Jens B Nielsen

Avdelningschef at Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens Nielsen has an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Danish Technical University (DTU), and after that established his independent research group and was appointed full Professor there in 1998. He was Fulbright visiting professor at MIT in 1995-1996. At DTU he founded and directed Center for Microbial Biotechnology. In 2008 he was recruited as Professor and Director to Chalmers University of Technology, Sweden, where he is currently directing a research group of about 60 people. Jens Nielsen has published so far more than 570 papers that have been cited more than 21,000 times according to Web of Science (current H-factor 71) 40,000 times according to Google Scholar (current H-factor 97), and co-authored more than 40 books. He is inventor of more than 50 patent and has founded several biotech companies. He has received numerous Danish and international awards and is member of the Academy of Technical Sciences in Denmark, National Academy of Engineering in USA, the Royal Danish Academy of Science and Letters, the American Institute for Medical and Biological Engineering, the American Academy of Microbiology, the Royal Swedish Academy of Engineering Sciences, the Royal Swedish Academy of Sciences, and the Royal Society of Arts and Sciences in Gothenburg. He is a founding president of the International Metabolic Engineering Society.

Source: orcid.org

Projects

2013–2017

Biobased production of diesel and jetfuel

Jens B Nielsen Systems and Synthetic Biology
Swedish Research Council (VR)

2014–2018

Integrating Modelling of Metabolism and Signalling towards an Application in Liver Cancer (ERASysAPP - IMOMESIC)

Jens B Nielsen Biology and Biological Engineering
Avlant Nilsson Systems and Synthetic Biology
Adil Mardinoglu Systems and Synthetic Biology
Swedish Research Council (VR)

2012–2017

Optimizing oil production in oleaginous yeast by cell-wide measurements and genome-based models

Jens B Nielsen Systems and Synthetic Biology
U.S. Department of Energy (DOE)

2016–2022

Gut microbiome effects on cardiometabolic disease through metabolism-modifying metabolites (Gut-MMM)

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk Fonden

2016–2020

Predictive and Accelerated Metabolic Engineering Network (PAcMEN)

Jens B Nielsen Systems and Synthetic Biology
European Commission (Horizon 2020)

2010–2014

Industrial Systems Biology of Yeast and A. oryzae (INSYSBIO)

Jens B Nielsen System Biology
European Commission (FP7)

57 publications exist
2012–2017

Metagenomics in Cardiometabolic Diseases (METACARDIS)

Jens B Nielsen System Biology
European Commission (FP7)

6 publications exist
2012–2015

Infrastructure for Systems Biology - Europe (ISBE)

Jens B Nielsen System Biology
European Commission (FP7)

2013–2017

Quantitative Biology for Fungal Secondary Metabolite Producers (QUANTFUNG)

Jens B Nielsen System Biology
European Commission (FP7)

2012–2017

Biomarkers For Enhanced Vaccine Safety (BioVacSafe)

Jens B Nielsen Biology and Biological Engineering
European Commission (EC)

2014–2018

Infect-ERA 2014. FunComPath. From colonization to infection of the commensal-to-pathogen shift of Candida albicans

Jens B Nielsen Biology and Biological Engineering
Swedish Research Council (VR)

2015–2016

Mathematical modelling of tissue metabolism in response to malnutrition, II

Jens B Nielsen Biology and Biological Engineering
Bill & Melinda Gates Foundation

2014–2015

Mathematical modeling of tissue metabolism in response to malnutrition

Jens B Nielsen Systems and Synthetic Biology
Bill & Melinda Gates Foundation

2014–2018

SysMilk. Designer microbial communities for fermented milk products: A Systems Biology Approach (ERASysAPP - SysMilk)

Jens B Nielsen Systems and Synthetic Biology
André Kelkkanen Innovationskontor Väst
Västra Götalandsregionen, Regional development committee

2013–2015

MetaboGen

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk Fonden

2014–2016

Biopetrolia

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk Fonden

2016–2019

Transkriptionsreglering i jäst på genomnivå

Jens B Nielsen Systems and Synthetic Biology
Swedish Research Council (VR)

2016–2017

Mapping the Transcription Factor Network of Yeast

Jens B Nielsen Systems and Synthetic Biology
Technical University of Denmark (DTU)

2016–2020

Bioinformatics Services for Data-Driven Design of Cell Factories and Communities (DD-DeCaF)

Jens B Nielsen Systems and Synthetic Biology
European Commission (Horizon 2020)

2012–2015

Utveckling av plattform för studier av metagenom och dess roll vid ämnesomsättningsrelaterade sjukdomar

Jens B Nielsen System Biology
Torsten Söderbergs Stiftelse

2016–2020

Model-Based Construction And Optimisation Of Versatile Chassis Yeast Strains For Production Of Valuable Lipid And Aromatic Compounds (CHASSY)

Jens B Nielsen Systems and Synthetic Biology
Verena Siewers Systems and Synthetic Biology
European Commission (Horizon 2020)

2017–2020

Biobaserad produktion av diesel och jetbränsle

Jens B Nielsen Systems and Synthetic Biology
Swedish Energy Agency

2015–2020

Biological Production Systems 2014

Jens B Nielsen Systems and Synthetic Biology
Verena Siewers Systems and Synthetic Biology
Swedish Foundation for Strategic Research (SSF)

2013–2017

Yeast Cell Factories: Training Researchers to Apply Modern Post-Genomic Methods In Yeast Biotechnology (YEASTCELL)

Verena Siewers System Biology
Jens B Nielsen System Biology
Leonie Wenning System Biology
European Commission (FP7)

There might be more projects where Jens B Nielsen participates, but you have to be logged in as a Chalmers employee to see them.

Publications

2017

Cocoa butter-like lipid production ability of non-oleaginous and oleaginous yeasts under nitrogen-limited culture conditions

Yongjun Wei, Verena Siewers, Jens B Nielsen
Applied Microbiology and Biotechnology. Vol. 101 (9), p. 3577-3585
Journal article
2017

Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae

Jichen Bao, Mingtao Huang, Dina Petranovic Nielsen et al
Applied and Environmental Microbiology. Vol. 83 (14), p. Article no. UNSP e03400-16
Journal article
2017

Systems Biology of Metabolism

Jens B Nielsen
Annual Review of Biochemistry. Vol. 86, p. 245-275
Chapter in monograph, book - peer reviewed
2017

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

Leif Väremo, T. I. Henriksen, C. Scheele et al
Genome Medicine. Vol. 9 (1), p. Article Number: 47-
Journal article
2017

Increasing cocoa butter-like lipid production of Saccharomyces cerevisiae by expression of selected cocoa genes

Yongjun Wei, Michael Gossing, David Bergenholm et al
AMB Express. Vol. 7 (1)
Journal article
2017

New challenges to study heterogeneity in cancer redox metabolism

Rui Benfeitas, Mathias Uhlen, Jens B Nielsen et al
Journal of Logic and Computation. Vol. 5 (JUL)
Journal article
2017

Genome scale metabolic modeling of cancer

Avlant Nilsson, Jens B Nielsen
Metabolic Engineering. Vol. 43, p. 103-112
Journal article
2017

Metabolic engineering of yeast for fermentative production of flavonoids

A. Rodriguez, T. Strucko, S. G. Stahlhut et al
Bioresource Technology. Vol. 245, p. 1645-1654
Journal article
2017

Exploiting off-targeting in guide-RNAs for CRISPR systems for simultaneous editing of multiple genes

Raphael Ferreira, Francesco Gatto, Jens B Nielsen
FEBS Letters. Vol. 591 (20), p. 3288-3295
Journal article
2017

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

Petri-Jaan Lahtvee, Benjamin José Sanchez Barja, Agata Smialowska et al
Cell Systems. Vol. 4 (5), p. 495-504.e5
Journal article
2017

Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity

Jens B Nielsen, J. Archer, M. Essack et al
Applied Microbiology and Biotechnology. Vol. 101 (12), p. 4837-4851
Journal article
2017

The yeast osmostress response is carbon source dependent

Roja Babazadeh, Petri-Jaan Lahtvee, Caroline B. Adiels et al
Scientific Reports. Vol. 7 (1)
Journal article
2017

Expanding the product portfolio of fungal type I fatty acid synthases

Zhu Zhiwei, Yongjin Zhou, Anastasia Krivoruchko et al
Nature Chemical Biology. Vol. 13 (4), p. 360-362
Journal article
2017

Systematic inference of functional phosphorylation events in yeast metabolism

Yu Chen, Y. H. Wang, Jens B Nielsen
Bioinformatics. Vol. 33 (13), p. 1995-2001
Journal article
2017

Effects of acetoacetyl-CoA synthase expression on production of farnesene in Saccharomyces cerevisiae

Stefan Tippmann, Raphael Ferreira, Verena Siewers et al
Journal of Industrial Microbiology and Biotechnology. Vol. 44 (6), p. 911-922
Journal article
2017

Engineering Robustness of Microbial Cell Factories

Z. W. Gong, Jens B Nielsen, Yongjin Zhou
Biotechnology journal. Vol. 12 (10)
Journal article
2017

Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine

Jens B Nielsen
Cell Metabolism. Vol. 25 (3), p. 572-579
Journal article
2017

Metabolic engineering of Saccharomyces cerevisiae for production of very long chain fatty acid-derived chemicals

Tao Yu, Yongjin Zhou, Leonie Wenning et al
Nature Communications. Vol. 8, p. Article number: 15587-
Journal article
2017

Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae

Paulo Teixeira, Raphael Ferreira, Yongjin Zhou et al
Microbial Cell Factories. Vol. 16 (1), p. 45-
Journal article
2017

Metabolic engineering of Saccharomyces cerevisiae for production of germacrene A, a precursor of beta-elemene

Yating Hu, Yongjin Zhou, Jichen Bao et al
Journal of Industrial Microbiology and Biotechnology. Vol. 44 (7), p. 1065-1072
Journal article
2017

Engineering central metabolism – a grand challenge for plant biologists

Lee J. Sweetlove, Jens B Nielsen, A. R. Fernie
Plant Journal. Vol. 90 (4), p. 749-763
Journal article
2017

Functional screening of aldehyde decarbonylases for long-chain alkane production by Saccharomyces cerevisiae

Min-Kyoung Kang, Yongjin Zhou, Nicolaas Buijs et al
Microbial Cell Factories. Vol. 16 (1), p. Article number 74-
Journal article
2017

Personal model-assisted identification of NAD(+) and glutathione metabolism as intervention target in NAFLD

Adil Mardinoglu, Elias Björnson, C. Zhang et al
Molecular Systems Biology. Vol. 13 (3)
Journal article
2017

