Jens Nielsen

Summary

Affiliation: Chalmers University of Technology
Country: Sweden

Publications

  1. ncbi Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis
    Margarita Salazar
    Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96, Goteborg, Sweden
    Mol Genet Genomics 282:571-86. 2009
  2. ncbi A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut
    Fredrik H Karlsson
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Microb Ecol 61:473-85. 2011
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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

Collaborators

Detail Information

Publications86

  1. ncbi Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis
    Margarita Salazar
    Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96, Goteborg, Sweden
    Mol Genet Genomics 282:571-86. 2009
    ..cerevisiae. Our study clearly demonstrates that cross-species evolutionary comparisons among filamentous fungi, using comparative genomics and transcriptomics, are a powerful tool for uncovering regulatory systems...
  2. ncbi A closer look at bacteroides: phylogenetic relationship and genomic implications of a life in the human gut
    Fredrik H Karlsson
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Microb Ecol 61:473-85. 2011
    ..Gut living Bacteroides have an enriched set of glycan, vitamin, and cofactor enzymes important for diet digestion...
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi 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
    ....
  6. ncbi 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...
  7. ncbi 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:..
  8. ncbi 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...
  9. ncbi 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
    ....
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...
  14. ncbi 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...
  15. ncbi 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...
  16. ncbi 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...
  17. ncbi 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...
  18. ncbi 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
    ....
  19. ncbi 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...
  20. ncbi 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...
  21. ncbi 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...
  22. ncbi 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...
  23. ncbi 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/...
  24. ncbi 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
    ....
  25. ncbi 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...
  26. ncbi 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
    ....
  27. ncbi 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...
  28. ncbi 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...
  29. ncbi 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...
  30. ncbi 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...
  31. ncbi 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
    ....
  32. ncbi Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress
    Keith E J Tyo
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 41296 Goteborg, Sweden
    BMC Biol 10:16. 2012
    ..In this study, we apply a systems biology approach to analyze secretory pathway dysfunctions resulting from heterologous production of a small protein (insulin precursor) or a larger protein (α-amylase)...
  33. ncbi Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production
    Yun Chen
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    FEMS Yeast Res 12:598-607. 2012
    ..We also demonstrated that this new expression vectors can be used to increase enzyme activity by improving patchoulol production by threefold...
  34. ncbi 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
    ....
  35. ncbi 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
    ....
  36. ncbi Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering
    Kuk Ki Hong
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Appl Environ Microbiol 78:7579-86. 2012
    ..Our study demonstrates how the identification of specific mutations by systems biology can direct new metabolic engineering strategies for improving galactose utilization by yeast...
  37. ncbi 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...
  38. ncbi 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...
  39. ncbi Codon usage variability determines the correlation between proteome and transcriptome fold changes
    Roberto Olivares-Hernández
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Gothenburg, Sweden
    BMC Syst Biol 5:33. 2011
    ..Thus, by using integrated analysis of omics data, genomic information, transcriptome and proteome, we aim to unravel important variables affecting translation...
  40. ncbi 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...
  41. ncbi 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...
  42. ncbi 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...
  43. ncbi 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...
  44. ncbi Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis
    Marta Papini
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemigården 4, Gothenburg, Sweden
    Appl Microbiol Biotechnol 95:1001-10. 2012
    ....
  45. ncbi 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...
  46. ncbi Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae
    Sakda Khoomrung
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Goteborg, Sweden
    Appl Microbiol Biotechnol 94:1637-46. 2012
    ..The new microwave-assisted derivatization method facilitates the preparation of FAMEs directly from yeast cells, but the method is likely to also be applicable for other biological samples...
  47. ncbi Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae
    Jin Hou
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    FEMS Yeast Res 12:491-510. 2012
    ..The objective of the review is to describe individual biological processes in the context of the larger, complex protein synthesis network...
  48. ncbi Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation
    Subir K Nandy
    Systems Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96, Gothenburg, Sweden
    BMC Syst Biol 4:68. 2010
    ..Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives...
  49. ncbi 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...
  50. ncbi 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...
  51. ncbi 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...
  52. ncbi Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae
    Siavash Partow
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Yeast 27:955-64. 2010
    ..These new vectors retain all the features from the pESC-URA plasmid except that gene expression is mediated by constitutive promoters...
  53. ncbi Aspergilli: systems biology and industrial applications
    Christoph Knuf
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol J 7:1147-55. 2012
    ..These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology...
  54. ncbi Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae
    Jin Hou
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Metab Eng 14:120-7. 2012
    ..Our study demonstrates that strengthening the protein trafficking in ER-to-Golgi and Golgi-to-plasma membrane process is a novel secretory engineering strategy for improving heterologous protein production in S. cerevisiae...
  55. ncbi Symptomatic atherosclerosis is associated with an altered gut metagenome
    Fredrik H Karlsson
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE 412 96, Sweden
    Nat Commun 3:1245. 2012
    ..Our findings suggest that the gut metagenome is associated with the inflammatory status of the host and patients with symptomatic atherosclerosis harbor characteristic changes in the gut metagenome...
