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 Systems Biology
European Commission (FP7)

56 publications exist
2012–2017

Metagenomics in Cardiometabolic Diseases (METACARDIS)

Jens B Nielsen Systems Biology
European Commission (FP7)

6 publications exist
2012–2015

Infrastructure for Systems Biology - Europe (ISBE)

Jens B Nielsen Systems Biology
European Commission (FP7)

2013–2017

Quantitative Biology for Fungal Secondary Metabolite Producers (QUANTFUNG)

Jens B Nielsen Systems 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 Systems 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 Systems Biology
Jens B Nielsen Systems Biology
Leonie Wenning Systems 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

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 & Biotechnology. Vol. 44 (7), p. 1065-1072
Scientific journal article - peer reviewed
2017

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

Petri-Jaan Lahtvee, Benjamin Sánchez, Agata Smialowska et al
Cell Systems. Vol. 4 (5), p. 495-504.e5
Scientific journal article - peer reviewed
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
Scientific journal article - 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, p. Article Number: 47
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2017

The yeast osmostress response is carbon source dependent

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

Engineering central metabolism – a grand challenge for plant biologists

Lee J. Sweetlove, Jens B. Nielsen, Alisdair R. Fernie et al
The Plant Journal. Vol. 90 (4), p. 749-763
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2017

Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production

Guokun Wang, Mingtao Huang, Jens B. Nielsen et al
Current Opinion in Biotechnology. Vol. 48, p. 77-84
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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 et al
Applied Microbiology and Biotechnology. Vol. 101 (9), p. 3577-3585
Scientific journal article - peer reviewed
2017

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

Jens Christian Froslev Nielsen, Sietske Grijseels, Sylvain Prigent et al
Nature Microbiology. Vol. 2
Scientific journal article - peer reviewed
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, p. 45
Scientific journal article - peer reviewed
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, p. 46
Scientific journal article - peer reviewed
2017

Expanding the product portfolio of fungal type I fatty acid synthases

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

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

Jens B. Nielsen,
Cell Metabolism. Vol. 25 (3), p. 572-579
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2017

A molecular genetic toolbox for Yarrowia lipolytica

Erin L. Bredeweg, Kyle R. Pomraning, Ziyu Dai et al
Biotechnology for Biofuels. Vol. 10 (1)
Scientific journal article - peer reviewed
2017

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

Min-Kyoung Kang, Jens B. Nielsen,
Journal of Industrial Microbiology & Biotechnology. Vol. 44 (4-5), p. 613-622
Scientific journal article - peer reviewed
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
Conference paper - non peer reviewed
2016

Flux control through protein phosphorylation in yeast

Yu Chen, Jens B. Nielsen,
Fems Yeast Research. Vol. 16 (8)
Scientific journal article - peer reviewed
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 et al
New Biotechnology. Vol. 33 ( Supplement: S Meeting Abstract: O18-3 ), p. S54-S54
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

Francesco Gatto, Marco Maruzzo, Cristina Magro et al
FRONTIERS IN ONCOLOGY. Vol. 6, p. Art. no. 253
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

José Luis Martinez Ruiz, Dina Petranovic, Jens B. Nielsen et al
Bioengineered. Vol. 7 (2), p. 112-5
Scientific journal article - peer reviewed
2016

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus.

John R Casey, Adil Mardinoglu, Jens B. Nielsen et al
mSystems. Vol. 1 (6)
Scientific journal article - peer reviewed
2016

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

Adil Mardinoglu, Jens B. Nielsen,
Frontiers in Physiology. Vol. 7
Scientific journal article - non peer reviewed
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 paper - non peer reviewed
2016

Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae.

Stefan Tippmann, Josefine Anfelt, Florian David et al
ACS synthetic biology
Scientific journal article - peer reviewed
2016

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

Eugene Fletcher, Amir Feizi, Markus M M Bisschops et al
Metabolic engineering. Vol. 39, p. 19-28
Scientific journal article - peer reviewed
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, p. 1025-1036
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

Engineering yeast for high-level production of stilbenoid antioxidants

M. J. Li, K. Schneider, M. Kristensen et al
Scientific Reports. Vol. 6, p. 36827
Scientific journal article - peer reviewed
2016

Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae

Alexandra Bergman, Verena Siewers, Jens B. Nielsen et al
AMB Express. Vol. 6
Scientific journal article - peer reviewed
2016

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

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

Integrative analysis of human omics data using biomolecular networks

Jonathan L. Robinson, Jens B. Nielsen,
Molecular Biosystems. Vol. 12 (10), p. 2953-2964
Scientific journal article - peer reviewed
2016

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

S. Grijseels, Jens Christian Froslev Nielsen, M. Randelovic et al
Scientific Reports. Vol. 6
Scientific journal article - peer reviewed
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 et al
mBio. Vol. 7 (3), p. e00559-16
Scientific journal article - non peer reviewed
2016