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

E. D. Jensen, Raphael Ferreira, T. Jakociunas et al
Microbial Cell Factories. Vol. 16 (1), p. 46-
Journal article
2017

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

Min-Kyoung Kang, Jens B Nielsen
Journal of Industrial Microbiology and Biotechnology. Vol. 44 (4-5), p. 613-622
Journal article
2017

A molecular genetic toolbox for Yarrowia lipolytica

Erin L. Bredeweg, Kyle R. Pomraning, Ziyu Dai et al
Biotechnology for Biofuels. Vol. 10 (1)
Journal article
2017

Selection of complementary foods based on optimal nutritional values

Partho Sen, Adil Mardinoglu, Jens B Nielsen
Scientific Reports. Vol. 7 (1), p. Article no 5413 -
Journal article
2017

Network analyses identify liver-specific targets for treating liver diseases

SangWook Lee, C. Zhang, Z. T. Liu et al
Molecular Systems Biology. Vol. 13 (8)
Journal article
2017

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

Eduard Kerkhoven, Y. M. Kim, S. W. Wei et al
mBio. Vol. 8 (3), p. Article no. e00857-17
Journal article
2017

Efficient protein production by yeast requires global tuning of metabolism

Mingtao Huang, Jichen Bao, B. M. Hallstrom et al
Nature Communications. Vol. 8 (1)
Journal article
2017

METABOLISM: Built on stable catalysts

Jens B Nielsen
Nature Microbiology. Vol. 2 (7), p. Art no: 17085-
Magazine article
2017

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Benjamin José Sanchez Barja, C. Zhang, Avlant Nilsson et al
Molecular Systems Biology. Vol. 13 (8), p. Article no 935 -
Journal article
2017

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species

Jens Christian Froslev Nielsen, S. Grijseels, Sylvain Prigent et al
Nature Microbiology. Vol. 2 (6)
Journal article
2017

Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production

Guokun Wang, Mingtao Huang, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 48, p. 77-84
Journal article
2017

Improving the economics of NASH/NAFLD treatment through the use of systems biology

J. Bosley, C. Boren, SangWook Lee et al
Drug Discovery Today. Vol. 22 (10), p. 1532-1538
Journal article
2017

Genome-scale metabolic models applied to human health and disease

Daniel Cook, Jens B Nielsen
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. Vol. 9 (6)
Journal article
2016

Editorial: The Impact of Systems Medicine on Human Health and Disease

Adil Mardinoglu, Jens B Nielsen
Frontiers in Physiology. Vol. 7 (NOV)
Magazine article
2016

Improved quantification of farnesene during microbial production from Saccharomyces cerevisiae in two-liquid-phase fermentations

Stefan Tippmann, Jens B Nielsen, Sakda Khoomrung
Talanta. Vol. 146, p. 100-106
Journal article
2016

In search for symmetries in the metabolism of cancer

Francesco Gatto, Jens B Nielsen
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. Vol. 8 (1), p. 23-35
Journal article
2016

The impact of respiration and oxidative stress response on recombinant ?-amylase production by Saccharomyces cerevisiae

Jose Luis Martinez Ruiz, Eugenio Meza, Dina Petranovic Nielsen et al
Metabolic Engineering Communications. Vol. 3, p. 205-210
Journal article
2016

Respiratory metabolism and calorie restriction relieve persistent endoplasmic reticulum stress induced by calcium shortage in yeast

Stefano Busti, Valeria Mapelli, Farida Tripodi et al
Scientific Reports. Vol. 6, p. Art. no. 27942-
Journal article
2016

EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

J. Maury, S. M. Germann, S. A. B. Jacobsen et al
PLoS ONE. Vol. 11 (3)
Journal article
2016

Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 degrees C

Luis Caspeta-Guadarrama, Yun Chen, Jens B Nielsen
Scientific Reports. Vol. 6, p. Art. no. 27003-
Journal article
2016

Integrative analysis of human omics data using biomolecular networks

Jonathan Robinson, Jens B Nielsen
Molecular BioSystems. Vol. 12 (10), p. 2953-2964
Journal article
2016

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma

Francesco Gatto, N. Volpi, H. Nilsson et al
Cell Reports. Vol. 15 (8), p. 1822-1836
Journal article
2016

Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids

Sara L Svahn, Leif Väremo, Britt Gabrielsson et al
PLoS ONE. Vol. 11 (5), p. Art. no. e0155099-
Journal article
2016

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics

Francesco Gatto, A. Schulze, Jens B Nielsen
Cell Reports. Vol. 16 (3), p. 878-895
Journal article
2016

Engineering yeast metabolism for production of fuels and chemicals

Jens B Nielsen
New Biotechnology. Vol. 33 (Supplement: S Meeting Abstract: PL3), p. S66-S66
Journal article
2016

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Avlant Nilsson, Jens B Nielsen
Scientific Reports. Vol. 6
Journal article
2016

Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae

Alexandra Linda Bergman, Verena Siewers, Jens B Nielsen et al
AMB Express. Vol. 6 (1)
Journal article
2016

All You Need Is Mentorship

R. A. Weinberg, M. Schuldiner, H. Wu et al
Cell. Vol. 164 (6), p. 1092-1093
Journal article
2016

Transcriptomics resources of human tissues and organs

M. Uhlen, B. M. Hallstrom, C. Lindskog et al
Molecular Systems Biology. Vol. 12 (4)
Journal article
2016

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.

Eugene Fletcher, Amir Feizi, Mark Bisschops et al
Metabolic Engineering. Vol. 39, p. 19-28
Journal article
2016

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus.

John R Casey, Adil Mardinoglu, Jens B Nielsen et al
mSystems. Vol. 1 (6), p. Article no UNSP e00065 -
Journal article
2016

Harnessing yeast peroxisomes for biosynthesis of fatty-acid-derived biofuels and chemicals with relieved side-pathway competition

Yongjin Zhou, Nicolaas Buijs, Zhu Zhiwei et al
Journal of the American Chemical Society. Vol. 138 (47), p. 15368-15377
Journal article
2016

Industrial systems biology and its impact on synthetic biology of yeast cell factories

Eugene Fletcher, Anastasia Krivoruchko, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 113 (6), p. 1164-1170
Journal article
2016

Prognostic Value of Plasma and Urine glycosaminoglycan scores in clear cell renal cell carcinoma

Francesco Gatto, M. Maruzzo, Cristina Magro et al
Frontiers in Oncology. Vol. 6 (NOV), p. Art. no. 253-
Journal article
2016

Engineering of synthetic, stress-responsive yeast promoters

Arun S. Rajkumar, Guodong Liu, David Bergenholm et al
Nucleic Acids Research. Vol. 44 (17), p. e136-
Journal article
2016

Flux control through protein phosphorylation in yeast

Yu Chen, Jens B Nielsen
FEMS Yeast Research. Vol. 16 (8)
Journal article
2016

Systematic analysis of overall survival and interactions between tumor mutations and drug treatment

Francesco Gatto, Jens B Nielsen
Journal of Hematology and Oncology. Vol. 9 (1)
Journal article
2016

Adaptation to different types of stress converge on mitochondrial metabolism

Petri-Jaan Lahtvee, Rahul Kumar, B. M. Hallstrom et al
Molecular Biology of the Cell. Vol. 27 (15), p. 2505-2514
Journal article
2016

Production of farnesene and santalene by Saccharomyces cerevisiae using fed-batch cultivations with RQ-controlled feed

Stefan Tippmann, Gionata Scalcinati, Verena Siewers et al
Biotechnology and Bioengineering. Vol. 113 (1), p. 72-81
Journal article
2016

Voluntary Running Suppresses Tumor Growth through Epinephrine- and IL-6-Dependent NK Cell Mobilization and Redistribution

L. Pedersen, M. Idorn, G. H. Olofsson et al
Cell Metabolism. Vol. 23 (3), p. 554-562
Journal article
2016

Engineering Cellular Metabolism

Jens B Nielsen, J.D. Keasling
Cell. Vol. 164 (6), p. 1185-1197
Journal article
2016

Integrated Network Analysis Reveals an Association between Plasma Mannose Levels and Insulin Resistance

SangWook Lee, C. Zhang, M. Kilicarslan et al
Cell Metabolism. Vol. 24 (1), p. 172-184
Journal article
2016

Improved production of fatty acids by Saccharomyces cerevisiae through screening a cDNA library from the oleaginous yeast Yarrowia lipolytica

Shuobo Shi, H. C. Ji, Verena Siewers et al
FEMS Yeast Research. Vol. 16 (1)
Journal article
2016

Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

Guodong Liu, David Bergenholm, Jens B Nielsen
mBio. Vol. 7 (3), p. e00559-16
Magazine article
2016

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

Yongjin Zhou, Nicolaas Buijs, Zhu Zhiwei et al
Nature Communications. Vol. 7, p. 11709-
Journal article
2016

Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae

Florian David, Jens B Nielsen, Verena Siewers
ACS Synthetic Biology. Vol. 5 (3), p. 224-233
Journal article
2016

Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae.

Stefan Tippmann, J. Anfelt, Florian David et al
ACS Synthetic Biology (1), p. 19-28
Journal article
2016

Engineering yeast for high-level production of stilbenoid antioxidants

M. Li, K. Schneider, M. Kristensen et al
Scientific Reports. Vol. 6, p. 36827-
Journal article
2016

Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae

Rui Pereira, Jens B Nielsen, I. Rocha
Metabolic Engineering Communications. Vol. 3, p. 153-163
Journal article
2016

Biosynthesis of very long-chain fatty alcohols and wax esters in metabolically engineered strains of Saccharomyces cerevisiae

Leonie Wenning, Verena Siewers, Jens B Nielsen
New Biotechnology. Vol. 33 (Supplement: S Meeting Abstract: O18-3), p. S54-S54
Journal article
2016

Physiological and transcriptional characterization of Saccharomyces cerevisiae engineered for production of fatty acid ethyl esters

Bouke Wim de Jong, Verena Siewers, Jens B Nielsen
FEMS Yeast Research. Vol. 16 (1)
Journal article
2016

Human gut microbiota and healthy aging: Recent developments and future prospective

Manish Kumar, Parizad Babaei, Boyang Ji et al
Nutrition and healthy aging. Vol. 4 (1), p. 3-16
Journal article
2016

Engineering and systems-level analysis of Saccharomyces cerevisiae for production of 3-hydroxypropionic acid via malonyl-CoA reductase-dependent pathway

K. R. Kildegaard, N. B. Jensen, K. Schneider et al
Microbial Cell Factories. Vol. 15 (53)
Journal article
2016

Glycosaminoglycan profiling in plasma and urine as a diagnostic and prognostic biomarker of clear cell renal cell carcinoma

Francesco Gatto, M. Maruzzo, U. Stierner et al
BJU International. Vol. 118, p. 12-13
Conference contribution
2016

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

Z. A. Irani, Eduard Kerkhoven, S. A. Shojaosadati et al
Biotechnology and Bioengineering. Vol. 113 (5), p. 961-969
Journal article
2016

Biobased organic acids production by metabolically engineered microorganisms

Yun Chen, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 37, p. 165-172
Journal article
2016

Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q in hepatocellular carcinoma metabolism

Ibrahim El-Semman, Adil Mardinoglu, Saeed Shoaie et al
Molecular BioSystems. Vol. 12 (5), p. 1496-1506
Journal article
2016

Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

Dan Fraenkel, Jens B Nielsen
FEMS Yeast Research. Vol. 16 (1)
Journal article
2016

Heme metabolism in stress regulation and protein production: From Cinderella to a key player.