  56. ncbi 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...
  57. ncbi Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries
    Kuk Ki Hong
    Novo Nordisk Centre for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
    Cell Mol Life Sci 69:2671-90. 2012
    ..cerevisiae. Finally, we discuss the perspectives of how technologies from systems biology and synthetic biology can be used to advance metabolic engineering of yeast...
  58. ncbi Prospects for microbial biodiesel production
    Shuobo Shi
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol J 6:277-85. 2011
    ..This work reviews both microbial approaches for renewable biodiesel production and evaluates the existing challenges in these two strategies...
  59. ncbi Systems biology of energy homeostasis in yeast
    Jie Zhang
    Systems Biology Group, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96 Goteborg, Sweden
    Curr Opin Microbiol 13:382-8. 2010
    ..This review will focus on how Snf1 regulates lipid metabolism based on the cellular energy status in yeast and drawing parallels with the mammalian system...
  60. ncbi Prospects for systems biology and modeling of the gut microbiome
    Fredrik H Karlsson
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96 Goteborg, Sweden
    Trends Biotechnol 29:251-8. 2011
    ..To this end, we propose the use of genome-scale metabolic models that have successfully been used in studying interactions between human hosts and microbes, as well as microbes in isolation and in communities...
  61. ncbi 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...
  62. ncbi Molecular basis for mycophenolic acid biosynthesis in Penicillium brevicompactum
    Torsten Bak Regueira
    Department of Systems Biology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
    Appl Environ Microbiol 77:3035-43. 2011
    ..brevicompactum. Our work sets the stage for engineering the production of MPA and analogues through metabolic engineering...
  63. ncbi Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels
    Bouke de Jong
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE412 96 Gothenburg, Sweden
    Curr Opin Biotechnol 23:624-30. 2012
    ..This review will cover the recent technological developments that support improvement of the advanced biofuels 1-butanol, biodiesels and jetfuels...
  64. ncbi Anaerobic α-Amylase Production and Secretion with Fumarate as the Final Electron Acceptor in Saccharomyces cerevisiae
    Zihe Liu
    Novo Nordisk Foundation Center for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Appl Environ Microbiol 79:2962-7. 2013
    ....
  65. ncbi 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...
  66. ncbi 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...
  67. ncbi 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...
  68. ncbi 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...
  69. ncbi Implementation of communication-mediating domains for non-ribosomal peptide production in Saccharomyces cerevisiae
    Verena Siewers
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE 412 96 Gothenburg, Sweden
    Biotechnol Bioeng 106:841-4. 2010
    ..This opens the possibility of using yeast as a eukaryotic platform for fast assessment of new module combinations for the development of novel NRP compounds...
  70. ncbi Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88
    Erik Larsson
    Sahlgrenska Center for Cardiovascular and Metabolic Research Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
    Gut 61:1124-31. 2012
    ..Microorganisms are recognised by pattern recognition receptors such as Toll-like receptors, which signal through the adaptor molecule MyD88...
  71. ncbi Lipid biosynthesis monitored at the single-cell level in Saccharomyces cerevisiae
    Pramote Chumnanpuen
    Systems and Synthetic Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Gothenburg, Sweden
    Biotechnol J 7:594-601. 2012
    ..cerevisiae, can be used for the biosynthesis of lipids and demonstrate the strength of CARS microscopy for monitoring the dynamics of lipid metabolism at the single-cell level of importance for optimized lipid production...
  72. ncbi Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology
    Madelene Lindqvist
    Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
    PLoS ONE 6:e20448. 2011
    ..These results could inform rational development of effective mucosal adjuvants for vaccination against STIs...
  73. ncbi Genome-scale metabolic models of Saccharomyces cerevisiae
    Intawat Nookaew
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Methods Mol Biol 759:445-63. 2011
    ..This will support and encourage researchers who are interested in systemic analysis of yeast metabolism and systems biology...
  74. ncbi Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group
    Roberto Olivares-Hernández
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    PLoS ONE 5:e12781. 2010
    ..The diversity of substrate specificities found in the FAE family shows that this family is old enough to have experienced the emergence and loss of many activities...
  75. ncbi Opportunities for yeast metabolic engineering: Lessons from synthetic biology
    Anastasia Krivoruchko
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol J 6:262-76. 2011
    ..Some examples of applications for yeast synthetic biology and metabolic engineering are also discussed...
  76. ncbi Fifteen years of large scale metabolic modeling of yeast: developments and impacts
    Tobias Osterlund
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol Adv 30:979-88. 2012
    ....
  77. ncbi Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism
    Dina Petranovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEMS Yeast Res 10:1046-59. 2010
    ....
  78. ncbi Industrial systems biology
    Jose Manuel Otero
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Goteborg, Sweden
    Biotechnol Bioeng 105:439-60. 2010
    ..Here we look into the history of these different techniques and review how they find application in industrial biotechnology, which will lead to what we here define as industrial systems biology...
  79. ncbi Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae
    Wanwipa Vongsangnak
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    Biotechnol Bioeng 108:1130-9. 2011
    ....
  80. ncbi 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...
  81. ncbi 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...
  82. ncbi Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level
    Roberto Olivares-Hernández
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivagen 10, Gothenburg SE 41296, Sweden
    Biotechnol Bioeng 107:865-75. 2010
    ....
  83. ncbi Identification of flux control in metabolic networks using non-equilibrium thermodynamics
    Sergio Bordel
    Systems Biology, Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
    Metab Eng 12:369-77. 2010
    ..These findings point to a wider use of the method for identification of novel targets for metabolic engineering of microorganisms used for sustainable production of fuels and chemicals...
  84. ncbi Systems biology of industrial microorganisms
    Marta Papini
    Chemical and Biological Engineering Systems Biology, Chalmers University of Technology, Kemigården 4, Goteborg, 41296, Sweden
    Adv Biochem Eng Biotechnol 120:51-99. 2010
    ....
  85. ncbi Can yeast systems biology contribute to the understanding of human disease?
    Dina Petranovic
    Department of Chemical and Biological Engineering, Chalmers University of Technology, SE 412 96 Gothenburg, Sweden
    Trends Biotechnol 26:584-90. 2008
    ....
  86. ncbi A systems-level approach for metabolic engineering of yeast cell factories
    Il Kwon Kim
    Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
    FEMS Yeast Res 12:228-48. 2012
    ....