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

S. Lee, Adil Mardinoglu, C. Zhang et al
Nucleic Acids Research. Vol. 44 (12), p. 5529-5539
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

José Luis Martinez Ruiz, Eugenio Meza, Dina Petranovic et al
Metabolic Engineering Communications. Vol. 3, p. 205-210
Scientific journal article - peer reviewed
2016

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

S. Lee, C. Zhang, M. Kilicarslan et al
Cell Metabolism. Vol. 24 (1), p. 172-184
Scientific journal article - peer reviewed
2016

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

Francesco Gatto, A. Schulze, Jens B. Nielsen et al
Cell Reports. Vol. 16 (3), p. 878-895
Scientific journal article - peer reviewed
2016

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

Rui Pereira, Jens B. Nielsen, Isabel Rocha et al
Metabolic Engineering Communications. Vol. 3, p. 153-163
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

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

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

Luis Caspeta, Yun Chen, Jens B. Nielsen et al
Scientific Reports. Vol. 6, p. Art. no. 27003
Scientific journal article - peer reviewed
2016

Transcriptomics resources of human tissues and organs

M. Uhlen, B. M. Hallstrom, C. Lindskog et al
Molecular Systems Biology. Vol. 12 (4)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

Eugene Fletcher, Anastasia Krivoruchko, Jens B. Nielsen et al
Biotechnology and Bioengineering. Vol. 113 (6), p. 1164-1170
Scientific journal article - peer reviewed
2016

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

Yongjin Zhou, Nicolaas Buijs, Zhiwei Zhu et al
Nature Communications. Vol. 7, p. 11709
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

All You Need Is Mentorship

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

Engineering Cellular Metabolism

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

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

Florian David, Jens B. Nielsen, Verena Siewers et al
ACS Synthetic Biology. Vol. 5 (3), p. 224-233
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2016

Trehalose-6-phosphate synthase and stabilization of yeast glycolysis

Dan Fraenkel, Jens B. Nielsen,
Fems Yeast Research. Vol. 16 (1)
Scientific journal article - peer reviewed
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 et al
FEMS Yeast Research. Vol. 16 (1)
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2016

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

Avlant Nilsson, Jens B. Nielsen,
Scientific Reports. Vol. 6
Scientific journal article - peer reviewed
2016

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

Francesco Gatto, Jens B. Nielsen,
Journal of Hematology & Oncology. Vol. 9
Scientific journal article - peer reviewed
2016

Biobased organic acids production by metabolically engineered microorganisms

Yun Chen, Jens B. Nielsen,
Current Opinion in Biotechnology. Vol. 37, p. 165-172
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2016

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

Stefan Tippmann, Jens B. Nielsen, Sakda Khoomrung et al
Talanta: The International Journal of Pure and Applied Analytical Chemistry. Vol. 146, p. 100-106
Scientific journal article - peer reviewed
2015

Modifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes.

Luis Caspeta, Tania Castillo, Jens B. Nielsen et al
Frontiers in bioengineering and biotechnology. Vol. 3, p. 184
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

Cancer Metabolism: A Modeling Perspective

Pouyan Ghaffari Nouran, Adil Mardinoglu, Jens B. Nielsen et al
Frontiers in Physiology. Vol. 6
Scientific journal article - peer reviewed
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, p. 12
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

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

David Jullesson, Florian David, B. Pfleger et al
Biotechnology Advances. Vol. 33 (7), p. 1395-1402
Scientific journal article - peer reviewed
2015

New insight into the gut microbiome through metagenomics

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

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

Sakda Khoomrung, José Luis Martinez Ruiz, Stefan Tippmann et al
Analytical Chemistry Research. Vol. 6, p. 9-16
Scientific journal article - peer reviewed
2015

New paradigms for metabolic modeling of human cells

Adil Mardinoglu, Jens B. Nielsen,
Current Opinion in Biotechnology. Vol. 34, p. 91-97
Scientific journal article - peer reviewed
2015

HCSD: The human cancer secretome database

Amir Feizi, Amir Banaei-Esfahani, Jens B. Nielsen et al
Database. Vol. 2015
Scientific journal article - peer reviewed
2015

Human metabolic atlas: an online resource for human metabolism

Natapol Pornputtapong, Intawat Nookaew, Jens B. Nielsen et al
Database-the Journal of Biological Databases and Curation. Vol. 2015
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

Glucose repression in Saccharomyces cerevisiae

Ömur Kayikci, Jens B. Nielsen,
Fems Yeast Research. Vol. 15 (6)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