Jose Luis Martinez Ruiz, Dina Petranovic Nielsen, Jens B Nielsen
Bioengineered Bugs. Vol. 7 (2), p. 112-5
Journal article
2016

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

SangWook Lee, Adil Mardinoglu, C. Zhang et al
Nucleic Acids Research. Vol. 44 (12), p. 5529-5539
Journal article
2016

Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

S. Grijseels, Jens Christian Froslev Nielsen, Jens B Nielsen et al
Scientific Reports. Vol. 6
Journal article
2016

Characterization of physiological and transcriptional properties of improved protein secretion yeast strains

Mingtao Huang, Jichen Bao, B. M. Hallstrom et al
11th Metabolic Engineering Conference 2016; Awaji Island; Japan, p. 639-640
Conference contribution
2016

Establishing very long-chain fatty alcohol and wax ester biosynthesis in Saccharomyces cerevisiae.

Leonie Wenning, Tao Yu, Florian David et al
Biotechnology and Bioengineering. Vol. 114 (5), p. 1025-1036
Journal article
2015

Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae

K. R. Kildegaard, Zheng Wang, Yun Chen et al
Metabolic Engineering Communications. Vol. 2, p. 132-136
Journal article
2015

The gut microbiota modulates host amino acid and glutathione metabolism in mice

Adil Mardinoglu, Saeed Shoaie, Mattias Bergentall et al
Molecular Systems Biology. Vol. 11 (10), p. Article Number: 834-
Journal article
2015

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

David Bergenholm, Florian David, B. F. Pfleger et al
Biotechnology Advances. Vol. 33 (7), p. 1395-1402
Journal article
2015

Genetic and nutrient modulation of acetyl-CoA levels in Synechocystis for n-butanol production

J. Anfelt, D. Kaczmarzyk, K. Shabestary et al
Microbial Cell Factories. Vol. 14 (1), p. 12-
Journal article
2015

New insight into the gut microbiome through metagenomics

Boyang Ji, Jens B Nielsen
Advances in Genomics and Genetics. Vol. 5, p. 77-91
Journal article
2015

Extensive weight loss reveals distinct gene expression changes in human subcutaneous and visceral adipose tissue

Adil Mardinoglu, J. T. Heiker, D. Gartner et al
Scientific Reports. Vol. 5, p. 14841-
Journal article
2015

Logical transformation of genome-scale metabolic models for gene level applications and analysis

C. Zhang, Boyang Ji, Adil Mardinoglu et al
Bioinformatics. Vol. 31 (14), p. 2324-2331
Journal article
2015

Applications of computational modeling in metabolic engineering of yeast

Eduard Kerkhoven, Petri-Jaan Lahtvee, Jens B Nielsen
FEMS Yeast Research. Vol. 15 (1)
Journal article
2015

Cancer Metabolism: A Modeling Perspective

Pouyan Ghaffari Nouran, Adil Mardinoglu, Jens B Nielsen
Frontiers in Physiology. Vol. 6 (DEC)
Journal article
2015

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Saeed Shoaie, Pouyan Ghaffari Nouran, P. Kovatcheva-Datchary et al
Cell Metabolism. Vol. 22 (2), p. 320-331
Journal article
2015

HCSD: The human cancer secretome database

Amir Feizi, Amir Banaei Esfahani, Jens B Nielsen
Database : the journal of biological databases and curation. Vol. 2015
Journal article
2015

De novo production of resveratrol from glucose or ethanol by engineered Saccharomyces cerevisiae

M. Li, K. R. Kildegaard, Yun Chen et al
Metabolic Engineering. Vol. 32, p. 1-11
Journal article
2015

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast

Mingtao Huang, Y. Bai, S. L. Sjostrom et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 112 (34), p. E4689-E4696
Journal article
2015

From next-generation sequencing to systematic modeling of the gut microbiome

Boyang Ji, Jens B Nielsen
Frontiers in Genetics. Vol. 6 (JUN)
Journal article
2015

Tissue-based map of the human proteome

M. Uhlen, L. Fagerberg, B.M. Hallström et al
Science. Vol. 347 (6220), p. 394-
Journal article
2015

Networking in metabolism and human disease

Leif Väremo, Jens B Nielsen
Oncotarget. Vol. 6 (18), p. 15708-15709
Journal article
2015

Molecular Mechanism of Flocculation Self-Recognition in Yeast and Its Role in Mating and Survival

K. V. Y. Goossens, F. S. Ielasi, Intawat Nookaew et al
mBio. Vol. 6 (2)
Journal article
2015

Functional pyruvate formate lyase pathway expressed with two different electron donors in Saccharomyces cerevisiae at aerobic growth

Yiming Zhang, Zongijie Dai, Anastasia Krivoruchko et al
FEMS Yeast Research. Vol. 15 (4)
Journal article
2015

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling

C. Lindskog, J. Linne, L. Fagerberg et al
BMC Genomics. Vol. 16 (1)
Journal article
2015

Production of beta-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae

J. Lopez, K. Essus, Il-Kwon Kim et al
Microbial Cell Factories. Vol. 14 (1), p. Art. no. 84-
Journal article
2015

Modular pathway rewiring of Saccharomyces cerevisiae enables high-level production of L-ornithine

J. Qin, Yongjin Zhou, Anastasia Krivoruchko et al
Nature Communications. Vol. 6 (Sept.), p. Art. no. 8224-
Journal article
2015

Microbial acetyl-CoA metabolism and metabolic engineering

Anastasia Krivoruchko, Yiming Zhang, Verena Siewers et al
Metabolic Engineering. Vol. 28, p. 28-42
Journal article
2015

New paradigms for metabolic modeling of human cells

Adil Mardinoglu, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 34, p. 91-97
Journal article
2015

Engineering the Oxygen Sensing Regulation Results in an Enhanced Recombinant Human Hemoglobin Production by Saccharomyces cerevisiae

Jose Luis Martinez Ruiz, Lifang Liu, Dina Petranovic Nielsen et al
Biotechnology and Bioengineering. Vol. 112 (1), p. 181-188
Journal article
2015

Establishment of a yeast platform strain for production of p-coumaric acid through metabolic engineering of aromatic amino acid biosynthesis

A. Rodriguez, K. R. Kildegaard, M. Li et al
Metabolic Engineering. Vol. 31, p. 181-188
Journal article
2015

RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH

Eugene Fletcher, Amir Feizi, S.S. Kim et al
Microbial Cell Factories. Vol. 14 (1)
Journal article
2015

Do genome-scale models need exact solvers or clearer standards?

A. Ebrahim, E. Almaas, E. Bauer et al
Molecular Systems Biology. Vol. 11 (10), p. Article Number: 831-
Journal article
2015

Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization

Elias Björnson, B. Mukhopadhyay, A. Asplund et al
Cell Reports. Vol. 13 (9), p. 2014-2026
Journal article
2015

Enabling Technologies to Advance Microbial Isoprenoid Production

Yun Chen, Yongjin Zhou, Verena Siewers et al
Advances in Biochemical Engineering/Biotechnology. Vol. 148, p. 143-160
Journal article
2015

Ach1 is involved in shuttling mitochondrial acetyl units for cytosolic C2 provision in Saccharomyces cerevisiae lacking pyruvate decarboxylase

Yun Chen, Yiming Zhang, Verena Siewers et al
FEMS Yeast Research. Vol. 15 (3), p. 1-8
Journal article
2015

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

S. Tymoshenko, R.D. Oppenheim, Rasmus Ågren et al
PLoS Computational Biology. Vol. 11 (5), p. Art. no. e1004261-
Journal article
2015

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

Pouyan Ghaffari Nouran, Adil Mardinoglu, A. Asplund et al
Scientific Reports. Vol. 5, p. Art. no. 8183-
Journal article
2015

Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain

Yiming Zhang, Guodong Liu, Martin Engqvist et al
Microbial Cell Factories. Vol. 14 (116)
Journal article
2015

Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes.

Luis Caspeta-Guadarrama, Tania Castillo, Jens B Nielsen
Frontiers in bioengineering and biotechnology. Vol. 3, p. 184-
Journal article
2015

Yeast cell factories on the horizon: Metabolic engineering in yeast gets increasingly more versatile

Jens B Nielsen
Science. Vol. 349 (6252), p. 1050-1051
Magazine article
2015

Expanded metabolite coverage of Saccharomyces cerevisiae extract through improved chloroform/methanol extraction and tert-butyldimethylsilyl derivatization

Sakda Khoomrung, Jose Luis Martinez Ruiz, Stefan Tippmann et al
Analytical Chemistry Research. Vol. 6, p. 9-16
Journal article
2015

Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via beta-alanine

I. Borodina, K. R. Kildegaard, N. B. Jensen et al
Metabolic Engineering. Vol. 27, p. 57-64
Journal article
2015

How to set up collaborations between academia and industrial biotech companies

J. Pronk, S. Y. Lee, J. Lievense et al
Nature Biotechnology. Vol. 33 (3), p. 237-240
Magazine article
2015

Metabolic engineering strategies for microbial synthesis of oleochemicals

B. F. Pfleger, Michael Gossing, Jens B Nielsen
Metabolic Engineering. Vol. 29, p. 1-11
Journal article
2015

Micro-droplet based directed evolution outperforms conventional laboratory evolution

S. L. Sjostrom, Mingtao Huang, Jens B Nielsen et al
18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014; United States; 26-30 October 2014, p. 169-171
Paper in proceedings
2015

Human metabolic atlas: an online resource for human metabolism

Natapol Pornputtapong, Intawat Nookaew, Jens B Nielsen
Database : the journal of biological databases and curation. Vol. 2015
Journal article
2015

