Jens B Nielsen

Full Professor at Systems and Synthetic Biology

Jens Nielsen has an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Technical University of Denmark (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 build a research group of more than 60 people. In 2019 he too the position as CEO of the BioInnovation Institute in Denmark. Jens Nielsen has published so far more than 700 papers that have been cited more than 68,000 times (current H-factor 119), and co-authored more than 40 books. He is inventor of more than 50 patents 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, National Academy of Science in USA, Chinese Academy of Engineering, 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.

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Showing 703 publications

2024

Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport

Johan Gustafsson, Jonathan Robinson, Henrik Zetterberg et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 121 (7)
Journal article
2024

Increased CO<inf>2</inf> fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast

Ning Qin, Lingyun Li, Xiaozhen Wan et al
Nature Communications. Vol. 15 (1)
Journal article
2024

Discriminating Benign from Malignant Lung Diseases Using Plasma Glycosaminoglycans and Cell-Free DNA

Alvida Qvick, Sinisa Bratulic, Jessica Carlsson et al
International Journal of Molecular Sciences. Vol. 25 (18)
Journal article
2024

The transition from 2G to 3G-feedstocks enabled efficient production of fuels and chemicals

Kai Wang, Changsheng Su, Haoran Bi et al
Green Energy and Environment. Vol. 9 (11), p. 1759-1770
Journal article
2024

Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms

Jiwei Mao, Hongyu Zhang, Yu Chen et al
Biotechnology Advances. Vol. 74
Review article
2024

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Chengyu Zhang, Benjamín José Sánchez, Feiran Li et al
Molecular Systems Biology. Vol. 20 (10), p. 1134-1150
Journal article
2024

De novo production of protoberberine and benzophenanthridine alkaloids through metabolic engineering of yeast

Xiang Jiao, Xiaozhi Fu, Qishuang Li et al
Nature Communications. Vol. 15, p. 8759-
Journal article
2024

Single-cell omics analysis with genome-scale metabolic modeling

Yu Chen, Johan Gustafsson, Jingyu Yang et al
Current Opinion in Biotechnology. Vol. 86
Review article
2024

Metabolic collaboration between cells in the tumor microenvironment has a negligible effect on tumor growth

Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål et al
Innovation. Vol. 5 (2)
Journal article
2024

TRYing to evaluate production costs in microbial biotechnology

Oliver Konzock, Jens B Nielsen
Trends in Biotechnology. Vol. 42 (11), p. 1339-1347
Review article
2024

Metabolic engineering of Saccharomyces cerevisiae for enhanced taxadiene production

Hülya Karaca Gencer, Murat Kaya, Handan Açelya Kapkac et al
Microbial Cell Factories. Vol. 23 (1)
Journal article
2024

Cell factory design with advanced metabolic modelling empowered by artificial intelligence

Hongzhong Lu, Luchi Xiao, Wenbin Liao et al
Metabolic Engineering. Vol. 85, p. 61-72
Journal article
2024

Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Yu Chen, Johan Gustafsson, Albert Tafur Rangel et al
Nature Protocols. Vol. 19 (3), p. 629-667
Journal article
2024

Autotrophic yeast

Jens B Nielsen
Nature Communications. Vol. 15 (1)
Other text in scientific journal
2024

Transcriptomic meta-analysis to identify potential antifungal targets in Candida albicans

Zeinab Abdelmoghis Hefny, Boyang Ji, Ibrahim El-Semman et al
BMC Microbiology. Vol. 24 (1)
Journal article
2024

Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease

Lingqi Meng, Han Jin, Burak Yulug et al
Alzheimers Research and Therapy. Vol. 16 (1), p. 213-
Journal article
2024

A long-term growth stable Halomonas sp. deleted with multiple transposases guided by its metabolic network model Halo-ecGEM

Lizhan Zhang, Jian Wen Ye, Gang Li et al
Metabolic Engineering. Vol. 84, p. 95-108
Journal article
2024

Urinary Free Glycosaminoglycans Identify Adults at High Risk of Developing Early-stage High-grade Bladder Cancer

Francesco Gatto, Sinisa Bratulic, F. Maccari et al
European Urology Open Science. Vol. 68, p. 40-47
Journal article
2024

Extending the G1 phase improves the production of lipophilic compounds in yeast by boosting enzyme expression and increasing cell size

He Hao, Mingdong Yao, Ying Wang et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 121 (47)
Journal article
2023

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 120 (6)
Journal article
2023

Protein engineering of invertase for enhancing yeast dough fermentation under high-sucrose conditions

Yijin Zhao, Kaiwen Meng, Jinyu Fu et al
Folia Microbiologica. Vol. 68 (2), p. 207-217
Journal article
2023

Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study

Francesco Gatto, Sinisa Bratulic, Eric Jonasch et al
JCO PRECISION ONCOLOGY. Vol. 7
Journal article
2023

Fine-tuning of p-coumaric acid synthesis to increase (2S)-naringenin production in yeast

Jiwei Mao, Marta Tous Mohedano, Jing Fu et al
Metabolic Engineering. Vol. 79, p. 192-202
Journal article
2023

Engineering yeast mitochondrial metabolism for 3-hydroxypropionate production

Yiming Zhang, Mo Su, Yu Chen et al
Biotechnology for Biofuels and Bioproducts. Vol. 16 (1)
Journal article
2023

Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica

Zhiyong Cui, Yutao Zhong, Zhijie Sun et al
Nature Communications. Vol. 14 (1)
Journal article
2023

Metabolic engineering of human gut microbiome: Recent developments and future perspectives

Peishun Li, Stefan Roos, Hao Luo et al
Metabolic Engineering. Vol. 79, p. 1-13
Review article
2023

Flux regulation through glycolysis and respiration is balanced by inositol pyrophosphates in yeast

Ning Qin, Lingyun Li, Xu Ji et al
Cell. Vol. 186 (4), p. 748-763.e15
Journal article
2023

Harnessing synthetic biology for mushroom farming

Gen Zou, Jens B Nielsen, Yongjun Wei
Trends in Biotechnology. Vol. 41 (4), p. 480-483
Other text in scientific journal
2023

Modeling the metabolic dynamics at the genome-scale by optimized yield analysis

Hao Luo, Peishun Li, Boyang Ji et al
Metabolic Engineering. Vol. 75, p. 119-130
Journal article
2023

Engineering yeast to produce plant-derived anti-obesity agent

Jens B Nielsen
Nature Chemistry. Vol. 15 (9), p. 1204-1205
Journal article
2023

Reprogramming methanol utilization pathways to convert Saccharomyces cerevisiae to a synthetic methylotroph

Chunjun Zhan, Xiaowei Li, Guangxu Lan et al
Nature Catalysis. Vol. 6 (5), p. 435-450
Journal article
2023

Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators

Hong Yang, Xiangyu Li, Han Jin et al
Free Radical Biology and Medicine. Vol. 204, p. 347-358
Journal article
2023

The acute effect of different NAD<sup>+</sup> precursors included in the combined metabolic activators

Xiangyu Li, Hong Yang, Han Jin et al
Free Radical Biology and Medicine. Vol. 205, p. 77-89
Journal article
2023

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide

Petros Andrikopoulos, Judith Aron-Wisnewsky, Rima Chakaroun et al
Nature Communications. Vol. 14 (1)
Journal article
2023

Engineering yeast for high-level production of diterpenoid sclareol

Xuan Cao, Wei Yu, Yu Chen et al
Metabolic Engineering. Vol. 75, p. 19-28
Journal article
2023

Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery

Dimitra Lappa, A. S. Meijnikman, Kimberly A. Krautkramer et al
PLoS ONE. Vol. 18 (3), p. e0279335-
Journal article
2023

Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

Burak Yulug, Ozlem Altay, Xiangyu Li et al
Translational Neurodegeneration. Vol. 12 (1)
Journal article
2023

GotEnzymes: an extensive database of enzyme parameter predictions

Feiran Li, Yu Chen, Petre Mihail Anton et al
Nucleic Acids Research. Vol. 51 (D1), p. D583-D586
Journal article
2023

Directed evolution of a wax ester synthase for production of fatty acid ethyl esters in Saccharomyces cerevisiae

Juan Octavio Valle Rodriguez, Verena Siewers, Jens B Nielsen et al
Applied Microbiology and Biotechnology. Vol. 107 (9), p. 2921-2932
Journal article
2023

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer

Le Yuan, Hongzhong Lu, Feiran Li et al
Briefings in Bioinformatics. Vol. 24 (2)
Journal article
2023

A highly efficient transcriptome-based biosynthesis of non-ethanol chemicals in Crabtree negative Saccharomyces cerevisiae

Zhen Yao, Yufeng Guo, Huan Wang et al
Biotechnology for Biofuels and Bioproducts. Vol. 16 (1)
Journal article
2023

Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation

Min Chen, Tingting Xie, Huan Li et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 120 (25)
Journal article
2023

Leveraging high-resolution omics data for predicting responses and adverse events to immune checkpoint inhibitors

Angelo Limeta, Francesco Gatto, M. J. Herrgard et al
Computational and Structural Biotechnology Journal. Vol. 21, p. 3912-3919
Review article
2023

A one-carbon chemicals conversion strategy to produce precursor of biofuels with Saccharomyces cerevisiae

Kai Wang, Yangyang Da, Haoran Bi et al
Renewable Energy. Vol. 208, p. 331-340
Journal article
2022

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Ibrahim El-Semman, Angelica Rodriguez Prado, Pranas Grigaitis et al
Nature Communications. Vol. 13 (1)
Journal article
2022

Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells

Rasool Saghaleyni, Magdalena Malm, Noah Moruzzi et al
Cell Reports. Vol. 39 (11)
Journal article
2022

Dual β-oxidation pathway and transcription factor engineering for methyl ketones production in Saccharomyces cerevisiae

Ge Zhang, Chao Zhang, Zheng Wang et al
Metabolic Engineering. Vol. 73, p. 225-234
Journal article
2022

Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction

Feiran Li, Le Yuan, Hongzhong Lu et al
Nature Catalysis. Vol. 5 (8), p. 662-672
Journal article
2022

Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation

Jianye Xia, Benjamín José Sánchez, Yu Chen et al
Nature Communications. Vol. 13 (1)
Journal article
2022

Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae

Olena Ishchuk, Iván Domenzain Del Castillo Cerecer, Benjamín José Sánchez et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 119 (30)
Journal article
2022

Analysis of normal levels of free glycosaminoglycans in urine and plasma in adults

Sinisa Bratulic, Angelo Limeta, F. Maccari et al
Journal of Biological Chemistry. Vol. 298 (2)
Journal article
2022

Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures

Fariba Roshanzamir, Jonathan Robinson, Daniel John Cook et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 119 (35)
Journal article
2022

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

Johan Gustafsson, Jonathan Robinson, Fariba Roshanzamir et al
Preprint
2022

Multi-omics analyses of the transition to the Crabtree effect in S. cerevisiae reveals a key role for the citric acid shuttle

Tingting Xie, Min Chen, Jens B Nielsen et al
FEMS Yeast Research. Vol. 22 (1)
Journal article
2022

Microbiome and metabolome features of the cardiometabolic disease spectrum

Sebastien Fromentin, Sofia K. Forslund, Kanta Chechi et al
Nature Medicine. Vol. 28 (2), p. 303-314
Journal article
2022

Multiscale models quantifying yeast physiology: towards a whole-cell model

Hongzhong Lu, Eduard Kerkhoven, Jens B Nielsen
Trends in Biotechnology. Vol. 40 (3), p. 291-305
Review article
2022

Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis

Mujdat Zeybel, Muhammad Arif, Xiangyu Li et al
Advanced Science. Vol. 9 (11)
Journal article
2022

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Iván Domenzain Del Castillo Cerecer, Benjamín José Sánchez, Petre Mihail Anton et al
Nature Communications. Vol. 13 (1)
Journal article
2022

Noninvasive detection of any-stage cancer using free glycosaminoglycans

Sinisa Bratulic, Angelo Limeta, Saeed Dabestani et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 119 (50)
Journal article
2022

Microbiome-derived ethanol in nonalcoholic fatty liver disease

A. S. Meijnikman, Mark Davids, H. Herrema et al
Nature Medicine. Vol. 28 (10), p. 2100-2106
Journal article
2022

Genome-scale modeling of yeast metabolism: retrospectives and perspectives

Yu Chen, Feiran Li, Jens B Nielsen
FEMS Yeast Research. Vol. 22 (1)
Review article
2022

Machine learning for data integration in human gut microbiome

Peishun Li, Hao Luo, Boyang Ji et al
Microbial Cell Factories. Vol. 21 (1)
Review article
2022

Mapping of Nonhomologous End Joining-Mediated Integration Facilitates Genome-Scale Trackable Mutagenesis in Yarrowia lipolytica

Xiaoqin Liu, Mengmeng Liu, Jin Zhang et al
ACS Synthetic Biology. Vol. 11 (1), p. 216-227
Journal article
2022

Metabolic reconfiguration enables synthetic reductive metabolism in yeast

Tao Yu, Quanli Liu, Xiang Wang et al
Nature Metabolism. Vol. 4 (11), p. 1551-1559
Journal article
2022

Type 2 diabetes is associated with increased circulating levels of 3-hydroxydecanoate activating GPR84 and neutrophil migration

Randi Bonke Mikkelsen, Tulika Arora, Kajetan Trošt et al
iScience. Vol. 25 (12)
Journal article
2022

