in Saccharomyces cerevisiae
    Siavash Partow
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    PLoS ONE 7:e52498. 2012
    ..coli genes fldA and fpr encoding flavodoxin and flavodoxin reductase believed to be responsible for electron transfer to IspG and IspH...
  11. pmc Profiling of cytosolic and peroxisomal acetyl-CoA metabolism in Saccharomyces cerevisiae
    Yun Chen
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    PLoS ONE 7:e42475. 2012
    ..This will be useful to further develop yeast as a cell factory for the biosynthesis of acetyl-CoA-derived products...
  12. pmc A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
    Intawat Nookaew
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296, Gothenburg, Sweden
    Nucleic Acids Res 40:10084-97. 2012
    ....
  13. pmc Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice
    Intawat Nookaew
    Life Sciences Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS ONE 5:e12361. 2010
    ..This will require methods for linking nutrient intake with specific metabolic processes in different tissues...
  14. pmc Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae
    Jie Zhang
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Mol Syst Biol 7:545. 2011
    ..Finally, we conclude that direct interactions between Snf1 and TORC1 pathways are unlikely under nutrient-limited conditions and propose that TORC1 is repressed in a manner that is independent of Snf1...
  15. pmc Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae
    Michael C Jewett
    Center for Microbial Biotechnology, DTU Systems Biology, Technical University of Denmark, DK 2800 Kongens Lyngby, Denmark
    G3 (Bethesda) 3:1979-95. 2013
    ....
  16. pmc Novel insights into obesity and diabetes through genome-scale metabolic modeling
    Leif Väremo
    Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
    Front Physiol 4:92. 2013
    ..This review will focus on the modeling of human metabolism in the field of obesity and diabetes, showing its vast range of applications of clinical importance as well as point out future challenges...
  17. ncbi request reprint Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
    Ibrahim E El-Semman
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    BMC Syst Biol 8:41. 2014
    ..This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs)...
  18. pmc Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway
    Bouke Wim de Jong
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Goteborg SE 412 96, Sweden
    Microb Cell Fact 13:39. 2014
    ..It is important to develop novel cell factories for efficient production of FAEEs and their precursors...
  19. pmc Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling
    Sven E F Borgos
    Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, N 7491, Norway
    BMC Syst Biol 7:19. 2013
    ....
  20. pmc Mapping the polysaccharide degradation potential of Aspergillus niger
    Mikael R Andersen
    Department of Systems Biology, Technical University of Denmark, Kgs Lyngby, Denmark
    BMC Genomics 13:313. 2012
    ..In plant-biomass degrading fungi, these enzymes are regulated and released by complex regulatory structures. In this study, we present a methodology for evaluating the potential of a given fungus for polysaccharide degradation...
  21. pmc FANTOM: Functional and taxonomic analysis of metagenomes
    Kemal Sanli
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Gothenburg SE 412 96, Sweden
    BMC Bioinformatics 14:38. 2013
    ..There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context...
  22. pmc Production of biopharmaceutical proteins by yeast: advances through metabolic engineering
    Jens Nielsen
    Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
    Bioengineered 4:207-11. 2013
    ..The involvement of directed metabolic engineering through the integration of tools from genetic engineering, systems biology and mathematical modeling, is also discussed. ..
  23. doi request reprint Metabolic engineering of yeast for production of fuels and chemicals
    Jens Nielsen
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
    Curr Opin Biotechnol 24:398-404. 2013
    ..Here we review recent scientific progress in metabolic engineering of S. cerevisiae for the production of bioethanol, advanced biofuels, and chemicals...
  24. pmc Specific growth rate and substrate dependent polyhydroxybutyrate production in Saccharomyces cerevisiae
    Kanokarn Kocharin
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Goteborg, SE 41296, Sweden
    AMB Express 3:18. 2013
    ..23 mg/L · h-1, at a dilution rate of 0.1 h-1...
  25. pmc Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae
    Kanokarn Kocharin
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96, Goteborg, Sweden
    AMB Express 2:52. 2012
    ....
  26. pmc De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
    Jurgen F Nijkamp
    The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
    Microb Cell Fact 11:36. 2012
    ..The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains...
  27. pmc Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production
    Shuobo Shi
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96, Goteborg, Sweden
    Biotechnol Biofuels 5:7. 2012
    ..abstract:..
  28. pmc Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae
    William A Rodríguez-Limas
    Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
    Microb Cell Fact 10:33. 2011
    ..In this work, the first steps required for the production of rotavirus-like particles (RLP) in S. cerevisiae were implemented and improved, in order to obtain the recombinant protein concentrations required for VLP assembly...
  29. 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
    ....
  30. pmc Systemic analysis of the response of Aspergillus niger to ambient pH
    Mikael R Andersen
    Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, DK 2800 Kgs Lyngby, Denmark
    Genome Biol 10:R47. 2009
    ..While it is known that the mechanisms regulating this production are tied to the levels of ambient pH, the reasons and mechanisms for this are poorly understood...