Finding directionality and gene-disease predictions in disease associations

Manuel Garcia, Jens B Nielsen
BMC Systems Biology. Vol. 9 (1)
Journal article
2015

Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Benjamin José Sanchez Barja, Jens B Nielsen
Integrative Biology (United Kingdom). Vol. 7 (8), p. 846-858
Journal article
2015

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

Leif Väremo, C. Scheele, C. Broholm et al
Cell Reports. Vol. 11 (6), p. 921-933
Journal article
2015

Improving heterologous protein secretion at aerobic conditions by activating hypoxia-induced genes in Saccharomyces cerevisiae

Lifang Liu, Yiming Zhang, Zihe Liu et al
FEMS Yeast Research. Vol. 15 (7), p. 10-
Journal article
2015

Controllability analysis of transcriptional regulatory networks reveals circular control patterns among transcription factors

Tobias Österlund, Sergio Velasco, Jens B Nielsen
Integrative Biology (United Kingdom). Vol. 7 (5), p. 560-568
Journal article
2015

Production of natural products through metabolic engineering of Saccharomyces cerevisiae

Anastasia Krivoruchko, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 35, p. 7-15
Journal article
2015

Glucose repression in Saccharomyces cerevisiae

Ömur Kayikci, Jens B Nielsen
FEMS Yeast Research. Vol. 15 (6)
Journal article
2015

Long-chain Alkane Production by the Yeast Saccharomyces cerevisiae

Nicolaas Buijs, Yongjin Zhou, Verena Siewers et al
Biotechnology and Bioengineering. Vol. 112 (6), p. 1275-1279
Journal article
2015

Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

Pouyan Ghaffari Nouran, Adil Mardinoglu, A. Asplund et al
Scientific Reports. Vol. 5, p. Art. no. 8183-
Journal article
2015

Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism

Francesco Gatto, H. Miess, A. Schulze et al
Scientific Reports. Vol. 5, p. Art. no. 10738-
Journal article
2015

Metabolic pathway engineering for fatty acid ethyl ester production in Saccharomyces cerevisiae using stable chromosomal integration

Bouke Wim de Jong, S. B. Shi, Juan Octavio Valle Rodriguez et al
Journal of Industrial Microbiology and Biotechnology. Vol. 42 (3), p. 477-486
Journal article
2015

FEMS yeast research: the yeast community journal

Jens B Nielsen
FEMS Yeast Research. Vol. 15 (2), p. Art. no. fou007-
Magazine article
2015

Enhanced amino acid utilization sustains growth of cells lacking Snf1/AMPK

Raffaele Nicastro, Farida Tripodi, C. Guzzi et al
Biochimica et Biophysica Acta - Molecular Cell Research. Vol. 1853 (7), p. 1615-1625
Journal article
2015

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation

Valentina Tremaroli, Fredrik Karlsson, Malin Werling et al
Cell Metabolism. Vol. 22 (2), p. 228-238
Journal article
2015

ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes

Martin Engqvist, Jens B Nielsen
ACS Synthetic Biology. Vol. 4 (8), p. 935-938
Journal article
2015

Advancing metabolic engineering through systems biology of industrial microorganisms

Zongijie Dai, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 36, p. 8-15
Journal article
2014

Most influential FEMS publications

J. I. Prosser, J. A. Cole, Jens B Nielsen et al
FEMS Microbiology Letters. Vol. 354 (2), p. 83-84
Journal article
2014

Management of the endoplasmic reticulum stress by activation of the heat shock response in yeast

Jin Hou, H. T. Tang, Zihe Liu et al
FEMS Yeast Research. Vol. 14 (3), p. 481-494
Journal article
2014

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

Fredrik Karlsson, Intawat Nookaew, Jens B Nielsen
PLoS Computational Biology. Vol. 10 (7)
Journal article
2014

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

Rasmus Ågren, Adil Mardinoglu, A. Asplund et al
Molecular Systems Biology. Vol. 10 (3)
Journal article
2014

Succinate dehydrogenase inhibition leads to epithelial-mesenchymal transition and reprogrammed carbon metabolism

P-J. Aspuria, S.Y. Lunt, Leif Väremo et al
Cancer & Metabolism. Vol. 2
Journal article
2014

High-throughput screening for industrial enzyme production hosts by droplet microfluidics

S. L. Sjostrom, Y. Bai, Mingtao Huang et al
Lab on a Chip - Miniaturisation for Chemistry and Biology. Vol. 14 (4), p. 806-813
Journal article
2014

Altered sterol composition renders yeast thermotolerant

Luis Caspeta-Guadarrama, Yun Chen, PAYAM GHIACI et al
Science. Vol. 346 (6205), p. 75-78
Journal article
2014

Engineering synergy in biotechnology

Jens B Nielsen, M. Fussenegger, J.D. Keasling et al
Nature Chemical Biology. Vol. 10 (5), p. 319-322
Magazine article
2014

Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast

Jens B Nielsen
mBio. Vol. 5 (6), p. Art. no. e02153-14
Magazine article
2014

Development of a yeast cell factory for production of aromatic products

A. R. Prado, K. Kildegaard, M. Li et al
New Biotechnology. Vol. 31, p. S130-S130
Magazine article
2014

Systems biology: Developments and applications

Rahul Kumar, Petri-Jaan Lahtvee, Jens B Nielsen
Molecular Mechanisms in Yeast Carbon Metabolism, p. 83-96
Chapter in monograph, book - peer reviewed
2014

Defining the Human Adipose Tissue Proteome To Reveal Metabolic Alterations in Obesity

Adil Mardinoglu, C. Kampf, A. Asplund et al
Journal of Proteome Research. Vol. 13 (11), p. 5106-5119
Journal article
2014

Maintaining a strong yeast research community

Jens B Nielsen
FEMS Yeast Research. Vol. 14 (4), p. 527-528
Magazine article
2014

Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii

R. Ledesma-Amaro, Eduard Kerkhoven, J. L. Revuelta et al
Biotechnology and Bioengineering. Vol. 111 (6), p. 1191-1199
Journal article
2014

Bridging the gaps in systems biology

Marija Cvijovic, Joachim E Almqvist, Jonas Hagmar et al
Molecular Genetics and Genomics. Vol. 289 (5), p. 727-734
Journal article
2014

Impact of protein uptake and degradation on recombinant protein secretion in yeast

Keith Tyo, Zihe Liu, Ylva Magnusson et al
Applied Microbiology and Biotechnology. Vol. 98 (16), p. 7149-7159
Journal article
2014

A dedicated database system for handling multi-level data in systems biology

Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson et al
Source Code for Biology and Medicine. Vol. 9 (1)
Journal article
2014

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data

Manuel Garcia, Subazini Thankaswamy-Kosalai, Avlant Nilsson et al
Nucleic Acids Research. Vol. 42 (W1), p. W175-W181
Journal article
2014

Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma

Francesco Gatto, Intawat Nookaew, Jens B Nielsen
Proceedings of the National Academy of Sciences of the United States of America. Vol. 111 (9), p. E866-E875
Journal article
2014

Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae

Pramote Chumnanpuen, M.A. Edberg Hansen, Jorn Smedsgaard et al
International Journal of Genomics. Vol. 2014, p. Art. no. 894296-
Journal article
2014

Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

K. R. Kildegaard, B. M. Hallstrom, T. H. Blicher et al
Metabolic Engineering. Vol. 26, p. 57-66
Journal article
2014

Genome-Scale Metabolic Models: A Link between Bioinformatics and Systems Biology

Jens B Nielsen, Sergio Velasco, Intawat Nookaew
Comprehensive Biomedical Physics, p. 165-173
Chapter in monograph, book - peer reviewed
2014

The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network

Guodong Liu, Antonio Marras, Jens B Nielsen
Quantitative Biology. Vol. 2 (1), p. 30-46
Journal article
2014

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

Ibrahim El-Semman, Fredrik Karlsson, Saeed Shoaie et al
BMC Systems Biology. Vol. 8 (41)
Journal article
2014

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

L. Fagerberg, B. M. Hallstrom, P. Oksvold et al
Molecular and Cellular Proteomics. Vol. 13 (2), p. 397-406
Journal article
2014

Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae

Yun Chen, Jichen Bao, Il-Kwon Kim et al
Metabolic Engineering. Vol. 22, p. 104-109
Journal article
2014

Balanced globin protein expression and heme biosynthesis improve production of human hemoglobin in Saccharomyces cerevisiae

Lifang Liu, Jose Luis Martinez Ruiz, Zihe Liu et al
Metabolic Engineering. Vol. 21, p. 9-16
Journal article
2014

The use of Genome-scale metabolic models for drug target and biomarker identification

Adil Mardinoglu, M. Uhlen, Jens B Nielsen
New Biotechnology. Vol. 31, p. S49-S49
Magazine article
2014

Improving Production of Malonyl Coenzyme A-Derived Metabolites by Abolishing Snf1-Dependent Regulation of Acc1

S. B. Shi, Yun Chen, Verena Siewers et al
mBio. Vol. 5 (3)
Journal article
2014

The human liver-specific proteome defined by transcriptomics and antibody-based profiling

C. Kampf, Adil Mardinoglu, L. Fagerberg et al
FASEB Journal. Vol. 28 (7), p. 2901-2914
Journal article
2014

Defining the human gallbladder proteome by transcriptomics and affinity proteomics

C. Kampf, Adil Mardinoglu, L. Fagerberg et al
Proteomics. Vol. 14 (21-22), p. 2498-2507
Journal article
2014

Physiological characterization of the high malic acid-producing Aspergillus oryzae strain 2103a-68

Christoph Knuf, Intawat Nookaew, Ilse Remmers et al
Applied Microbiology and Biotechnology. Vol. 98 (8), p. 3517-3527
Journal article
2014

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

Adil Mardinoglu, Rasmus Ågren, C. Kampf et al
Nature Communications. Vol. 5, p. 11-
Journal article
2014

EasyClone: method for iterative chromosomal integration of multiple genes in Saccharomyces cerevisiae

N. B. Jensen, T. Strucko, K. R. Kildegaard et al
FEMS Yeast Research. Vol. 14 (2), p. 238-248
Journal article
2014

Improved Production of a Heterologous Amylase in Saccharomyces cerevisiae by Inverse Metabolic Engineering

Zihe Liu, Lifang Liu, Tobias Österlund et al
Applied and Environmental Microbiology. Vol. 80 (17), p. 5542-5550
Journal article
2014

Kinetic models in industrial biotechnology - Improving cell factory performance

Joachim E Almqvist, Marija Cvijovic, V. Hatzimanikatis et al
Metabolic Engineering. Vol. 24, p. 38-60
Journal article
2014