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

Cheng Zhang, Mengnan Shi, Woonghee Kim et al
EBioMedicine. Vol. 83
Journal article
2022

Controlling gene expression with deep generative design of regulatory DNA

Jan Zrimec, Xiaozhi Fu, Muhammad Azam Sheikh et al
Nature Communications. Vol. 13 (1), p. 5099-
Journal article
2022

Microbial production of chemicals driven by CRISPR-Cas systems

Shuobo Shi, Nailing Qi, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 73, p. 34-42
Review article
2022

Integrative functional analysis uncovers metabolic differences between Candida species

Neelu Begum, Sunjae Lee, Theo John Portlock et al
Communications Biology. Vol. 5 (1), p. 1013-
Journal article
2022

A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

Hongzhong Lu, Eduard Kerkhoven, Jens B Nielsen
Biomolecules. Vol. 12 (11)
Journal article
2022

A systems biology approach to study non-alcoholic fatty liver (NAFL) in women with obesity

A. S. Meijnikman, Dimitra Lappa, H. Herrema et al
iScience. Vol. 25 (8)
Journal article
2022

Yeast synthetic biology advances biofuel production

Zihe Liu, Junyang Wang, Jens B Nielsen
Current Opinion in Microbiology. Vol. 65, p. 33-39
Review article
2022

Hyperinsulinemia Is Highly Associated With Markers of Hepatocytic Senescence in Two Independent Cohorts

A. S. Meijnikman, C. C. Van Olden, O. Aydin et al
Diabetes. Vol. 71 (9), p. 1929-1936
Journal article
2022

The integration of bio-catalysis and electrocatalysis to produce fuels and chemicals from carbon dioxide

Xinyi Tan, Jens B Nielsen
Chemical Society Reviews. Vol. 51 (11), p. 4763-4785
Review article
2022

Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints

Feiran Li, Yu Chen, Qi Qi et al
Nature Communications. Vol. 13 (1)
Journal article
2022

Professor Stefan Hohmann (08.09.1956-02.07.2021)

Jens B Nielsen, Markus J. Tamás
FEMS Yeast Research. Vol. 22 (1)
Other text in scientific journal
2022

Rewiring regulation on respiro-fermentative metabolism relieved Crabtree effects in Saccharomyces cerevisiae

Yiming Zhang, Mo Su, Zheng Wang et al
Synthetic and Systems Biotechnology. Vol. 7 (4), p. 1034-1043
Journal article
2022

Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast Kluyveromyces marxianus

Noemi Montini, Tyler Doughty, Iván Domenzain Del Castillo Cerecer et al
Microbiology. Vol. 168 (3)
Journal article
2022

Cellular limitation of enzymatic capacity explains glutamine addiction in cancers

Johan Gustafsson, Fariba Roshanzamir, Anders Hagnestål et al
Preprint
2022

Innovation trends in industrial biotechnology

Jens B Nielsen, Christian Brix Tillegreen, Dina Petranovic Nielsen
Trends in Biotechnology. Vol. 40 (10), p. 1160-1172
Review article
2022

Yeast has evolved to minimize protein resource cost for synthesizing amino acids

Yu Chen, Jens B Nielsen
Proceedings of the National Academy of Sciences of the United States of America. Vol. 119 (4)
Journal article
2022

Bioactive metabolites: The double-edged sword in your food

Jens B Nielsen
Cell. Vol. 185 (24), p. 4469-4471
Other text in scientific journal
2022

Learning deep representations of enzyme thermal adaptation

Gang Li, Filip Buric, Jan Zrimec et al
Protein Science. Vol. 31 (12)
Journal article
2022

Plasma and Urine Free Glycosaminoglycans as Monitoring Biomarkers in Nonmetastatic Renal Cell Carcinoma—A Prospective Cohort Study

Francesco Gatto, Saeed Dabestani, Sinisa Bratulic et al
European Urology Open Science. Vol. 42, p. 30-39
Journal article
2022

Adipose Tissue, Bile Acids, and Gut Microbiome Species Associated With Gallstones After Bariatric Surgery

M. S.S. Guman, J. B. Hoozemans, S. Haal et al
Journal of Lipid Research. Vol. 63 (11), p. 100280-
Journal article
2022

Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach

Xiangyu Li, Koeun Shong, Woonghee Kim et al
EBioMedicine. Vol. 78
Journal article
2021

Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Ozlem Altay, Cheng Zhang, Hasan Turkez et al
Metabolites. Vol. 11 (4)
Journal article
2021

Combined Metabolic Activators Accelerates Recovery in Mild-to-Moderate COVID-19

Ozlem Altay, Muhammad Arif, Xiangyu Li et al
Advanced Science. Vol. 8 (17)
Journal article
2021

Performance of Regression Models as a Function of Experiment Noise

Gang Li, Jan Zrimec, Boyang Ji et al
Bioinformatics and Biology Insights. Vol. 15
Journal article
2021

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Sonja Blasche, Yongkyu Kim, Ruben A.T. Mars et al
Nature Microbiology. Vol. 6 (2), p. 196-208
Journal article
2021

GTR 2.0: GRNA-tRNA Array and Cas9-NG Based Genome Disruption and Single-Nucleotide Conversion in Saccharomyces cerevisiae

Guiping Gong, Yueping Zhang, Zibai Wang et al
ACS Synthetic Biology. Vol. 10 (6), p. 1328-1337
Journal article
2021

Machine learning-based investigation of the cancer protein secretory pathway

Rasool Saghaleyni, Muhammad Azam Sheikh, Pramod Bangalore et al
PLoS Computational Biology. Vol. 17 (4)
Journal article
2021

Metabolic Alterations in Older Women With Low Bone Mineral Density Supplemented With Lactobacillus reuteri

Peishun Li, Daniel Sundh, Boyang Ji et al
JBMR Plus. Vol. 5 (4)
Journal article
2021

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

Rosemary Brown, Egor Vorontsov, C. Sihlbom et al
eLife. Vol. 10
Journal article
2021

Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis

Xiaowei Li, Yanyan Wang, Gang Li et al
Nature Catalysis. Vol. 4 (9), p. 783-796
Journal article
2021

Systems biology based drug repositioning for development of cancer therapy

Beste Turanli, Ozlem Altay, Jan Borén et al
Seminars in Cancer Biology. Vol. 68, p. 47-58
Review article
2021

Informing Pharmacokinetic Models With Physiological Data: Oral Population Modeling of L-Serine in Humans

Jim Bosley, Elias Björnson, C. Zhang et al
Frontiers in Pharmacology. Vol. 12
Journal article
2021

Production of β-carotene in Saccharomyces cerevisiae through altering yeast lipid metabolism

Yijin Zhao, Yueping Zhang, Jens B Nielsen et al
Biotechnology and Bioengineering. Vol. 118 (5), p. 2043-2052
Journal article
2021