  31. pmc MEMOSys: Bioinformatics platform for genome-scale metabolic models
    Stephan Pabinger
    Institute for Genomics and Bioinformatics, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
    BMC Syst Biol 5:20. 2011
    ..One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models...
  32. pmc OptFlux: an open-source software platform for in silico metabolic engineering
    Isabel Rocha
    IBB Institute for Biotechnology and Bioengineering Centre of Biological Engineering, University of Minho, 4710 057 Campus de Gualtar, Braga, Portugal
    BMC Syst Biol 4:45. 2010
    ..However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications...
  33. 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...
  34. pmc Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae
    Tobias S Christensen
    Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    BMC Syst Biol 3:7. 2009
    ..This process is complex due to the presence of feedback loops and crosstalk between different pathways, complicating the use of intuitive approaches to analyze the system...
  35. pmc Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3
    Donatella Cimini
    Second University of Naples, Department of Experimental Medicine, Naples, Italy
    BMC Syst Biol 3:17. 2009
    ..We therefore explored the physiological and transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3, that codes for an essential subunit of the Sdhp...
  36. pmc Natural computation meta-heuristics for the in silico optimization of microbial strains
    Miguel Rocha
    Department of Informatics CCTC, University of Minho, Braga, Portugal
    BMC Bioinformatics 9:499. 2008
    ....
  37. pmc Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications
    Jose Manuel Otero
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
    BMC Genomics 11:723. 2010
    ..The exact genetic modification or resulting genotype that leads to the improved phenotype is often not identified or understood to enable further metabolic engineering...
  38. doi request reprint Systems biology of lipid metabolism: from yeast to human
    Jens Nielsen
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEBS Lett 583:3905-13. 2009
    ..Hereby yeast systems biology can assist to improve our understanding of how lipid metabolism is regulated...
  39. 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...
  40. 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
    ....
  41. 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
    ....
  42. 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...
  43. 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...
  44. 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
    ....
  45. ncbi request reprint Genome-wide analysis of maltose utilization and regulation in aspergilli
    Wanwipa Vongsangnak
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
    Microbiology 155:3893-902. 2009
    ..our study not only helps to understand the sugar preference in industrial fermentation processes, but also indicates how maltose affects gene expression and overall metabolism...
  46. ncbi 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...
  47. 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...
  48. 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...
  49. 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...
  50. 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
    ....
  51. doi request reprint Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae
    Jin Hou
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 41296 Goteborg, Sweden
    Appl Microbiol Biotechnol 97:3559-68. 2013
    ..cerevisiae is not limited by secretion. Our results provide an effective strategy to improve protein secretion and demonstrated an approach that can induce ER and cytosolic chaperones simultaneously...
  52. ncbi request reprint The beta-subunits of the Snf1 kinase in Saccharomyces cerevisiae, Gal83 and Sip2, but not Sip1, are redundant in glucose derepression and regulation of sterol biosynthesis
    Jie Zhang
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Gothenburg, Sweden
    Mol Microbiol 77:371-83. 2010
    ..Furthermore, we found that Sip2, but not Sip1, can take over when Gal83 is deleted, but to a lesser extent. However, Sip1 may be sufficient for some other processes such as regulation of the nitrogen metabolism and meiosis...
  53. 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
    ....
  54. 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...
  55. 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...
  56. 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...
  57. pmc Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae
    Marta Papini
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, SE, 412 96, Sweden
    Microb Cell Fact 11:136. 2012
    ..Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of S. stipitis during aerobic growth on glucose under batch and chemostat cultivations...
  58. doi request reprint Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production
    Rasmus Agren
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296, Gothenburg, Sweden
    J Ind Microbiol Biotechnol 40:735-47. 2013
    ..While far from industrial titers, this proof-of-concept suggests that in silico predictions coupled with experimental validation can be used to identify novel and non-intuitive metabolic engineering strategies...
  59. 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
    ....
  60. ncbi 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
    ....
  61. 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...
  62. 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...
  63. 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
    ....
  64. ncbi 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...
  65. pmc Combined metabolic engineering of precursor and co-factor supply to increase α-santalene production by Saccharomyces cerevisiae
    Gionata Scalcinati
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96, Goteborg, Sweden
    Microb Cell Fact 11:117. 2012
    ..The hydrocarbon α-santalene is a precursor of sesquiterpenes with relevant commercial applications. Here, we construct an efficient Saccharomyces cerevisiae cell factory for α-santalene production...
  66. doi request reprint Dynamic control of gene expression in Saccharomyces cerevisiae engineered for the production of plant sesquitepene α-santalene in a fed-batch mode
    Gionata Scalcinati
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Metab Eng 14:91-103. 2012
    ..18mg/gDCWh. The titer was further increased by deleting DPP1 encoding a second FPP consuming pyrophosphate phosphatase yielding a final productivity and titer, respectively, of 0.21mg/gDCWh and 92mg/l of α-santalene...