Engineering of Chromosomal Wax Ester Synthase Integrated Saccharomyces Cerevisiae Mutants for Improved Biosynthesis of Fatty Acid Ethyl Esters

Shuobo Shi, Juan Octavio Valle Rodriguez, Verena Siewers et al
Biotechnology and Bioengineering. Vol. 111 (9), p. 1740-1747
Journal article
2014

Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae

Lifang Liu, Amir Feizi, Tobias Österlund et al
BMC Systems Biology. Vol. 8 (73)
Journal article
2014

Enhanced ethanol production and reduced glycerol formation in fps1∆ mutants of Saccharomyces cerevisiae engineered for improved redox balancing

Clara Navarrete Roman, Jens B Nielsen, Verena Siewers
AMB Express. Vol. 4 (1), p. 1-8
Journal article
2014

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling

Saeed Shoaie, Jens B Nielsen
Frontiers in Genetics. Vol. 5 (APR)
Journal article
2014

Kiwi: a tool for integration and visualization of network topology and gene-set analysis

Leif Väremo, Francesco Gatto, Jens B Nielsen
BMC Bioinformatics. Vol. 15 (1)
Journal article
2014

Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals

I. Borodina, Jens B Nielsen
Biotechnology journal. Vol. 9 (5), p. 609-620
Journal article
2013

FANTOM: Functional and taxonomic analysis of metagenomes

Kemal Sanli, Fredrik Karlsson, Intawat Nookaew et al
BMC Bioinformatics. Vol. 14 (1), p. artikel nr 38-
Journal article
2013

Yeast as a platform cell factory in future biorefineries

Jens B Nielsen
4th International Conference on Biomolecular Engineering, ICBE 2013, Fort Lauderdale, United States, 13-16 January 2013, p. 56-79
Paper in proceedings
2013

Genome-Scale Modeling of the Protein Secretory Machinery in Yeast

Amir Feizi, Tobias Österlund, Dina Petranovic Nielsen et al
PLoS ONE. Vol. 8 (5)
Journal article
2013

Droplet based directed evolution of yeast cell factories doubles production of industrial enzymes

S. L. Sjostrom, Y. Bai, M. Huang et al
17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013, p. 1270-1272
Paper in proceedings
2013

Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast

Pramote Chumnanpuen, Intawat Nookaew, Jens B Nielsen
BMC Systems Biology. Vol. 7 (Suppl 3) (S7)
Journal article
2013

Anaerobic alpha-Amylase Production and Secretion with Fumarate as the Final Electron Acceptor in Saccharomyces cerevisiae

Zihe Liu, Tobias Österlund, Jin Hou et al
Applied and Environmental Microbiology. Vol. 79 (9), p. 2962-2967
Journal article
2013

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

Adil Mardinoglu, Rasmus Ågren, C. Kampf et al
Molecular Systems Biology. Vol. 9 (1), p. 649-
Journal article
2013

Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker

Intawat Nookaew, Kaisa Thorell, Kuntal Worah et al
BMC Medical Genomics. Vol. 6 (41)
Journal article
2013

Economic and environmental impacts of microbial biodiesel

Luis Caspeta-Guadarrama, Jens B Nielsen
Nature Biotechnology. Vol. 31 (9), p. 789-793
Journal article
2013

Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production

Rasmus Ågren, José Manuel Otero, Jens B Nielsen
Journal of Industrial Microbiology and Biotechnology. Vol. 40 (7), p. 735-747
Journal article
2013

Adaptively evolved yeast mutants on galactose show trade-offs in carbon utilization on glucose

Kuk-ki Hong, Jens B Nielsen
Metabolic Engineering. Vol. 16 (1), p. 78-86
Journal article
2013

Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism

Yun Chen, L. Daviet, M. Schalk et al
Metabolic Engineering. Vol. 15 (1), p. 48-54
Journal article
2013

A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study

R. G. E. van Eijsden, C. Stassen, L. Daenen et al
Biotechnology Letters. Vol. 35 (6), p. 891-900
Journal article
2013

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Tobias Österlund, Intawat Nookaew, Sergio Velasco et al
BMC Systems Biology. Vol. 7
Journal article
2013

Rapid Quantification of Yeast Lipid using Microwave-Assisted Total Lipid Extraction and HPLC-CAD

Sakda Khoomrung, Pramote Chumnanpuen, Suwanee Jansa-Ard et al
Analytical Chemistry. Vol. 85 (10), p. 4912-4919
Journal article
2013

Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism

Anastasia Krivoruchko, Cristina Serrano-Amatriain, Yun Chen et al
Journal of Industrial Microbiology and Biotechnology. Vol. 40 (9), p. 1051-1056
Journal article
2013

Genome-scale modeling of human metabolism - a systems biology approach.

Adil Mardinoglu, Francesco Gatto, Jens B Nielsen
Biotechnology journal. Vol. 8
Journal article
2013

Production of biopharmaceutical proteins by yeast Advances through metabolic engineering

Jens B Nielsen
Bioengineered Bugs. Vol. 4 (4), p. 207-211
Journal article
2013

Metabolic engineering of yeast for production of fuels and chemicals

Jens B Nielsen, Christer Larsson, A. van Maris et al
Current Opinion in Biotechnology. Vol. 24 (3), p. 398-404
Journal article
2013

Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels

Luis Caspeta-Guadarrama, Jens B Nielsen
Biotechnology journal. Vol. 8 (5), p. 534-544
Journal article
2013

Adipose Tissue Resting Energy Expenditure and Expression of Genes Involved in Mitochondrial Function Are Higher in Women than in Men.

Intawat Nookaew, Per-Arne Svensson, Peter Jacobson et al
The Journal of clinical endocrinology and metabolism. Vol. 98 (2), p. E370-E378
Journal article
2013

Using Transcriptomics To Improve Butanol Tolerance of Synechocystis sp Strain PCC 6803

J. Anfelt, B. M. Hallstrom, Jens B Nielsen et al
Applied and Environmental Microbiology. Vol. 79 (23), p. 7419-7427
Journal article
2013

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

Adil Mardinoglu, Rasmus Ågren, C. Kampf et al
Molecular Systems Biology. Vol. 9 (1), p. 649-
Journal article
2013

Novel insights into obesity and diabetes through genome-scale metabolic modeling

Leif Väremo, Intawat Nookaew, Jens B Nielsen
Frontiers in Physiology. Vol. 4 (92)
Journal article
2013

Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae

M. C. Jewett, C. T. Workman, Intawat Nookaew et al
G3: Genes, Genomes, Genetics. Vol. 3 (11), p. 1979-1995
Journal article
2013

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Leif Väremo, Jens B Nielsen, Intawat Nookaew
Nucleic Acids Research. Vol. 41 (8), p. 4378-4391
Journal article
2013

Assessing the human gut microbiota in metabolic diseases.

Fredrik Karlsson, Valentina Tremaroli, Jens B Nielsen et al
Journal of Logic and Computation. Vol. 62 (10), p. 3341-9
Journal article
2013

Understanding the interactions between bacteria in the human gut through metabolic modeling

Saeed Shoaie, Fredrik Karlsson, Adil Mardinoglu et al
Scientific Reports. Vol. 3
Journal article
2013

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

Elzbieta Petelenz-Kurdziel, C. Kuehn, Bodil Nordlander et al
PLoS Computational Biology. Vol. 9 (6), p. artikel nr e1003084-
Journal article
2013

Advances in metabolic pathway and strain engineering paving the way for sustainable production of chemical building blocks

Yun Chen, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 24 (6), p. 956-972
Journal article
2013

Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae

Jin Hou, Tobias Österlund, Zihe Liu et al
Applied Microbiology and Biotechnology. Vol. 97 (8), p. 3559-3568
Journal article
2013

From flavors and pharmaceuticals to advanced biofuels: Production of isoprenoids in Saccharomyces cerevisiae

Stefan Tippmann, Yun Chen, Verena Siewers et al
Biotechnology journal. Vol. 8 (12), p. 1435-1444
Journal article
2013

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

José Manuel Otero, D. Cimini, K. R. Patil et al
PLoS ONE. Vol. 8 (1)
Journal article
2013

Systems biology methods and developments of filamentous fungi in relation to the production of food ingredients

Wanwipa Vongsangnak, Jens B Nielsen
Microbial Production of Food Ingredients, Enzymes and Nutraceuticals, p. 19-41
Chapter in monograph, book - peer reviewed
2013

The role of biofuels in the future energy supply

Luis Caspeta-Guadarrama, Nicolaas Buijs, Jens B Nielsen
Energy and Environmental Sciences. Vol. 6 (4), p. 1077-1082
Journal article
2013

Advanced biofuel production by the yeast Saccharomyces cerevisiae

Nicolaas Buijs, Verena Siewers, Jens B Nielsen
Current Opinion in Chemical Biology. Vol. 17 (3), p. 480-488
Journal article
2013

Metabolic engineering of isoprenoid production: Reconstruction of multistep heterologous pathways in tractable hosts

J. Maury, M. A. Asadollahi, L. R. Formenti et al
Isoprenoid Synthesis in Plants and Microorganisms: New Concepts and Experimental Approaches, p. 73-89
Chapter in monograph, book - peer reviewed
2013

Improved polyhydroxybutyrate production by Saccharomyces cerevisiae through the use of the phosphoketolase pathway

Kanokarn Kocharin, Verena Siewers, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 110 (8), p. 2216-2224
Journal article
2013

Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling

S. Borgos, Sergio Velasco, H. Sletta et al
BMC Systems Biology. Vol. 7
Journal article
2013

Investigation of Malic Acid Production in Aspergillus oryzae under Nitrogen Starvation Conditions

Christoph Knuf, Intawat Nookaew, Stephen H. Brown et al
Applied and Environmental Microbiology. Vol. 79 (19), p. 6050-6058
Journal article
2013

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Rasmus Ågren, Liming Liu, Saeed Shoaie et al
PLoS Computational Biology. Vol. 9 (3), p. e1002980-
Journal article
2013

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Rasmus Ågren, Liming Liu, Saeed Shoaie et al
PLoS Computational Biology. Vol. 9 (3), p. e1002980-
Journal article
2013

A community-driven global reconstruction of human metabolism

I. Thiele, N. Swainston, R. M. T. Fleming et al
Nature Biotechnology. Vol. 31 (5), p. 419-+
Journal article
2013

Application of genome-scale metabolic models in metabolic engineering

Manuel Garcia, Jens B Nielsen
Industrial Biotechnology. Vol. 9 (4), p. 203-214
Journal article
2013