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

Boyang Ji, Jens B. Nielsen,
Frontiers in Genetics. Vol. 6 (JUN)
Scientific journal article - peer reviewed
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
Conference paper - peer reviewed
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)
Scientific journal article - peer reviewed
2015

Advancing metabolic engineering through systems biology of industrial microorganisms

Zongjie Dai, Jens B. Nielsen,
Current Opinion in Biotechnology. Vol. 36, p. 8-15
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

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

Cheng Zhang, Boyang Ji, Adil Mardinoglu et al
Bioinformatics. Vol. 31 (14), p. 2324-2331
Scientific journal article - peer reviewed
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
Scientific journal article - non peer reviewed
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
Scientific journal article - peer reviewed
2015

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

Mingtao Huang, Y. P. 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
Scientific journal article - peer reviewed
2015

Minimum Information about a Biosynthetic Gene cluster

M. H. Medema, R. Kottmann, P. Yilmaz et al
Nature Chemical Biology. Vol. 11 (9), p. 625-631
Scientific journal article - peer reviewed
2015

Tissue-based map of the human proteome

M. Uhlén, L. Fagerberg, B.M. Hallström et al
Science. Vol. 347 (6220), p. 394-
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

Networking in metabolism and human disease

Leif Väremo, Jens B. Nielsen,
OncoTarget. Vol. 6 (18), p. 15708-15709
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2015

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

Benjamin Sánchez, Jens B. Nielsen,
Integrative Biology. Vol. 7 (8), p. 846-858
Scientific journal article - peer reviewed
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 H. Karlsson, Malin Werling et al
Cell Metabolism. Vol. 22 (2), p. 228-238
Scientific journal article - peer reviewed
2015

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

Yiming Zhang, Zongjie Dai, Anastasia Krivoruchko et al
Fems Yeast Research. Vol. 15 (4)
Scientific journal article - peer reviewed
2015

Finding directionality and gene-disease predictions in disease associations

Manuel Garcia-Albornoz, Jens B. Nielsen,
BMC Systems Biology. Vol. 9 (1)
Scientific journal article - peer reviewed
2015

Applications of computational modeling in metabolic engineering of yeast

Eduard Kerkhoven, Petri-Jaan Lahtvee, Jens B. Nielsen et al
Fems Yeast Research. Vol. 15 (1)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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, p. Art. no. 84
Scientific journal article - peer reviewed
2015

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

R. Nicastro, F. Tripodi, C. Guzzi et al
Biochimica Et Biophysica Acta-Molecular Cell Research. Vol. 1853 (7), p. 1615-1625
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

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

Tobias Österlund, Sergio Bordel Velasco, Jens B. Nielsen et al
Integrative Biology. Vol. 7 (5), p. 560-568
Scientific journal article - peer reviewed
2015

Metabolic engineering strategies for microbial synthesis of oleochemicals

B. F. Pfleger, Michael Gossing, Jens B. Nielsen et al
Metabolic Engineering. Vol. 29, p. 1-11
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

FEMS yeast research: the yeast community journal

Jens B. Nielsen,
Fems Yeast Research. Vol. 15 (2), p. Art. no. fou007
Scientific journal article - non peer reviewed
2015

Microbial acetyl-CoA metabolism and metabolic engineering

Anastasia Krivoruchko, Yiming Zhang, Verena Siewers et al
Metabolic Engineering. Vol. 28, p. 28-42
Scientific journal article - peer reviewed
2015

How to set up collaborations between academia and industrial biotech companies

J. T. Pronk, S. Y. Lee, J. Lievense et al
Nature Biotechnology. Vol. 33 (3), p. 237-240
Scientific journal article - non peer reviewed
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 & Biotechnology. Vol. 42 (3), p. 477-486
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2015

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

José Luis Martinez Ruiz, Lifang Liu, Dina Petranovic et al
Biotechnology and Bioengineering. Vol. 112 (1), p. 181-188
Scientific journal article - peer reviewed
2014

Systems biology: Developments and applications

Rahul Kumar, Petri-Jaan Lahtvee, Jens B. Nielsen et al
Molecular Mechanisms in Yeast Carbon Metabolism
Chapter in monograph, book
2014

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

Guodong Liu, Antonio Marras, Jens B. Nielsen et al
Quantitative Biology. Vol. 2 (1), p. 30-46
Scientific journal article - peer reviewed
2014

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

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

Altered sterol composition renders yeast thermotolerant

Luis Caspeta, Yun Chen, Payam Ghiaci et al
Science. Vol. 346 (6205), p. 75-78
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2014

Development of a yeast cell factory for production of aromatic products

A. R. Prado, K. Kildegaard, M. J. Li et al
New Biotechnology. Vol. 31, p. S130-S130
Scientific journal article - non peer reviewed
2014