Urine free glycosaminoglycans as monitoring biomarkers in confined renal cell carcinoma - A prospective observational study

Francesco Gatto, Sinisa Bratulic, U. Stierner et al
European Urology. Vol. 79, p. S900-S900
Other conference contribution
2021

Preface

Sang Yup Lee, Jens B Nielsen, Gregory Stephanopoulos
Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. xv-xvi
Book chapter
2021

Proteome Constraints in Genome-Scale Models

Yu Chen, Jens B Nielsen, Eduard Kerkhoven
Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. 137-152
Book chapter
2021

Characterization of cross-species transcription and splicing from Penicillium to Saccharomyces cerevisiae

Zhenquan Lin, Kang Xu, Guang Cai et al
Journal of Industrial Microbiology and Biotechnology. Vol. 48 (9-10)
Journal article
2021

Transcriptomic response of Saccharomyces cerevisiae to octanoic acid production

Leonie Baumann, Tyler Doughty, Verena Siewers et al
FEMS Yeast Research. Vol. 21 (2)
Journal article
2021

Engineering yeast metabolism for the discovery and production of polyamines and polyamine analogues

Jiufu Qin, Anastasia Krivoruchko, Boyang Ji et al
Nature Catalysis. Vol. 4 (6), p. 498-509
Journal article
2021

Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Carl Malina, Rosemary Brown, Johan Björkeroth et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (51)
Journal article
2021

Synthetic biology advanced natural product discovery

Junyang Wang, Jens B Nielsen, Zihe Liu
Metabolites. Vol. 11 (11)
Review article
2021

Metabolic Engineering of Yeast

Rui Pereira, Olena Ishchuk, Xiaowei Li et al
Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. 689-733
Book chapter
2021

Genome-scale metabolic network reconstruction of model animals as a platform for translational research

Hao Wang, Jonathan Robinson, Pinar Kocabas et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (30)
Journal article
2021

In vitro turnover numbers do not reflect in vivo activities of yeast enzymes

Yu Chen, Jens B Nielsen
Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (32)
Journal article
2021

Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients

Mujdat Zeybel, Ozlem Altay, Muhammad Arif et al
Molecular Systems Biology. Vol. 17 (10)
Journal article
2021

Discovery of Functional Alternatively Spliced PKM Transcripts in Human Cancers

Xiangyu Li, Woonghee Kim, Muhammad Arif et al
Cancers. Vol. 13 (2), p. 1-23
Journal article
2021

Metabolic Engineering: Concepts and Applications: Volume 13a and 13b

Sang Yup Lee, Jens B Nielsen, Gregory Stephanopoulos
Edited book
2021

A systems biology approach to understand gut microbiota and host metabolism in morbid obesity: design of the BARIA Longitudinal Cohort Study

C. C. Van Olden, A. W. Van de Laar, A. S. Meijnikman et al
Journal of Internal Medicine. Vol. 289 (3), p. 340-354
Journal article
2021

Kinetic Models of Metabolism

Hongzhong Lu, Yu Chen, Jens B Nielsen et al
Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. 153-170
Book chapter
2021

Mathematical modeling of proteome constraints within metabolism

Yu Chen, Jens B Nielsen
Current Opinion in Systems Biology. Vol. 25, p. 50-56
Review article
2021

Rational gRNA design based on transcription factor binding data

David Bergenholm, Yasaman Dabirian, Raphael Ferreira et al
Synthetic Biology. Vol. 6 (1)
Journal article
2021

Draft genome sequences of five fungal strains isolated from Kefir

Simonas Marcisauskas, Yongkyu Kim, Sonja Blasche et al
Microbiology Resource Announcements. Vol. 10 (21)
Journal article
2021

Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning

Xiangyu Li, Woonghee Kim, Kajetan Juszczak et al
iScience. Vol. 24 (7)
Journal article
2021

Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteri

Hao Luo, Peishun Li, Hao Wang et al
BMC Biotechnology. Vol. 21 (1)
Journal article
2021

The Translational Status of Cancer Liquid Biopsies

Sinisa Bratulic, Francesco Gatto, Jens B Nielsen
Regenerative Engineering and Translational Medicine. Vol. 7 (3), p. 312-352
Journal article
2021

Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Yu Chen, Feiran Li, Jiwei Mao et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (12)
Journal article
2021

Cyanobacteria Biotechnology

Paul Hudson, Sang Y. Lee, Jens B Nielsen et al
Book
2021

Analytical performance of a standardized kit for mass spectrometry-based measurements of human glycosaminoglycans

Davide Tamburro, Sinisa Bratulic, Souad Abou Shameh et al
Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences. Vol. 1177
Journal article
2021

BUTTERFLY: addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

Johan Gustafsson, Jonathan Robinson, Jens B Nielsen et al
Genome Biology. Vol. 22 (1)
Journal article
2021

Production of 10-methyl branched fatty acids in yeast

Hannah G. Blitzblau, Andrew L. Consiglio, Paulo Teixeira et al
Biotechnology for Biofuels. Vol. 14 (1)
Journal article
2021

De novo biosynthesis of bioactive isoflavonoids by engineered yeast cell factories

Quanli Liu, Yi Liu, Gang Li et al
Nature Communications. Vol. 12 (1)
Journal article
2021

Yeast based biorefineries for oleochemical production

Yiming Zhang, Jens B Nielsen, Zihe Liu
Current Opinion in Biotechnology. Vol. 67, p. 26-34
Review article
2021

Expression of fungal biosynthetic gene clusters in S. cerevisiae for natural product discovery

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Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

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Addressing the heterogeneity in liver diseases using biological networks

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Perspective: Metabotyping—A Potential Personalized Nutrition Strategy for Precision Prevention of Cardiometabolic Disease

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Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning

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The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability

Christoph Sebastian Börlin, Jens B Nielsen, Verena Siewers
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MEMOTE for standardized genome-scale metabolic model testing

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Other text in scientific journal
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DSAVE: Detection of misclassified cells in single-cell RNA-Seq data

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Engineering carboxylic acid reductase for selective synthesis of medium-chain fatty alcohols in yeast

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The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease

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Exercise-Mediated Lowering of Glutamine Availability Suppresses Tumor Growth and Attenuates Muscle Wasting

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Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma

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Editorial: yeast synthetic biology

Jin Hou, Jens B Nielsen
FEMS Yeast Research. Vol. 20 (6)
Other text in scientific journal
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Yeast systems biology in understanding principles of physiology underlying complex human diseases

Rosemary Yu, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 63, p. 63-69
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Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids

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Metabolic Engineering of Saccharomyces cerevisiae for Rosmarinic Acid Production

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Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

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Frontiers in Bioengineering and Biotechnology. Vol. 8
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Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production

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Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast

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Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products

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A systems biology approach for studying neurodegenerative diseases

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Drug Discovery Today. Vol. 25 (7), p. 1146-1159
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The role of peroxisomes in xylose alcoholic fermentation in the engineered Saccharomyces cerevisiae