Specific growth rate and substrate dependent polyhydroxybutyrate production in Saccharomyces cerevisiae

Kanokarn Kocharin, Jens B Nielsen
AMB Express. Vol. 3 (18), p. 1-6
Journal article
2013

Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae

Zihe Liu, Jin Hou, Jose Luis Martinez Ruiz et al
Applied Microbiology and Biotechnology. Vol. 97 (20), p. 8955-8962
Journal article
2013

Gut metagenome in European women with normal, impaired and diabetic glucose control

Fredrik Karlsson, Valentina Tremaroli, Intawat Nookaew et al
Nature. Vol. 498 (7452), p. 99-103
Journal article
2013

Bridging omics technologies with synthetic biology in yeast industrial biotechnology

Antonio Roldao, Il-Kwon Kim, Jens B Nielsen
Systems Metabolic Engineering, p. 271-327
Chapter in monograph, book - peer reviewed
2013

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

Leif Väremo, Jens B Nielsen, Intawat Nookaew
Nucleic Acids Research. Vol. 41 (8), p. 4378-4391
Journal article
2012

Systems biology: the 'new biotechnology' Editorial overview

Jens B Nielsen, S. Y. Lee
Current Opinion in Biotechnology. Vol. 23 (4), p. 583-584
Magazine article
2012

Pharmaceutical protein production by yeast: towards production of human blood proteins by microbial fermentation

Jose Luis Martinez Ruiz, Lifang Liu, Dina Petranovic Nielsen et al
Current Opinion in Biotechnology. Vol. 23 (6), p. 965-971
Journal article
2012

Mapping the polysaccharide degradation potential of Aspergillus niger

M.R. Andersen, M. Giese, R.P. de Vries et al
BMC Genomics. Vol. 13
Journal article
2012

Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels

Bouke Wim de Jong, Verena Siewers, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 23 (4), p. 624-630
Journal article
2012

Profiling of Cytosolic and Peroxisomal Acetyl-CoA Metabolism in Saccharomyces cerevisiae

Yun Chen, Verena Siewers, Jens B Nielsen
PLoS ONE. Vol. 7 (8), p. e42475-
Journal article
2012

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress

Keith Tyo, Zihe Liu, Dina Petranovic Nielsen et al
BMC Biology. Vol. 10 (16), p. Art. no 16-
Journal article
2012

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

Gionata Scalcinati, José Manuel Otero, J. R. H. Van Vleet et al
FEMS Yeast Research. Vol. 12 (5), p. 582-597
Journal article
2012

Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production

Shuobo Shi, Juan Octavio Valle Rodriguez, Sakda Khoomrung et al
Biotechnology for Biofuels. Vol. 5, p. Art. no. 7-
Journal article
2012

Genome-scale metabolic representation of Amycolatopsis balhimycina

Wanwipa Vongsangnak, L. F. Figueiredo, J. Forster et al
Biotechnology and Bioengineering. Vol. 109 (7), p. 1798-1807
Journal article
2012

Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae

Jin Hou, Keith Tyo, Zihe Liu et al
FEMS Yeast Research. Vol. 12 (5), p. 491-510
Journal article
2012

Dynamic (13) C-labelling experiments prove important differences in protein turnover rate between two Saccharomyces cerevisiae strains

Kuk-ki Hong, Jin Hou, Saeed Shoaie et al
FEMS Yeast Research. Vol. 12 (7), p. 741-747
Journal article
2012

Aspergilli: Systems biology and industrial applications

Christoph Knuf, Jens B Nielsen
Biotechnology journal. Vol. 7 (9), p. 1147-1155
Journal article
2012

Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response

Cecilia Geijer, Ivan Pirkov, Wanwipa Vongsangnak et al
BMC Genomics. Vol. 13 (1), p. artikel nr 554-
Journal article
2012

Symptomatic atherosclerosis is associated with an altered gut metagenome

Fredrik Karlsson, Frida Fåk, Intawat Nookaew et al
Nature Communications. Vol. 3
Journal article
2012

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Rasmus Ågren, Sergio Velasco, Adil Mardinoglu et al
PLoS Computational Biology (5)
Journal article
2012

dynamic control of gene expression in saccharomyces cerevisiae engineered for the production of plant sesquiterpene alpha-santalene in a fed-batch mode

Gionata Scalcinati, Christoph Knuf, Siavash Partow et al
Metabolic Engineering. Vol. 14 (2), p. 91-103
Journal article
2012

Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

Kuk-ki Hong, Jens B Nielsen
Applied and Environmental Microbiology. Vol. 78 (21), p. 7579-7586
Journal article
2012

Applied systems biology - vanillin production in Saccharomyces cerevisiae

T. Strucko, J. C. Eriksen, Jens B Nielsen et al
FEBS Journal. Vol. 279 (Special Issue: SI Supplement: 1), p. 525-525
Conference contribution
2012

A systems-level approach for metabolic engineering of yeast cell factories

Il-Kwon Kim, Antonio Roldao, Verena Siewers et al
FEMS Yeast Research. Vol. 12 (2), p. 228-248
Journal article
2012

Metabolic engineering, synthetic biology and systems biology

Jens B Nielsen, J. Pronk
FEMS Yeast Research. Vol. 12 (2), p. 103-103
Magazine article
2012

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88

E. G. Larsson, Valentina Tremaroli, Ying Shiuan Lee et al
Gut. Vol. 61 (8), p. 1124-1131
Journal article
2012

Combined metabolic engineering of precursor and co-factor supply to increase α-santalene production by Saccharomyces cerevisiae

Gionata Scalcinati, Siavash Partow, Verena Siewers et al
Microbial Cell Factories. Vol. 11, p. Article Number: 117-
Journal article
2012

Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

Kuk-ki Hong, Jens B Nielsen
Applied and Environmental Microbiology. Vol. 78 (21), p. 7579-7586
Journal article
2012

Translational and systems medicine Introduction

Jens B Nielsen
Journal of Internal Medicine. Vol. 271 (2), p. 108-110
Magazine article
2012

Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases

J. K. Michener, Jens B Nielsen, C. D. Smolke
Proceedings of the National Academy of Sciences of the United States of America. Vol. 109 (47), p. 19504-19509
Journal article
2012

Fifteen years of large scale metabolic modeling of yeast: Developments and impacts

Tobias Österlund, Intawat Nookaew, Jens B Nielsen
Biotechnology Advances. Vol. 30 (5), p. 979-988
Journal article
2012

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, Marta Papini, Natapol Pornputtapong et al
Nucleic Acids Research. Vol. 40 (20), p. 10084-10097
Journal article
2012

Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae

Zihe Liu, Keith Tyo, Jose Luis Martinez Ruiz et al
Biotechnology and Bioengineering. Vol. 109 (5), p. 1259-1268
Journal article
2012

Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through (13)C-based metabolic flux analysis.

Marta Papini, Intawat Nookaew, Verena Siewers et al
Applied Microbiology and Biotechnology. Vol. 95 (4), p. 1001-1010
Journal article
2012

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Marta Papini, Intawat Nookaew, M. Uhlen et al
Microbial Cell Factories. Vol. 11, p. Article Number: 136 -
Journal article
2012

Reconstruction and Evaluation of the Synthetic Bacterial MEP Pathway in Saccharomyces cerevisiae

Siavash Partow, Verena Siewers, L. Daviet et al
PLoS ONE. Vol. 7 (12), p. Article Number: e52498 -
Journal article
2012

Engineering of acetyl-CoA metabolism for the improved production of polyhydroxybutyrate in Saccharomyces cerevisiae

Kanokarn Kocharin, Yun Chen, Verena Siewers et al
AMB Express. Vol. 2 (1)
Journal article
2012

Fast and accurate preparation fatty acid methyl esters by microwave-assisted derivatization in the yeast Saccharomyces cerevisiae

Sakda Khoomrung, Pramote Chumnanpuen, Suwanee Jansa-Ard et al
Applied Microbiology and Biotechnology. Vol. 94 (6), p. 1637-1646
Journal article
2012

Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity

L. Pedersen, K. Hansen, Jens B Nielsen et al
Biotechnology and Bioengineering. Vol. 109 (1), p. 116-124
Journal article
2012

Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae

Jin Hou, Keith Tyo, Zihe Liu et al
Metabolic Engineering. Vol. 14 (2), p. 120-127
Journal article
2012

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

Luis Caspeta-Guadarrama, Saeed Shoaie, Rasmus Ågren et al
BMC Systems Biology. Vol. 6 (24)
Journal article
2012

Systems medicine and metabolic modelling

Adil Mardinoglu, Jens B Nielsen
Journal of Internal Medicine. Vol. 271 (2), p. 142-154
Journal article
2012

Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production

Yun Chen, Siavash Partow, Gionata Scalcinati et al
FEMS Yeast Research. Vol. 12 (5), p. 598-607
Journal article
2012

Integrated analysis of transcriptome and lipid profiling reveals the co-influences of inositol-choline and Snf1 in controlling lipid biosynthesis in yeast

Pramote Chumnanpuen, Jie Zhang, Intawat Nookaew et al
Molecular Genetics and Genomics. Vol. 287 (7), p. 541-554
Journal article
2012

De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology

J. F. Nijkamp, M. van den Broek, E. Datema et al
Microbial Cell Factories. Vol. 11, p. Article Number: 36-
Journal article
2012

Metabolic Engineering of Saccharomyces cerevisiae: A Key Cell Factory Platform for Future Biorefineries

Kuk-ki Hong, Jens B Nielsen
Cellular and Molecular Life Sciences (16), p. 2671-2690
Journal article
2011

A Closer Look at Bacteroides: Phylogenetic Relationship and Genomic Implications of a Life in the Human Gut

Fredrik Karlsson, D. W. Ussery, Jens B Nielsen et al
Microbial Ecology. Vol. 61 (3), p. 473-485
Journal article
2011

MEMOSys: Bioinformatics platform for genome-scale metabolic models

S. Pabinger, R. Rader, Rasmus Ågren et al
BMC Systems Biology. Vol. 5
Journal article
2011

Lipid biosynthesis monitored at the single-cell level in Saccharomyces cerevisiae

Pramote Chumnanpuen, Christian Brackmann, Subir Kumar Nandy et al
Biotechnology journal (5), p. 594-601
Journal article
2011

BIOFUELS Chimeric synthetic pathways

Jens B Nielsen
Nature Chemical Biology. Vol. 7 (4), p. 195-196
Journal article
2011

Mathematical models of cell factories: moving towards the core of industrial biotechnology

Marija Cvijovic, Sergio Velasco, Jens B Nielsen
Microbial Biotechnology. Vol. 4 (5), p. 572-584
Journal article
2011