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

Adil Mardinoglu, M. Uhlen, Jens B. Nielsen et al
New Biotechnology. Vol. 31, p. S49-S49
Scientific journal article - non peer reviewed
2014

Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast

Jens B. Nielsen,
Mbio. Vol. 5 (6), p. Art. no. e02153-14
Scientific journal article - non peer reviewed
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
Scientific journal article - peer reviewed
2014

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

Clara Navarrete, Jens B. Nielsen, Verena Siewers et al
AMB Express. Vol. 4
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

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

Leif Väremo, Francesco Gatto, Jens B. Nielsen et al
BMC Bioinformatics. Vol. 15
Scientific journal article - peer reviewed
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
Scientific journal article - 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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

Bridging the gaps in systems biology

Marija Cvijovic, Joachim Almquist, Jonas Hagmar et al
Molecular Genetics and Genomics. Vol. 289 (5), p. 727-734
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

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

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

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

Fredrik H. Karlsson, Intawat Nookaew, Jens B. Nielsen et al
Plos Computational Biology. Vol. 10 (7)
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2014

Kinetic models in industrial biotechnology - Improving cell factory performance

Joachim Almquist, Marija Cvijovic, V. Hatzimanikatis et al
Metabolic Engineering. Vol. 24, p. 38-60
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

Maintaining a strong yeast research community

Jens B. Nielsen,
Fems Yeast Research. Vol. 14 (4), p. 527-528
Scientific journal article - non peer reviewed
2014

Gcn4p and the Crabtree effect of yeast: drawing the causal model of the Crabtree effect in Saccharomyces cerevisiae and explaining evolutionary trade-offs of adaptation to galactose through systems biology

José Luis Martinez Ruiz, Sergio Bordel Velasco, Kuk-Ki Hong et al
Fems Yeast Research. Vol. 14 (4), p. 654-662
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

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

Ibrahim El-Semman, Fredrik H. Karlsson, Saeed Shoaie et al
Bmc Systems Biology. Vol. 8 (41)
Scientific journal article - peer reviewed
2014

Engineering synergy in biotechnology

Jens B. Nielsen, M. Fussenegger, J. Keasling et al
Nature Chemical Biology. Vol. 10 (5), p. 319-322
Scientific journal article - non peer reviewed
2014

Improved production of fatty acid ethyl esters in Saccharomyces cerevisiae through up-regulation of the ethanol degradation pathway and expression of the heterologous phosphoketolase pathway

Bouke Wim de Jong, S. Shi, Verena Siewers et al
Microbial Cell Factories. Vol. 13
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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 et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 111 (9), p. E866-E875
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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 & Cellular Proteomics. Vol. 13 (2), p. 397-406
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2014

Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid ethyl esters, an advanced biofuel, by eliminating non-essential fatty acid utilization pathways

Juan Octavio Valle Rodriguez, Shuobo Shi, Verena Siewers et al
Applied Energy. Vol. 115, p. 226-232
Scientific journal article - peer reviewed
2014

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

S. L. Sjostrom, Y. P. Bai, Mingtao Huang et al
Lab on a Chip. Vol. 14 (4), p. 806-813
Scientific journal article - peer reviewed
2014

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

Pramote Chumnanpuen, M.A. Edberg Hansen, J. Smedsgaard et al
International Journal of Genomics. Vol. 2014, p. Art. no. 894296
Scientific journal article - peer reviewed
2014

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

Lifang Liu, José Luis Martinez Ruiz, Zihe Liu et al
Metabolic Engineering. Vol. 21, p. 9-16
Scientific journal article - peer reviewed
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
Conference paper - peer reviewed
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
2013

Bridging omics technologies with synthetic biology in yeast industrial biotechnology

António Roldão, Il-Kwon Kim, Jens B. Nielsen et al
Systems Metabolic Engineering, p. 271-327
Chapter in monograph, book
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
Conference paper - peer reviewed
2013

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

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

Application of genome-scale metabolic models in metabolic engineering

M.A. Garcia-Albornoz, Jens B. Nielsen,
Industrial Biotechnology. Vol. 9 (4), p. 203-214
Scientific journal article - peer reviewed
2013

Production of biopharmaceutical proteins by yeast Advances through metabolic engineering

Jens B. Nielsen,
BIOENGINEERED. Vol. 4 (4), p. 207-211
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

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

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

A maternal diet of fatty fish reduces body fat of offspring compared with a maternal diet of beef and a post-weaning diet of fish improves insulin sensitivity and lipid profile in adult C57BL/6 male mice.

A. Hussain, Intawat Nookaew, Sakda Khoomrung et al
Acta Physiologica. Vol. 209 (3), p. 220-234
Scientific journal article - peer reviewed
2013

Assessing the human gut microbiota in metabolic diseases.