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Expressing a cytosolic pyruvate dehydrogenase complex to increase free fatty acid production in Saccharomyces cerevisiae

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Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media

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Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift

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Molecular natural history of breast cancer: Leveraging transcriptomics to predict breast cancer progression and aggressiveness

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Cancer Medicine. Vol. 9 (10), p. 3551-3562
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Improvement in the Current Therapies for Hepatocellular Carcinoma Using a Systems Medicine Approach

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Classification of clear cell renal cell carcinoma based on PKM alternative splicing

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Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

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Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

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Rewiring Central Carbon Metabolism Ensures Increased Provision of Acetyl-CoA and NADPH Required for 3-OH-Propionic Acid Production

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Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum

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Third-generation biorefineries as the means to produce fuels and chemicals from CO2

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Nature Catalysis. Vol. 3 (3), p. 274-288
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Qi Qi, Feiran Li, Rosemary Yu et al
mBio. Vol. 11 (6), p. 1-12
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Pan-cancer analysis of the metabolic reaction network

Francesco Gatto, Raphael Ferreira, Jens B Nielsen
Metabolic Engineering. Vol. 57, p. 51-62
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2019

Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes

T. I. Henriksen, Leif Wigge, Jens B Nielsen et al
Scientific Reports. Vol. 9 (1)
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Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies

Rui Pereira, P. Vilaca, P. Maia et al
ACS Synthetic Biology. Vol. 8 (5), p. 976-988
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Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Simonas Marcisauskas, Boyang Ji, Jens B Nielsen
BMC Bioinformatics. Vol. 20 (1)
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A bioinformatic pipeline to analyze ChIP-exo datasets

Christoph Sebastian Börlin, David Bergenholm, Petter Holland et al
Biology Methods and Protocols. Vol. 4 (1)
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Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

Christoph Sebastian Börlin, Nevena Cvetesic, Petter Holland et al
FEMS Yeast Research. Vol. 19 (2)
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Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose

Gheorghe M. Borja, A. Rodriguez, Kate Campbell et al
Microbial Cell Factories. Vol. 18 (1)
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Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima

Gang Li, Kersten S. Rabe, Jens B Nielsen et al
ACS Synthetic Biology. Vol. 8 (6), p. 1411-1420
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Recent trends in metabolic engineering of microbial chemical factories

Yi Liu, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 60, p. 188-197
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Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi

Jens Christian Froslev Nielsen, Sylvain Prigent, Sietske Grijseels et al
mSystems. Vol. 4 (2)
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Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Ghofran Othoum, Sylvain Prigent, Abderahmane Derouiche et al
Scientific Reports. Vol. 9 (1)
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The human secretome

Mathias Uhlen, Max J. Karlsson, Andreas Hober et al
Science signaling. Vol. 12 (609)
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Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota

Ling Qun Ye, Promi Das, Peishun Li et al
FEMS microbiology ecology. Vol. 95 (11)
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The pan-genome of Saccharomyces cerevisiae

Gang Li, Boyang Ji, Jens B Nielsen
FEMS Yeast Research. Vol. 19 (7)
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Tackling Cancer with Yeast-Based Technologies

Raphael Ferreira, Angelo Limeta, Jens B Nielsen
Trends in Biotechnology. Vol. 37 (6), p. 592-603
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Systems biology perspective for studying the gut microbiota in human physiology and liver diseases

Ozlem Altay, Jens B Nielsen, Mathias Uhlen et al
EBioMedicine. Vol. 49 (November), p. 363-373
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Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression

Yongjun Wei, Boyang Ji, Verena Siewers et al
Applied Microbiology and Biotechnology. Vol. 103 (9), p. 3727-3736
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Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges

Yu Chen, Gang Li, Jens B Nielsen
Methods in Molecular Biology. Vol. 2049, p. 329-345
Book chapter
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FadR-Based Biosensor-Assisted Screening for Genes Enhancing Fatty Acyl-CoA Pools in Saccharomyces cerevisiae

Yasaman Dabirian, Paulo Teixeira, Jens B Nielsen et al
ACS Synthetic Biology. Vol. 8 (8), p. 1788-1800
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Metagenomic analysis of bile salt biotransformation in the human gut microbiome

Promi Das, Simonas Marcisauskas, Boyang Ji et al
BMC Genomics. Vol. 20 (1)
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Assembly and analysis of the genome sequence of the yeast Brettanomyces naardenensis CBS 7540

Ievgeniia Tiukova, Huifeng Jiang, Jacques Dainat et al
Microorganisms. Vol. 7 (11)
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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Hongzhong Lu, Feiran Li, Benjamín José Sánchez et al
Nature Communications. Vol. 10 (1)
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Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis

Rui Benfeitas, G. Bidkhori, B. Mukhopadhyay et al
EBioMedicine. Vol. 40, p. 471-487
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ChIP-exo analysis highlights Fkh1 and Fkh2 transcription factors as hubs that integrate multi-scale networks in budding yeast

Thierry D.G.A. Mondeel, Petter Holland, Jens B Nielsen et al
Nucleic Acids Research. Vol. 47 (15), p. 7825-7841
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SLIMEr: Probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Benjamín José Sánchez, Feiran Li, Eduard Kerkhoven et al
BMC Systems Biology. Vol. 13 (1)
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Yeast Systems Biology: Model Organism and Cell Factory

Jens B Nielsen
Biotechnology journal. Vol. 14 (9)
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METABOLISM: A stress-coping strategy for yeast cells

Jens B Nielsen
Nature. Vol. 572 (7768), p. 184-185
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2019

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Rui Pereira, Yongjun Wei, Elsayed Mohamed et al
Metabolic Engineering. Vol. 56, p. 130-141
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Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

Ievgeniia Tiukova, Jule Brandenburg, Johanna Blomqvist et al
Biotechnology for Biofuels. Vol. 12 (1)
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Model-Assisted Fine-Tuning of Central Carbon Metabolism in Yeast through dCas9-Based Regulation

Raphael Ferreira, Christos Skrekas, Alex Hedin et al
ACS Synthetic Biology. Vol. 8 (11), p. 2457-2463
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A Systematic Investigation of the Malignant Functions and Diagnostic Potential of the Cancer Secretome

Jonathan Robinson, Amir Feizi, Mathias Uhlen et al
Cell Reports. Vol. 26 (10), p. 2622-2635.e5
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RNAi expression tuning, microfluidic screening, and genome recombineering for improved protein production in Saccharomyces cerevisiae

Guokun Wang, Sara M. Björk, Mingtao Huang et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 116 (19), p. 9324-9332
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Increasing jojoba-like wax ester production in Saccharomyces cerevisiae by enhancing very long-chain, monounsaturated fatty acid synthesis