Unraveling molecular signatures of immunostimulatory adjuvants in the female genital tract through systems biology

M. Lindqvist, Intawat Nookaew, Ingrid Brinkenberg et al
PLoS ONE. Vol. 6 (6), p. e20448-
Journal article
2011

The Influence of Microgravity on Invasive Growth in Saccharomyces cerevisiae

S. E. Van Mulders, C. Stassen, L. Daenen et al
Astrobiology. Vol. 11 (1), p. 45-55
Journal article
2011

Diversion of Flux toward Sesquiterpene Production in Saccharomyces cerevisiae by Fusion of Host and Heterologous Enzymes

L. Albertsen, Yun Chen, L. S. Bach et al
Applied and Environmental Microbiology. Vol. 77 (3), p. 1033-1040
Journal article
2011

Comparative Metabolic Capabilities for Micrococcus luteus NCTC 2665, the "Fleming" Strain, and Actinobacteria

J. S. Rokem, Wanwipa Vongsangnak, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 108 (11), p. 2770-2775
Journal article
2011

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

M. R. Andersen, Margarita Salazar Pena, P. J. Schaap et al
Genome Research. Vol. 21 (6), p. 885-897
Journal article
2011

Genome-scale metabolic models of Saccharomyces cerevisiae

Intawat Nookaew, Roberto Olivares Hernandez, S. Bhumiratana et al
Methods in molecular biology (Clifton, N.J.), p. 445-463
Chapter in monograph, book - peer reviewed
2011

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

Kuk-ki Hong, Wanwipa Vongsangnak, Goutham Vemuri et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 108 (29), p. 12179-12184
Journal article
2011

Synergies between synthetic biology and metabolic engineering

Jens B Nielsen, J.D. Keasling
Nature Biotechnology. Vol. 29 (8), p. 693-695
Magazine article
2011

Transcriptional control of metabolic fluxes

Jens B Nielsen
Molecular Systems Biology. Vol. 7
Journal article
2011

Industrial systems biology

Jens B Nielsen
Biotechnology journal. Vol. 6 (3), p. 255-255
Journal article
2011

Molecular Basis for Mycophenolic Acid Biosynthesis in Penicillium brevicompactum

T. B. Regueira, K. R. Kildegaard, B. G. Hansen et al
Applied and Environmental Microbiology. Vol. 77 (9), p. 3035-3043
Journal article
2011

Molecular and process design for rotavirus-like particle production in Saccharomyces cerevisiae

W. A. Rodriguez-Limas, Keith Tyo, Jens B Nielsen et al
Microbial Cell Factories. Vol. 10, p. Art. no. 33-
Journal article
2011

Prospects for microbial biodiesel production

Shuobo Shi, Juan Octavio Valle Rodriguez, Verena Siewers et al
Biotechnology journal. Vol. 6 (3), p. 277-285
Journal article
2011

Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques

M. P. Piddocke, A. Fazio, Wanwipa Vongsangnak et al
Microbial Cell Factories. Vol. 10
Journal article
2011

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

B. G. Hansen, B. Salomonsen, M. T. Nielsen et al
Applied and Environmental Microbiology. Vol. 77 (9), p. 3044-3051
Journal article
2011

Opportunities for yeast metabolic engineering: Lessons from synthetic biology

Verena Siewers, Jens B Nielsen, Anastasia Krivoruchko
Biotechnology journal. Vol. 6 (3), p. 262-276
Journal article
2011

Codon usage variability determines the correlation between proteome and transcriptome fold changes

Roberto Olivares Hernandez, Sergio Velasco, Jens B Nielsen
BMC Systems Biology. Vol. 5
Journal article
2011

Integrated Analysis of the Global Transcriptional Response to alpha-Amylase Over-Production by Aspergillus oryzae

Wanwipa Vongsangnak, K. Hansen, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 108 (5), p. 1130-1139
Journal article
2011

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

Jie Zhang, S. Vaga, Pramote Chumnanpuen et al
Molecular Systems Biology. Vol. 7
Journal article
2011

Linking Genotype and Phenotype of Saccharomyces cerevisiae Strains Reveals Metabolic Engineering Targets and Leads to Triterpene Hyper-Producers

Karina M. Madsen, Gupta Udatha, Saori Semba et al
PLoS ONE. Vol. 6 (3), p. e14763-
Journal article
2011

Prospects for systems biology and modeling of the gut microbiome

Fredrik Karlsson, Intawat Nookaew, Dina Petranovic Nielsen et al
Trends in Biotechnology. Vol. 29 (6), p. 251-258
Journal article
2010

Systems Biology of lipid metabolism: From yeast to human

José Manuel Otero, Jens B Nielsen
FEBS Letters. Vol. 583 (24), p. 3905-3913
Journal article
2010

Transcriptional progression of atrophic gastritis development in humans

S. Lundin, Intawat Nookaew, K. Worah et al
Helicobacter. Vol. 15 (4), p. 323-324
Journal article
2010

Identification of flux control in metabolic networks using non-equilibrium thermodynamics

Sergio Velasco, Jens B Nielsen
Metabolic Engineering. Vol. 12 (4), p. 369-377
Journal article
2010

Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

José Manuel Otero, Wanwipa Vongsangnak, M. A. Asadollahi et al
BMC Genomics. Vol. 11 (1), p. 723-
Journal article
2010

The b-subunits of the Snf1 kinase in Saccharomyces cerevisae, Gal83 and Sip2, but not Sip1 are redundant in glucose derepression and regulation of sterol biosynthesis

Jie Zhang, Lisbeth Olsson, Jens B Nielsen
Molecular Microbiology. Vol. 77 (2), p. 371-383
Journal article
2010

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

Sergio Velasco, Rasmus Ågren, Jens B Nielsen
PLoS Computational Biology. Vol. 6 (7), p. 16-
Journal article
2010

Identifying molecular effects of diet through systems biology: influence of herring diet on sterol metabolism and protein turnover in mice

Intawat Nookaew, Britt Gabrielsson, Agneta Holmäng et al
PLoS ONE. Vol. 5 (8), p. e12361-
Journal article
2010

BioMet Toolbox: genome-wide analysis of metabolism

Marija Cvijovic, Roberto Olivares Hernandez, Rasmus Ågren et al
Nucleic Acids Research. Vol. 38 (SUPPL. 2), p. W144-W149
Journal article
2010

OptFlux: an open-source software platform for in silico metabolic engineering

I. Rocha, P. Maia, P. Evangelista et al
BMC Systems Biology. Vol. 4
Journal article
2010

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

A.B. Canelas, N. Harrison, A. Fazio et al
Nature Communications. Vol. 1 (9)
Journal article
2010

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

Sergio Velasco, Rasmus Ågren, Jens B Nielsen
PLoS Computational Biology. Vol. 6 (7), p. 16-
Journal article
2010

Industrial Systems Biology

José Manuel Otero, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 105 (3), p. 439-460
Journal article
2010

Industrial Systems Biology

José Manuel Otero, Jens B Nielsen
Industrial Biotechnology: Sustainable Growth and Economic Success, p. 79-147
Chapter in monograph, book - peer reviewed
2010

Toward Design-based Engineering of Industrial Microbes

Keith Tyo, Kanokarn Kocharin, Jens B Nielsen
Current Opinion in Microbiology. Vol. 13 (3), p. 255-262
Journal article
2010

Yeast Biological Networks Unfold the Interplay of Antioxidants, Genome and Phenotype, and Reveal a Novel Regulator of the Oxidative Stress Response

José Manuel Otero, M.A. Papadakis, Gupta Udatha et al
PLoS ONE. Vol. 5 (10), p. e13606-
Journal article
2010

Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae

Siavash Partow, Verena Siewers, S. Bjorn et al
Yeast. Vol. 27 (11), p. 955-964
Journal article
2010

Systems biology of microorganisms

Jens B Nielsen, Marc Vidal
Current Opinion in Microbiology. Vol. 13 (3), p. 335-336
Journal article
2010

Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group

Roberto Olivares Hernandez, Hampus Sunner, J. C. Frisvad et al
PLoS ONE. Vol. 5 (9), p. Article Number: e12781-
Journal article
2010

Use of genome-scale metabolic models for understanding microbial physiology

Liming Liu, Rasmus Ågren, Sergio Velasco et al
FEBS Letters. Vol. 584 (12), p. 2556-2564
Journal article
2010

Prospects of yeast systems biology for human health: integrating lipid, protein and energy metabolism

Dina Petranovic Nielsen, Keith Tyo, Goutham Vemuri et al
FEMS Yeast Research. Vol. 10 (8), p. 1046-1059
Journal article
2010

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation

Subir Kumar Nandy, Paula Jouhten, Jens B Nielsen
BMC Systems Biology. Vol. 4, p. 68-
Journal article
2010

Measuring enzyme activities under standardized in-vivo like conditions for systems biology

K. Van Eunen, J. Bouwman, P. Daran-Lapujade et al
FEBS Journal. Vol. 277 (3), p. 749-760
Journal article
2010

Systems Biology of Industrial Microorganisms

Marta Papini, Margarita Salazar Pena, Jens B Nielsen
Advances in Biochemical Engineering/Biotechnology. Vol. 120, p. 51-99
Journal article
2010

Systems biology of energy homeostasis in yeast

Jie Zhang, Goutham Vemuri, Jens B Nielsen
Current Opinion in Microbiology. Vol. 13 (3), p. 382-388
Journal article
2010

Analysis of Genome-Wide Coexpression and Coevolution of Aspergillus oryzae and Aspergillus niger

Wanwipa Vongsangnak, Intawat Nookaew, Margarita Salazar Pena et al
OMICS A Journal of Integrative Biology. Vol. 14 (2), p. 165-175
Journal article
2010

Implementation of communication-mediating domains for non-ribosomal peptide production in Saccharomyces cerevisae

Verena Siewers, Rita San-Bento, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 106 (5), p. 841-844
Journal article
2010

Enhancement of Farnesyl Diphosphate Pool as Direct Precursor of Sesquiterpenes Through Metabolic Engineering of the Mevalonate Pathway in Saccharomyces cerevisiae

M. A. Asadollahi, J. Maury, M. Schalk et al
Biotechnology and Bioengineering. Vol. 106 (1), p. 86-96
Journal article
2010

Phosphoglycerate mutase knock-out mutant Saccharomyces cerevisiae: Physiological investigation and transcriptome analysis

Marta Papini, Intawat Nookaew, Gionata Scalcinati et al
Biotechnology journal. Vol. 5 (10), p. 1016-1027
Journal article
2010