Fredrik H. Karlsson, Valentina Tremaroli, Jens B. Nielsen et al
Diabetes. Vol. 62 (10), p. 3341-9
Scientific journal article - peer reviewed
2013

Economic and environmental impacts of microbial biodiesel

Luis Caspeta, Jens B. Nielsen,
Nature Biotechnology. Vol. 31 (9), p. 789-793
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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 et al
BMC Systems Biology. Vol. 7 (Suppl 3) (S7)
Scientific journal article - peer reviewed
2013

Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae

Zihe Liu, Jin Hou, José Luis Martinez Ruiz et al
Applied Microbiology and Biotechnology. Vol. 97 (20), p. 8955-8962
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

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

Saeed Shoaie, Fredrik H. Karlsson, Adil Mardinoglu et al
Scientific Reports. Vol. 3
Scientific journal article - peer reviewed
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 & Biotechnology. Vol. 40 (9), p. 1051-1056
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

Advanced biofuel production by the yeast Saccharomyces cerevisiae

Nicolaas Buijs, Verena Siewers, Jens B. Nielsen et al
Current Opinion in Chemical Biology. Vol. 17 (3), p. 480-488
Scientific journal article - peer reviewed
2013

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

Rasmus Ågren, José Manuel Otero Romero, Jens B. Nielsen et al
Journal of Industrial Microbiology & Biotechnology. Vol. 40 (7), p. 735-747
Scientific journal article - peer reviewed
2013

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

Kanokarn Kocharin, Verena Siewers, Jens B. Nielsen et al
Biotechnology and Bioengineering. Vol. 110 (8), p. 2216-2224
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

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

Fredrik H. Karlsson, Valentina Tremaroli, Intawat Nookaew et al
Nature. Vol. 498 (7452), p. 99-103
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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-+
Scientific journal article - peer reviewed
2013

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

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

Genome-Scale Modeling of the Protein Secretory Machinery in Yeast

Amir Feizi, Tobias Österlund, Dina Petranovic et al
PLoS ONE. Vol. 8 (5)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

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

Tobias Österlund, Intawat Nookaew, Sergio Bordel Velasco et al
BMC Systems Biology. Vol. 7
Scientific journal article - peer reviewed
2013

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

S. Borgos, Sergio Bordel Velasco, H. Sletta et al
BMC Systems Biology. Vol. 7
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

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

Adil Mardinoglu, Francesco Gatto, Jens B. Nielsen et al
Biotechnology Journal. Vol. 8
Scientific journal article - peer reviewed
2013

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

Leif Väremo, Intawat Nookaew, Jens B. Nielsen et al
Frontiers in Physiology. Vol. 4 (92)
Scientific journal article - 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 et al
Nucleic Acids Research. Vol. 41 (8), p. 4378-4391
Scientific journal article - peer reviewed
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, p. 649
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2013

The role of biofuels in the future energy supply

Luis Caspeta, Nicolaas Buijs, Jens B. Nielsen et al
Energy & Environmental Science. Vol. 6 (4), p. 1077-1082
Scientific journal article - peer reviewed
2013

Specific growth rate and substrate dependent polyhydroxybutyrate production in Saccharomyces cerevisiae

Kanokarn Kocharin, Jens B. Nielsen,
AMB Express. Vol. 3 (18)
Scientific journal article - peer reviewed
2013

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

José Manuel Otero Romero, D. Cimini, K. R. Patil et al
PLoS ONE. Vol. 8 (1)
Scientific journal article - peer reviewed
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, p. 48-54
Scientific journal article - peer reviewed
2013

FANTOM: Functional and taxonomic analysis of metagenomes

Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew et al
BMC Bioinformatics. Vol. 14, p. artikel nr 38
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

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

José Luis Martinez Ruiz, Lifang Liu, Dina Petranovic et al
Current Opinion in Biotechnology. Vol. 23 (6), p. 965-971
Scientific journal article - peer reviewed
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 et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 109 (47), p. 19504-19509
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

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

Marta Papini, Intawat Nookaew, M. Uhlén et al
Microbial Cell Factories. Vol. 11, p. Article Number: 136
Scientific journal article - peer reviewed
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, p. artikel nr 554
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

Symptomatic atherosclerosis is associated with an altered gut metagenome

Fredrik H. Karlsson, Frida Fåk, Intawat Nookaew et al
Nature Communications. Vol. 3
Scientific journal article - peer reviewed
2012

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

Tobias Österlund, Intawat Nookaew, Jens B. Nielsen et al
Biotechnology Advances. Vol. 30 (5), p. 979-988
Scientific journal article - peer reviewed
2012

Systems biology: the 'new biotechnology' Editorial overview

Jens B. Nielsen, S. Y. Lee,
Current Opinion in Biotechnology. Vol. 23 (4), p. 583-584
Scientific journal article - non peer reviewed
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 et al
Current Opinion in Biotechnology. Vol. 23 (4), p. 624-630
Scientific journal article - peer reviewed
2012