  67. 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...
  68. 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...
  69. 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...
  70. 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...
  71. 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...
  72. ncbi request reprint Microbial isoprenoid production: an example of green chemistry through metabolic engineering
    Jerome Maury
    Center for Microbial Biotechnology, BioCentrum DTU, Building 223, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
    Adv Biochem Eng Biotechnol 100:19-51. 2005
    ..Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described...
  73. 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...
  74. 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...
  75. 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...
  76. 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...
  77. ncbi 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...
  78. pmc Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    Sergio Bordel
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS Comput Biol 6:e1000859. 2010
    ..This has not been previously reported. The information provided by the presented method could guide the discovery of new metabolic engineering strategies or the identification of drug targets for treatment of metabolic diseases...
  79. doi request reprint Dynamic 13C-labeling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains
    Kuk Ki Hong
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEMS Yeast Res 12:741-7. 2012
    ..PK 113-7D, which makes these processes the dominant nonbiosynthetic drain of ATP in living cells, and hence, it represents an energetic parameter of great relevance...
  80. doi request reprint Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae
    Zihe Liu
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol Bioeng 109:1259-68. 2012
    ....
  81. doi request reprint Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae
    Zihe Liu
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 41296, Goteborg, Sweden
    Appl Microbiol Biotechnol 97:8955-62. 2013
    ....
  82. 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...
  83. 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
    ....
  84. 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...
  85. 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...
  86. pmc Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response
    Cecilia Geijer
    Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Gothenburg, S 40530, Sweden
    BMC Genomics 13:554. 2012
    ....
  87. ncbi request reprint Analysis of genome-wide coexpression and coevolution of Aspergillus oryzae and Aspergillus niger
    Wanwipa Vongsangnak
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
    OMICS 14:165-75. 2010
    ....
  88. ncbi request reprint Use of genome-scale metabolic models for understanding microbial physiology
    Liming Liu
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEBS Lett 584:2556-64. 2010
    ..We further describe the reconstruction process of genome-scale metabolic models and different algorithms that can be used to apply these models to gain improved insight into microbial physiology...
  89. pmc Genome-scale modeling of the protein secretory machinery in yeast
    Amir Feizi
    Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
    PLoS ONE 8:e63284. 2013
    ....
  90. pmc Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
    Luis Caspeta
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    BMC Syst Biol 6:24. 2012
    ..As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research...
  91. doi request reprint Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism
    Yun Chen
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
    Metab Eng 15:48-54. 2013
    ..This strain would be a useful tool to produce a wide range of acetyl-CoA-derived products...
  92. doi request reprint Gut metagenome in European women with normal, impaired and diabetic glucose control
    Fredrik H Karlsson
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
    Nature 498:99-103. 2013
    ..Therefore, metagenomic predictive tools for T2D should be specific for the age and geographical location of the populations studied...
  93. pmc Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling
    Tobias Osterlund
    Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg SE412 96, Sweden
    BMC Syst Biol 7:36. 2013
    ..Since then continuous efforts have been made in order to improve and expand the yeast metabolic network...
  94. 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...
  95. doi request reprint Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast
    Pramote Chumnanpuen
    Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, 412 96 Gothenburg, Sweden
    Mol Genet Genomics 287:541-54. 2012
    ..The analysis showed the strength of using both transcriptome and lipid profiling analysis for mapping the co-influence of inositol-choline and Snf1 on phospholipid metabolism...
  96. doi request reprint Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption
    Gionata Scalcinati
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEMS Yeast Res 12:582-97. 2012
    ..The resulting strain is a desirable platform for the industrial production of biomass-related products using xylose as a sole carbon source...
  97. pmc Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis
    Kuk Ki Hong
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
    Proc Natl Acad Sci U S A 108:12179-84. 2011
    ....
  98. pmc Toward design-based engineering of industrial microbes
    Keith E J Tyo
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg SE 412 96, Sweden
    Curr Opin Microbiol 13:255-62. 2010
    ..Genome-scale metabolic models, new tools for controlling expression, and integrated -omics analysis are described as key contributors in moving the field toward Design-based Engineering...
  99. doi request reprint Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation
    Jose L Martinez
    Novo Nordisk Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
    Curr Opin Biotechnol 23:965-71. 2012
    ....
  100. doi request reprint Phosphoglycerate mutase knock-out mutant Saccharomyces cerevisiae: physiological investigation and transcriptome analysis
    Marta Papini
    Systems Biology, Chemical and Biological Engineering Department, Chalmers University of Technology, Kemigården, Goteborg, Sweden
    Biotechnol J 5:1016-27. 2010
    ..These results indicate an attempt to compensate for the energy imbalance caused by the deletion of the glycolytic/gluconeogenic gene within the mutant...