Integrative Analysis Using Proteome and Transcriptome Data From Yeast to Unravel Regulatory Patterns at Post-Transcriptional Level

Roberto Olivares Hernandez, R. Usaite, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 107 (5), p. 865-875
Journal article
2009

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3

D. Cimini, K. R. Patil, C. Schiraldi et al
BMC Systems Biology. Vol. 3, p. 17 (artno)-
Journal article
2009

Nutritional Systems Biology: Definitions and Approaches

G. Panagiotou, Jens B Nielsen
Annual Review of Nutrition. Vol. 29, p. 329-339
Journal article
2009

In-depth analysis of Aspergillus niger metabolism during industrial fed-batch fermentations

L. Pedersen, K. Hansen, K. F. Nielsen et al
New Biotechnology. Vol. 25 (Suppl. 1; SEP 2009; Meeting Abstract), p. S210-S211
Journal article
2009

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

T. S. Christensen, A. P. Oliveira, Jens B Nielsen
BMC Systems Biology. Vol. 3, p. 7 (artno)-
Journal article
2009

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering

M. A. Asadollahi, J. Maury, K. R. Patil et al
Metabolic Engineering. Vol. 11 (6), p. 328-334
Journal article
2009

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

J. R. Wortman, J. M. Gilsenan, V. Joardar et al
Fungal Genetics and Biology. Vol. 46, p. S2-S13
Journal article
2009

Overexpression of isocitrate lyase-glyoxylate bypass influence on matabolism in Aspergillus niger

S Meijer, J Otero, R Olivares et al
Metabolic Engineering (11), p. 107-116
Journal article
2009

Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Renata Usaite, Michael C Jewett, Ana Paula Oliveira et al
Molecular Systems Biology. Vol. 5 (319), p. 1-12
Journal article
2009

Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis

Margarita Salazar Pena, Wanwipa Vongsangnak, G. Panagiotou et al
Molecular Genetics and Genomics. Vol. 282 (6), p. 571-586
Journal article
2009

Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger

G. Hofmann, A. Diano, Jens B Nielsen
Metabolic Engineering. Vol. 11 (1), p. 8-12
Journal article
2009

Studies of the Production of Fungal Polyketides in Aspergillus nidulans by Using Systems Biology Tools

Gianni Panagiotou, Mikael R. Andersen, Thomas Grotkjær et al
Applied and Environmental Microbiology. Vol. 75 (7), p. 2212-2220
Journal article
2009

Linking transcriptional regulation and high resolution metabolic fluxes in yeast modulated by the global regulator Gcn4p

J.F. Moxley, M.C. Jewett, M.R Antoniewicz et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 106 (16), p. 6477-6482
Journal article
2009

Comparative Transcriptomic Approach To Investigate Differences in Wine Yeast Physiology and Metabolism during Fermentation

D. Rossouw, Roberto Olivares Hernandez, Jens B Nielsen et al
Applied and Environmental Microbiology. Vol. 75 (20), p. 6600-6612
Journal article
2009

Linking transcriptional regulation and high resolution metabolic fluxes in yeast modulated by the global regulator Gcn4p

J.F. Moxley, M.C. Jewett, M.R Antoniewicz et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 106 (16), p. 6477-6482
Journal article
2009

Gene deletion of cytosolic ATP: citrate lyase leads to altered organic acid production in Aspergillus niger

S. L. Meijer, M. L. Nielsen, Lisbeth Olsson et al
Journal of Industrial Microbiology and Biotechnology. Vol. 36 (10), p. 1275-1280
Journal article
2009

Heterologous production of non-ribosomal peptide LLD-ACV in Saccharomyces cerevisiae

V. Siewers, X. Chen, L. Huang et al
Metabolic Engineering. Vol. 11 (6), p. 391-397
Journal article
2009

Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae

D. B. Flagfeldt, V. Siewers, L. Huang et al
Yeast. Vol. 26 (10), p. 545-551
Journal article
2009

Systems biology of lipid metabolism: From yeast to human

Jens B Nielsen
FEBS Letters. Vol. 583 (24), p. 3905-3913
Journal article
2009

Random sampling of metabolic networks

Sergio Velasco, Jens B Nielsen
New Biotechnology. Vol. 25 (Suppl. 1 Published: SEP 2009 ; Meeting abstract), p. S336-S336
Journal article
2009

Vintage paper - Introduction

Jens B Nielsen
Biotechnology and Bioengineering. Vol. 103 (1), p. 1-
Journal article
2009

Current status of systems biology in Aspergilli

M.R. Andersen, Jens B Nielsen
Fungal Genetics and Biology. Vol. 46 (584-590), p. 180-190
Journal article
2009

Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae

P. M. Coutinho, M. R. Andersen, K. Kolenova et al
Fungal Genetics and Biology. Vol. 46 (Suppl 1), p. S161-S169
Journal article
2009

Qualification of flux control in metabolic pathways

Jens B Nielsen
Biotechnology and Bioengineering. Vol. 104, p. 1-2
Journal article
2009

Physiological characterisation of acuB deletion in Aspergillus niger

S. L. Meijer, W. A. de Jongh, Lisbeth Olsson et al
Applied Microbiology and Biotechnology. Vol. 84 (1), p. 157-167
Journal article
2009

Systemic analysis of the response of Aspergillus niger to ambient pH

M. R. Andersen, L. Lehmann, Jens B Nielsen
Genome Biology. Vol. 10 (5)
Journal article
2009

Disruption of the NADPH-dependent glutamate dehydrogenase affects the morphology of two industrial strains of Penicillium chrysogenum

J. Thykaer, K. Rueksomtawin, H. Noorman et al
Journal of Biotechnology. Vol. 139 (4), p. 280-282
Journal article
2009

Yeast as a Prototype for Systems Biology

Goutham Vemuri, Jens B Nielsen
Systems Biology and Synthetic Biology, p. 287-353
Chapter in monograph, book - peer reviewed
2009

In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network.

K.R. Kjeldsen, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 102 (2), p. 583-597
Journal article
2009

Physiology of Aspergillus niger in Oxygen-Limited Continuous Cultures: Influence of Aeration, Carbon Source Concentration and Dilution Rate

A. Diano, J. Peeters, J. Dynesen et al
Biotechnology and Bioengineering. Vol. 103 (5), p. 956-965
Journal article
2009

Genome-wide analysis of maltose utilization and regulation in aspergilli

Wanwipa Vongsangnak, Margarita Salazar Pena, Kim Hansen et al
Microbiology. Vol. 155 (12), p. 3893-3902
Journal article
2008

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Wanwipa Vongsangnak, Peter Olsen, Kim Hansen et al
BMC Genomics. Vol. 9 (245)
Journal article
2008

Systems Analysis Unfolds the Relationship between the Phosphoketolase Pathway and Growth in Aspergillus nidulans

Gianni Panagiotou, Mikael R. Andersen, Thomas Grotkjær et al
PLoS ONE. Vol. 3 (12)
Journal article
2008

Metabolic footprinting in microbiology: methods and applications in functional genomics and biotechnology

Valeria Mapelli, Lisbeth Olsson, Jens B Nielsen
Trends in Biotechnology. Vol. 26 (9), p. 490-497
Journal article
2008

Can yeast systems biology contribute to the understanding of human disease?

Dina Petranovic Nielsen, Jens B Nielsen
Trends in Biotechnology. Vol. 26 (11), p. 584-590
Journal article
2008

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

Ana Paula Oliveira, Kiran Raosaheb Patil, Jens B Nielsen
BMC Systems Biology. Vol. 2 (17)
Journal article
2008

Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus Niger

Jens B Nielsen, MR Andersen, ML Nielsen
Mol Syst Biol.. Vol. 4, p. 178-
Journal article
2008

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Markus J Herrgård, Neil Swainston, Paul Dobson et al
Nature Biotechnology. Vol. 26 (10), p. 1155-1160
Journal article
2008

Penicillium chrysogenum is involved in regulation of b-lactam production

Jens B Nielsen, J. Thykaer, K. Rueksomtawin et al
Microbiol.. Vol. 154, p. 1242-1250
Journal article
2008

A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species

MR Andersen, W Vongsangnak, G Panagiotou et al
Proc. Nat. Acad. Sci.. Vol. 105, p. 4387-4392
Journal article
2008

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, James Wohlschlegel, John D. Venable et al
Journal of Proteome Research. Vol. 266 (7), p. 266-275
Journal article
2008

Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply

S. Wattanachaisaereekul, A.E. Lantz, M.L. Nielsen et al
Metabolic Eng.. Vol. 10, p. 246-254
Journal article
2008

Systems biology: Is the hope worth the hype

G. Vemuri, Jens B Nielsen
SIM News. Vol. 58, p. 178-188
Journal article
2008

Natural computation meta-heuristics for the in silico optimization of microbial strains

M. Rocha, P. Maia, R. Mendes et al
BMC Bioinformatics. Vol. 9, p. 499-
Journal article
2008

The Roles of Galactitol, Galactose-1-Phosphate, and Phosphoglucomutase in Galactose-Induced Toxicity in Saccharomyces cerevisiae

Willem A. de Jongh, Christoffer Bro, Simon Ostergaard et al
Biotechnology and Bioengineering. Vol. 101 (2), p. 317-326
Journal article
2008

Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion

I Borodina, J. Siebring, J. Zhang et al
J. Biol. Chem.. Vol. 283, p. 25186-25199
Journal article
2008

Physiological characterization of glucose repression in the strains with SNF1 and SNF4 genes deleted

Renata Usaite, Jens B Nielsen, Lisbeth Olsson
Journal of Biotechnology (133), p. 73-81
Journal article
2008

Analysis of Aspergillus nidulans metabolism at the genome-scale

H David, I. Ozcelik, G. Hofmann et al
BMC Genomics. Vol. 9, p. 163-
Journal article
2008

Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae

J. Maury, M. A. Asadollahi, K. Moller et al
FEBS Letters. Vol. 582 (29), p. 4032-4038
Journal article
2008

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design

Allessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade et al
BMC Genomics. Vol. 9 (341)
Journal article
2008

Growth temperature exerts a differential physiological and transcriptional response in laboratory and wine strains of Saccharomyces cerevisiae

F. Pizarro, M.C. Jewett, Jens B Nielsen et al
Appl. Environ. Microbiol.. Vol. 74, p. 6358-6368
Journal article
2008

The genome-scale metabolic model ilN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

Intawat Nookaew, Michael C Jewett, Asawin Meechai et al
BMC Systems Biology. Vol. 2 (71)
Journal article
2008

Metabolomics. Topics in Current Genetics

Jens B Nielsen
Springer Verlag, Heidelberg. Vol. 18
Journal article