Aspergilli: Systems biology and industrial applications

Christoph Knuf, Jens B. Nielsen,
Biotechnology Journal. Vol. 7 (9)
Scientific journal article - peer reviewed
2012

Applied systems biology - vanillin production in Saccharomyces cerevisiae

T. Strucko, J. C. Eriksen, Jens B. Nielsen et al
Febs Journal: 22nd IUBMB Congress/37th FEBS Congress. Vol. 279 (Special Issue: SI Supplement: 1 ), p. 525-525
Conference paper - non peer reviewed
2012

Mapping the polysaccharide degradation potential of Aspergillus niger

M.R. Andersen, M. Giese, R.P. de Vries et al
BMC Genomics. Vol. 13
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

Gionata Scalcinati, José Manuel Otero Romero, J. R. H. Van Vleet et al
Fems Yeast Research. Vol. 12 (5), p. 582-597
Scientific journal article - peer reviewed
2012

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

Yun Chen, Verena Siewers, Jens B. Nielsen et al
PLoS ONE. Vol. 7 (8), p. e42475
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

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

Rasmus Ågren, Sergio Bordel Velasco, Adil Mardinoglu et al
PLoS Computational Biology
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

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

Luis Caspeta, Saeed Shoaie, Rasmus Ågren et al
BMC Systems Biology. Vol. 6 (24)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae

Zihe Liu, Keith Tyo, José Luis Martinez Ruiz et al
Biotechnology and Bioengineering. Vol. 109 (5), p. 1259-1268
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

Metabolic engineering, synthetic biology and systems biology

Jens B. Nielsen, J. T. Pronk,
Fems Yeast Research. Vol. 12 (2), p. 103-103
Scientific journal article - non peer reviewed
2012

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

Il-Kwon Kim, António Roldão, Verena Siewers et al
Fems Yeast Research. Vol. 12 (2), p. 228-248
Scientific journal article - peer reviewed
2012

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

Keith Tyo, Zihe Liu, Dina Petranovic et al
BMC Biology. Vol. 10 (16), p. Art. no 16
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2012

Translational and systems medicine Introduction

Jens B. Nielsen,
Journal of Internal Medicine. Vol. 271 (2), p. 108-110
Scientific journal article - non peer reviewed
2012

Systems medicine and metabolic modelling

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

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, Valentina Tremaroli, Ying Shiuan Lee et al
Gut. Vol. 61, p. 1124-1131
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2011

Genome-scale metabolic models of Saccharomyces cerevisiae

Intawat Nookaew, Roberto Olivares Hernandez, S. Bhumiratana et al
Methods in Molecular Biology, vol. 759, p. 445-463
Chapter in monograph, book
2011

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

M. R. Andersen, M. P. Salazar, P. J. Schaap et al
Genome Research. Vol. 21 (6), p. 885-897
Scientific journal article - peer reviewed
2011

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

Madelene Lindqvist, Intawat Nookaew, Ingrid Brinkenberg et al
PLoS ONE. Vol. 6 (6), p. e20448
Scientific journal article - peer reviewed
2011

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

Pramote Chumnanpuen, Christian Brackmann, Subir Kumar Nandy et al
Biotechnology Journal, p. n/a-n/a
Scientific journal article - peer reviewed
2011

Synergies between synthetic biology and metabolic engineering

Jens B. Nielsen, J.D. Keasling,
Nature Biotechnology. Vol. 29 (8), p. 693-695
Scientific journal article - non peer reviewed
2011

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

Jie Zhang, S. Vaga, Pramote Chumnanpuen et al
Molecular Systems Biology. Vol. 7
Scientific journal article - peer reviewed
2011

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

J. S. Rokem, Wanwipa Vongsangnak, Jens B. Nielsen et al
Biotechnology and Bioengineering. Vol. 108 (11), p. 2770-2775
Scientific journal article - peer reviewed
2011

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

Marija Cvijovic, Sergio Bordel Velasco, Jens B. Nielsen et al
Microbial Biotechnology. Vol. 4 (5), p. 572-584
Scientific journal article - peer reviewed
2011

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

Kuk-Ki Hong, Wanwipa Vongsangnak, Goutham N. Vemuri et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 108 (29), p. 12179-12184
Scientific journal article - peer reviewed
2011

MEMOSys: Bioinformatics platform for genome-scale metabolic models

S. Pabinger, R. Rader, Rasmus Ågren et al
BMC Systems Biology. Vol. 5
Scientific journal article - peer reviewed
2011

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

Roberto Olivares Hernandez, Sergio Bordel Velasco, Jens B. Nielsen et al
BMC Systems Biology. Vol. 5
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2011