Leonie Wenning, Christer S. Ejsing, Florian David et al
Microbial Cell Factories. Vol. 18 (1)
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Cell factory engineering for improved production of natural products

Jens B Nielsen
Natural Product Reports. Vol. 36 (9), p. 1233-1236
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Big data in yeast systems biology

Tao Yu, Jens B Nielsen
FEMS Yeast Research. Vol. 19 (7)
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Antibiotic Lethality Is Impacted by Nutrient Availabilities: New Insights from Machine Learning

Jens B Nielsen
Cell. Vol. 177 (6), p. 1373-1374
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2019

Modelling approaches for studying the microbiome

Manish Kumar, Boyang Ji, Karsten Zengler et al
Nature Microbiology. Vol. 4 (8), p. 1253-1267
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Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Yating Hu, Zhu Zhiwei, Jens B Nielsen et al
Open Biology. Vol. 9 (5)
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Energy metabolism controls phenotypes by protein efficiency and allocation

Yu Chen, Jens B Nielsen
Proceedings of the National Academy of Sciences of the United States of America. Vol. 116 (35), p. 17592-17597
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Genome-scale model of Rhodotorula toruloides metabolism

Ievgeniia Tiukova, Sylvain Prigent, Jens B Nielsen et al
Biotechnology and Bioengineering. Vol. 116 (12), p. 3396-3408
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Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

Quanli Liu, Tao Yu, Xiaowei Li et al
Nature Communications. Vol. 10 (1)
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Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome

Alexandra Linda Bergman, Dóra Vitay, John Hellgren et al
FEMS Yeast Research. Vol. 19 (3)
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Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions

Petter Holland, David Bergenholm, Christoph Sebastian Börlin et al
Nucleic Acids Research. Vol. 47 (10), p. 4986-5000
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Complex I is bypassed during high intensity exercise

Avlant Nilsson, Elias Björnson, Mikael Flockhart et al
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Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das, Parizad Babaei, Jens B Nielsen
BMC Genomics. Vol. 20 (1)
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Expanding the Dynamic Range of a Transcription Factor-Based Biosensor in Saccharomyces cerevisiae

Yasaman Dabirian, Xiaowei Li, Yun Chen et al
ACS Synthetic Biology. Vol. 8 (9), p. 1968-1975
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Identification and characterisation of two high-affinity glucose transporters from the spoilage yeast Brettanomyces bruxellensis

Ievgeniia Tiukova, Iben Møller-Hansen, Zeinu M. Belew et al
FEMS microbiology letters. Vol. 366 (17)
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Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree negative

Zongijie Dai, Mingtao Huang, Yun Chen et al
Nature Communications. Vol. 9 (1)
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Balanced trafficking between the ER and the Golgi apparatus increases protein secretion in yeast

Jichen Bao, Mingtao Huang, Dina Petranovic Nielsen et al
AMB Express. Vol. 8 (1)
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Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production

Mingtao Huang, Guokun Wang, Jiufu Qin et al
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An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans

Adil Mardinoglu, Hao Wu, Elias Björnson et al
Cell Metabolism. Vol. 27 (3), p. 559-571.e5
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Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

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Metabolomics. Vol. 14 (4)
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Heterologous transporter expression for improved fatty alcohol secretion in yeast

Yating Hu, Zhu Zhiwei, Verena Siewers et al
Metabolic Engineering. Vol. 45, p. 51-58
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Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

David Bergenholm, Michael Gossing, Yongjun Wei et al
Biotechnology and Bioengineering. Vol. 115 (4), p. 932-942
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Metabolic Network-Based Identification and Prioritization o f Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma

Gholamreza Bidkhori, Rui Benfeitas, Ezgi Elmas et al
Frontiers in Physiology. Vol. 9 (JUL)
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Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae

Michael Gossing, Agata Smialowska, Jens B Nielsen
FEMS Yeast Research. Vol. 18 (8)
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Integrated analysis of the yeast NADPH-regulator Stb5 reveals distinct differences in NADPH requirements and regulation in different states of yeast metabolism

Liming Ouyang, Petter Holland, Hongzhong Lu et al
FEMS Yeast Research. Vol. 18 (8)
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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira et al
Nucleic Acids Research. Vol. 46 (7)
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Regulation of yeast-to-hyphae transition in Yarrowia lipolytica

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mSphere. Vol. 3 (6)
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RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

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Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid–derived hydrocarbons

Yiming Zhang, Jens B Nielsen, Zihe Liu
Biotechnology and Bioengineering. Vol. 115 (9), p. 2139-2147
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Guidelines and recommendations on yeast cell death nomenclature

Didac Carmona-Gutierrez, Maria Anna Bauer, Andreas Zimmermann et al
Microbial Cell. Vol. 5 (1), p. 4-31
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Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors

Alireza Azimi, Stefano Caramuta, Brinton Seashore-Ludlow et al
Molecular Systems Biology. Vol. 14 (3)
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Plasma Glycosaminoglycans as Diagnostic and Prognostic Biomarkers in Surgically Treated Renal Cell Carcinoma

Francesco Gatto, Kyle A. Blum, Seyedeh Shaghayegh Hosseini et al
European Urology Oncology. Vol. 1 (5), p. 364-377
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Reconstruction of 24 Penicillium genome-scale metabolic models shows diversity based on their secondary metabolism

Sylvain Prigent, Jens Christian Froslev Nielsen, J. C. Frisvad et al
Biotechnology and Bioengineering. Vol. 115 (10), p. 2604-2612
Journal article
2018

Screening of 2A peptides for polycistronic gene expression in yeast

Tatiana M. Souza-Moreira, Clara Navarrete Roman, Xin Chen et al
FEMS Yeast Research. Vol. 18 (5)
Journal article
2018

High-throughput microfluidics for the screening of yeast libraries

Mingtao Huang, H. N. Joensson, Jens B Nielsen
Methods in Molecular Biology. Vol. 1671, p. 307-317
Book chapter
2018

Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

Tao Yu, Yongjin Zhou, Mingtao Huang et al
Cell. Vol. 174 (6), p. 1549-1572
Journal article
2018

TCSBN: A database of tissue and cancer specific biological networks

Sunjae Lee, C. Zhang, M. Arif et al
Nucleic Acids Research. Vol. 46 (D1), p. D595-D600
Journal article
2018

Expression of cocoa genes in Saccharomyces cerevisiae improves cocoa butter production

Yongjun Wei, David Bergenholm, Michael Gossing et al
Microbial Cell Factories. Vol. 17 (1)
Journal article
2018

Coupling cell division to metabolic pathways through transcription

Petter Holland, Jens B Nielsen, Thierry D.G.A. Mondeel et al
Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Vol. 1-3, p. 74-93
Book chapter
2018

Systems biology in hepatology: Approaches and applications

Adil Mardinoglu, Jan Borén, Ulf Smith et al
Nature Reviews Gastroenterology and Hepatology. Vol. 15 (6), p. 365-377
Review article
2018