Prospects for systems biology and modeling of the gut microbiome

Fredrik H. Karlsson, Intawat Nookaew, Dina Petranovic et al
Trends in Biotechnology. Vol. 29 (6), p. 251-258
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2011

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

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

Transcriptional control of metabolic fluxes

Jens B. Nielsen,
Molecular Systems Biology. Vol. 7
Scientific journal article - peer reviewed
2011

Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress

R. Ruenwai, A. Neiss, K. Laoteng et al
Biotechnology Journal. Vol. 6 (3), p. 343-356
Scientific journal article - peer reviewed
2011

Prospects for microbial biodiesel production

Shuobo Shi, J. O. Valle-Rodriguez, Verena Siewers et al
Biotechnology Journal. Vol. 6 (3), p. 277-285
Scientific journal article - peer reviewed
2011

Opportunities for yeast metabolic engineering: Lessons from synthetic biology

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

Industrial systems biology

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

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

Wanwipa Vongsangnak, K. Hansen, Jens B. Nielsen et al
Biotechnology and Bioengineering. Vol. 108 (5), p. 1130-1139
Scientific journal article - peer reviewed
2011

BIOFUELS Chimeric synthetic pathways

Jens B. Nielsen,
Nature Chemical Biology. Vol. 7 (4), p. 195-196
Scientific journal article - peer reviewed
2011

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

Karina M. Madsen, D.B.R.K. Gupta Udatha, Saori Semba et al
PLoS ONE. Vol. 6 (3), p. e14763
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

Industrial Systems Biology

José Manuel Otero Romero, Jens B. Nielsen,
Industrial Biotechnology: Sustainable Growth and Economic Success
Chapter in monograph, book
2010

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

Intawat Nookaew, Britt G. Gabrielsson, Agneta Holmäng et al
PLoS ONE. Vol. 5 (8), p. e12361
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

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

José Manuel Otero Romero, Wanwipa Vongsangnak, Mohammad Asadollahi et al
BMC Genomics. Vol. 11, p. 723
Scientific journal article - peer reviewed
2010

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

Dina Petranovic, Keith Tyo, Goutham N. Vemuri et al
Fems Yeast Research. Vol. 10 (8), p. 1046-1059
Scientific journal article - peer reviewed
2010

Industrial Systems Biology

José Manuel Otero Romero, Jens B. Nielsen,
Biotechnology and Bioengineering. Vol. 105 (3), p. 439-460
Scientific journal article - peer reviewed
2010

BioMet Toolbox: genome-wide analysis of metabolism

Marija Cvijovic, Roberto Olivares Hernandez, Rasmus Ågren et al
Nucleic Acids Research. Vol. 38, p. W144-W149
Scientific journal article - peer reviewed
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 et al
Biotechnology and Bioengineering. Vol. 107 (5), p. 865-875
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

Systems Biology of Industrial Microorganisms

Marta Papini, Margarita Salazar, Jens B. Nielsen et al
Biosystems Engineering I: Creating Superior Biocatalysts; Book Series: Advances in Biochemical Engineering-Biotechnology. Vol. 120, p. 51-99
Scientific journal article - peer reviewed
2010

Transcriptional progression of atrophic gastritis development in humans

S. Lundin, Intawat Nookaew, K. Worah et al
HELICOBACTER; 23rd International Workshop on Helicobacter and Related Bacteria in Chronic Digestive Inflammation and Gastric Cancer. Vol. 15 (4), p. 323-324
Scientific journal article - peer reviewed
2010

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

J.M Otero, M.A. Papadakis, D.B.R.K. Gupta Udatha et al
PLoS ONE. Vol. 5 (10), p. e13606
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

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

Sergio Bordel Velasco, Rasmus Ågren, Jens B. Nielsen et al
PLoS Computational Biology. Vol. 6 (7)
Scientific journal article - peer reviewed
2010

Systems biology of microorganisms

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

Systems biology of energy homeostasis in yeast

Jie Zhang, Goutham N. Vemuri, Jens B. Nielsen et al
Curr. Op. Microbiol.. Vol. 13 (3), p. 382-388
Scientific journal article - peer reviewed
2010

Toward Design-based Engineering of Industrial Microbes

Keith Tyo, Kanokarn Kocharin, Jens B. Nielsen et al
Curr. Op. Microbiol.. Vol. 13 (3), p. 255-262
Scientific journal article - peer reviewed
2010

Systems Biology of lipid metabolism: From yeast to human

J.M Otero, Jens B. Nielsen,
FEBS Letters. Vol. 583 (24), p. 3905-3913
Scientific journal article - peer reviewed
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 et al
Molecular micobiology. Vol. 77 (2), p. 371-383
Scientific journal article - peer reviewed
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 et al
BMC Systems Biology. Vol. 4, p. 68
Scientific journal article - peer reviewed
2010