Barriers and opportunities in bio-based production of hydrocarbons

Yongjin Zhou, Eduard Kerkhoven, Jens B Nielsen
Nature Energy. Vol. 3 (11), p. 925-935
Review article
2018

Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols

Raphael Ferreira, Paulo Teixeira, Michael Gossing et al
Metabolic Engineering Communications. Vol. 6, p. 22-27
Journal article
2018

Metabolite Depletion Affects Flux Profiling of Cell Lines

Avlant Nilsson, J. R. Haanstra, B. Teusink et al
Trends in Biochemical Sciences. Vol. 43 (6), p. 395-397
Other text in scientific journal
2018

Investigation of putative regulatory acetylation sites in Fas2p of Saccharomyces cerevisiae

Alexandra Linda Bergman, Leonie Wenning, Verena Siewers et al
Preprint
2018

Evolution of the Metabolic Engineering Community

Jens B Nielsen, Sang Yup Lee
Metabolic Engineering. Vol. 48, p. A1-A2
Other text in scientific journal
2018

Advancing biotechnology with CRISPR/Cas9: recent applications and patent landscape

Raphael Ferreira, Florian David, Jens B Nielsen
Journal of Industrial Microbiology and Biotechnology. Vol. 45 (7), p. 467-480
Review article
2018

Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion

Raphael Ferreira, Paulo Teixeira, Verena Siewers et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 115 (6), p. 1262-1267
Journal article
2018

Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling

Manish Kumar, Boyang Ji, Parizad Babaei et al
Metabolic Engineering. Vol. 49, p. 128-142
Journal article
2018

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis

Promi Das, Boyang Ji, P. Kovatcheva-Datchary et al
PLoS ONE. Vol. 13 (3)
Journal article
2018

Engineering lipid droplet assembly mechanisms for improved triacylglycerol accumulation in Saccharomyces cerevisiae

Paulo Teixeira, Florian David, Verena Siewers et al
FEMS Yeast Research. Vol. 18 (6)
Journal article
2018

Challenges in modeling the human gut microbiome

Parizad Babaei, Saeed Shoaie, Boyang Ji et al
Nature Biotechnology. Vol. 36 (8), p. 682-686
Other text in scientific journal
2018

DCEO Biotechnology: Tools to Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals

Xiulai Chen, Cong Gao, Liang Guo et al
Chemical Reviews. Vol. 118 (1), p. 4-72
Review article
2018

Dynamic engineering of 1-alkenes biosynthesis and secretion in yeast.

Yongjin Zhou, Yating Hu, Zhu Zhiwei et al
ACS Synthetic Biology. Vol. 7 (2), p. 584-590
Journal article
2018

Identification of the decumbenone biosynthetic gene cluster in penicillium decumbens and the importance for production of calbistrin

S. Grijseels, Carsten Pohl, Jens Christian Froslev Nielsen et al
Fungal Biology and Biotechnology. Vol. 5 (1), p. 1-17
Journal article
2018

Drug Repositioning for Effective Prostate Cancer Treatment

Beste Turanli, Morten Grötli, Jan Boren et al
Frontiers in Physiology. Vol. 9 (MAY)
Review article
2018

Changes in lipid metabolism convey acid tolerance in Saccharomyces cerevisiae

Zhongpeng Guo, Sakda Khoomrung, Jens B Nielsen et al
Biotechnology for Biofuels. Vol. 11 (Issue 1)
Journal article
2018

Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes

G. Bidkhori, Rui Benfeitas, M. Klevstig et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 115 (50), p. E11874-E11883
Journal article
2018

All you need is mentorship

Robert A. Weinberg, Maya Schuldiner, Hong Wu et al
Getting to Good: Research Integrity in the Biomedical Sciences, p. 256-258
Book chapter
2018

Multiplexed CRISPR/Cas9 Genome Editing and Gene Regulation Using Csy4 in Saccharomyces cerevisiae

Raphael Ferreira, Christos Skrekas, Jens B Nielsen et al
ACS Synthetic Biology. Vol. 7 (1), p. 10-15
Journal article
2018

Yeast mitochondria: An overview of mitochondrial biology and the potential of mitochondrial systems biology

Carl Malina, Christer Larsson, Jens B Nielsen
FEMS Yeast Research. Vol. 18 (5)
Other text in scientific journal
2017

Efficient protein production by yeast requires global tuning of metabolism

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

METABOLISM: Built on stable catalysts

Jens B Nielsen
Nature Microbiology. Vol. 2, p. Art no: 17085-
Other text in scientific journal
2017

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

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

Comparison of the metabolic response to over-production of p-coumaric acid in two yeast strains

A. Rodriguez, Yun Chen, Sakda Khoomrung et al
Metabolic Engineering. Vol. 44, p. 265-272
Journal article
2017

Editorial: Where is scientific publishing heading?

Jens B Nielsen
FEMS Yeast Research. Vol. 17 (7)
Other text in scientific journal
2017

Affibody Scaffolds Improve Sesquiterpene Production in Saccharomyces cerevisiae.

Stefan Tippmann, J. Anfelt, Florian David et al
ACS Synthetic Biology. Vol. 6 (1), p. 19-28
Journal article
2017

Metabolic Models of Protein Allocation Call for the Kinetome

Avlant Nilsson, Jens B Nielsen, Bernhard O Palsson
Cell Systems. Vol. 5 (6), p. 538-541
Other text in scientific journal
2017

Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae

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

Genome-scale metabolic models applied to human health and disease

Daniel Cook, Jens B Nielsen
Wiley Interdisciplinary Reviews: Systems Biology and Medicine. Vol. 9 (6)
Review article
2017

The yeast osmostress response is carbon source dependent

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

Systems Biology of Metabolism

Jens B Nielsen
Annual Review of Biochemistry. Vol. 86, p. 245-275
Review article
2017

Engineering yeast metabolism for production of terpenoids for use as perfume ingredients, pharmaceuticals and biofuels

Yueping Zhang, Jens B Nielsen, Zihe Liu
FEMS Yeast Research. Vol. 17 (8)
Other text in scientific journal
2017

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

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

Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism

Jens Christian Froslev Nielsen, Jens B Nielsen
Synthetic and Systems Biotechnology. Vol. 2 (1), p. 5-12
Review article
2017

Human protein secretory pathway genes are expressed in a tissue-specific pattern to match processing demands of the secretome

Amir Feizi, Francesco Gatto, Mathias Uhlen et al
npj Systems Biology and Applications. Vol. 3 (1)
Journal article
2017

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

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

Model forms most useful

K. R. Patil, Jens B Nielsen
Current Opinion in Systems Biology. Vol. 6, p. iv-vi
Other text in scientific journal
2017

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

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

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

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

Predicting growth of the healthy infant using a genome scale metabolic model.