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

Verena Siewers, Rita San-Bento, Jens B. Nielsen et al
Biotechnology and Bioengineering. Vol. 106 (5), p. 841-844
Scientific journal article - peer reviewed
2010

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

S. Bordel, Jens B. Nielsen,
Met. Eng.. Vol. 12 (4), p. 369-377
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

Use of genome-scale metabolic models for understanding microbial physiology

Liming Liu, Rasmus Ågren, Sergio Bordel Velasco et al
Febs Letters. Vol. 584 (12), p. 2556-2564
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2010

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

Wanwipa Vongsangnak, Intawat Nookaew, Margarita Salazar et al
Omics-a Journal of Integrative Biology. Vol. 14 (2), p. 165-175
Scientific journal article - peer reviewed
2009

Random sampling of metabolic networks

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

Qualification of flux control in metabolic pathways

Jens B. Nielsen,
Biotechnology and Bioengineering. Vol. 104, p. 1-2
Scientific journal article - peer reviewed
2009

Vintage paper - Introduction

Jens B. Nielsen,
Biotechnology and Bioengineering. Vol. 103 (1), p. 1
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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. Vol. 106 (16), p. 6477-6482
Scientific journal article - 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
Scientific journal article - peer reviewed
2009

Physiological characterisation of acuB deletion in Aspergillus niger

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

Nutritional Systems Biology: Definitions and Approaches

G. Panagiotou, Jens B. Nielsen,
Annual Review of Nutrition. Vol. 29, p. 329-339
Scientific journal article - peer reviewed
2009

Systems biology of lipid metabolism: From yeast to human

Jens B. Nielsen,
Febs Letters. Vol. 583 (24), p. 3905-3913
Scientific journal article - peer reviewed
2009

Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger

G. Hofmann, A. Diano, Jens B. Nielsen et al
Metabolic Engineering. Vol. 11 (1), p. 8-12
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2009

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

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

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

T. S. Christensen, A. P. Oliveira, Jens B. Nielsen et al
BMC Systems Biology. Vol. 3, p. 7 (artno)
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2009

Systemic analysis of the response of Aspergillus niger to ambient pH

M. R. Andersen, L. Lehmann, Jens B. Nielsen et al
Genome Biology. Vol. 10 (5)
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2009

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

Susan Meijer, Michael Lynge Nielsen, Lisbeth Olsson et al
Journal of Industrial Microbiology & Biotechnology. Vol. 36, p. 1275-1280
Scientific journal article - peer reviewed
2009

Genome-wide analysis of maltose utilization and regulation in aspergilli

Wanwipa Vongsangnak, Margarita Salazar, Kim Hansen et al
Microbiology. Vol. 155 (12), p. 3893-3902
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2008

Metabolomics. Topics in Current Genetics

Jens B. Nielsen,
Springer Verlag, Heidelberg. Vol. 18
Scientific journal article - peer reviewed
2008

Systems biology: Is the hope worth the hype

G. Vemuri, Jens B. Nielsen,
SIM News. Vol. 58, p. 178-188
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2008

Analysis of Aspergillus nidulans metabolism at the genome-scale

H David, I. Ozcelik, G. Hofmann et al
BMC Genomics. Vol. 9, p. 163
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2008

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

Jens B. Nielsen, MR Andersen, ML Nielsen et al
Mol Syst Biol.. Vol. 4, p. 178
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2008

The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry

Jesper Hojer-Pedersen, Jorn Smedsgaard, Jens B. Nielsen et al
Metabolomics. Vol. 4 (4), p. 393-405
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2008

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

Wanwipa Vongsangnak, Peter Olsen, Kim Hansen et al
BMC Genomics. Vol. 9 (245)
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed
2008

The yeast metabolome addressed by electrospray ionization mass spectrometry: Initiation of a mass spectral library and its applications for metabolic footprinting by direct infusion mass spectrometry

Jesper Højer-Pedersen, Jørn Smedsgaard, Jens B. Nielsen et al
Metabolomics (4), p. 393-405
Scientific journal article - peer reviewed
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 et al
BMC Systems Biology. Vol. 2 (17)
Scientific journal article - peer reviewed
2008

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

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

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

Valeria Mapelli, Lisbeth Olsson, Jens B. Nielsen et al
Trends in Biotechnology. Vol. 26 (9), p. 490-497
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
2008

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

Renata Usaite, Jens B. Nielsen, Lisbeth Olsson et al
Journal of Biotechnology (133), p. 73-81
Scientific journal article - peer reviewed
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
Scientific journal article - peer reviewed
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)
Scientific journal article - peer reviewed