Avlant Nilsson, Adil Mardinoglu, Jens B Nielsen
npj Systems Biology and Applications. Vol. 3, p. 3-
Journal article
2017

Anticancer drug discovery through genome-scale metabolic modeling

Jonathan Robinson, Jens B Nielsen
Current Opinion in Systems Biology. Vol. 4, p. 1-8
Review article
2017

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

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

Exploring the potential of Saccharomyces cerevisiae for biopharmaceutical protein production

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

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

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

Systematic inference of functional phosphorylation events in yeast metabolism

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

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

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

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

Eugene Fletcher, Amir Feizi, Mark Bisschops et al
Metabolic Engineering. Vol. 39, p. 19-28
Journal article
2017

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

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

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

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

Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast

Zhu Zhiwei, Yongjin Zhou, Min-Kyoung Kang et al
Metabolic Engineering. Vol. 44 (NOV), p. 81-88
Journal article
2017

Metabolic engineering frontiers emerging with advanced tools and methodologies

X. Q. Zhao, Jens B Nielsen
Biotechnology Advances. Vol. 35 (8), p. 933-933
Other text in scientific journal
2017

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

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

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

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

The Impact of Systems Biology on Bioprocessing

Kate Campbell, Jianye Xia, Jens B Nielsen
Trends in Biotechnology. Vol. 35 (12), p. 1156-1168
Review article
2017

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

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

A molecular genetic toolbox for Yarrowia lipolytica

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

Physiological characterization of secondary metabolite producing Penicillium cell factories

S. Grijseels, Jens Christian Froslev Nielsen, Jens B Nielsen et al
Fungal Biology and Biotechnology. Vol. 4, p. 8-
Journal article
2017

Engineering Robustness of Microbial Cell Factories

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

Systems Biology

Jens B Nielsen, Stefan Hohmann
Book
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
Review article
2017

Engineering central metabolism – a grand challenge for plant biologists

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

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

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

Network analyses identify liver-specific targets for treating liver diseases

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

In silico analysis of human metabolism: Reconstruction, contextualization and application of genome-scale models

Jun Geng, Jens B Nielsen
Current Opinion in Systems Biology. Vol. 2, p. 29-38
Review article
2017

Selection of complementary foods based on optimal nutritional values

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

Elimination of the last reactions in ergosterol biosynthesis alters the resistance of Saccharomyces cerevisiae to multiple stresses

Guodong Liu, Yun Chen, N. J. Faergeman et al
FEMS Yeast Research. Vol. 17 (6)
Journal article
2017

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

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

In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis

Kaisa Thorell, Johan Bengtsson Palme, Oscar Hsin Fu Liu et al
Infection and Immunity. Vol. 85 (10)
Journal article
2017

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

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

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

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

Expanding the product portfolio of fungal type I fatty acid synthases

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

New challenges to study heterogeneity in cancer redox metabolism

Rui Benfeitas, Mathias Uhlen, Jens B Nielsen et al
Frontiers in Cell and Developmental Biology. Vol. 5 (JUL)
Review article
2017

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

Leonie Wenning, Tao Yu, Florian David et al
Biotechnology and Bioengineering. Vol. 114 (5), p. 1025-1035
Journal article
2017

Genome scale metabolic modeling of cancer

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

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

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

Metabolic engineering of yeast for fermentative production of flavonoids

A. Rodriguez, T. Strucko, S. G. Stahlhut et al
Bioresource Technology. Vol. 245, p. 1645-1654
Journal article
2016

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

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

Regulation of amino-acid metabolism controls flux to lipid accumulation in yarrowia lipolytica

Eduard Kerkhoven, Kyle R. Pomraning, S. E. Baker et al
npj Systems Biology and Applications. Vol. 2
Journal article
2016

Engineering yeast metabolism for production of fuels and chemicals

Jens B Nielsen
New Biotechnology. Vol. 33 (Supplement: S Meeting Abstract: PL3), p. S66-S66
Other text in scientific journal
2016

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

Adil Mardinoglu, Jens B Nielsen
Frontiers in Physiology. Vol. 7 (NOV)
Other text in scientific journal
2016

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

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

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

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

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

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

Engineering yeast for high-level production of stilbenoid antioxidants

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

Flux control through protein phosphorylation in yeast

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

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

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

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

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

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

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

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

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

Engineering Cellular Metabolism

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

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

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

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis

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

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

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

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

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

All You Need Is Mentorship

R. A. Weinberg, M. Schuldiner, H. Wu et al
Cell. Vol. 164 (6), p. 1092-1093
Other text in scientific journal
2016

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

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

Transcriptomics resources of human tissues and organs

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

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

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

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

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

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

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

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

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

Adaptive Evolution of Phosphorus Metabolism in Prochlorococcus.

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

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

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

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
Review article
2016

Engineering of synthetic, stress-responsive yeast promoters

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

Functional expression and evaluation of heterologous phosphoketolases in Saccharomyces cerevisiae

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

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

Jose Luis Martinez Ruiz, Dina Petranovic Nielsen, Jens B Nielsen
Bioengineered. Vol. 7 (2), p. 1-4
Other text in scientific journal
2016

sTrehalose-6-phosphate synthase and stabilization of yeast glycolysis

Dan Fraenkel, Jens B Nielsen
FEMS Yeast Research. Vol. 16 (1)
Other text in scientific journal
2016

Adaptation to different types of stress converge on mitochondrial metabolism

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

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

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

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

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

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

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

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

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

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
Other conference contribution
2016

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

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

Integrative analysis of human omics data using biomolecular networks

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

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

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

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

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

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

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

Biobased organic acids production by metabolically engineered microorganisms

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

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

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

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

Mingtao Huang, Jichen Bao, B. M. Hallstrom et al
Metabolic Engineering, p. 639-640
Paper in proceeding
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 (1)
Journal article
2016

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

S. Grijseels, Jens Christian Froslev Nielsen, Jens B Nielsen et al
Scientific Reports. Vol. 6
Journal article
2015

Long-chain Alkane Production by the Yeast Saccharomyces cerevisiae

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

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

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

HCSD: The human cancer secretome database

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

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

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

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

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

Modifying yeast tolerance to inhibitory conditions of ethanol production processes

Luis Caspeta-Guadarrama, Tania Castillo, Jens B Nielsen
Frontiers in Bioengineering and Biotechnology. Vol. 3 (Nov), p. 184-
Review article
2015

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

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

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

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

Microbial acetyl-CoA metabolism and metabolic engineering

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

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

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

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

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

New insight into the gut microbiome through metagenomics

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

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

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

How to set up collaborations between academia and industrial biotech companies

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

Tissue-based map of the human proteome

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

Metabolic engineering strategies for microbial synthesis of oleochemicals

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

New paradigms for metabolic modeling of human cells

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

Networking in metabolism and human disease

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

Micro-droplet based directed evolution outperforms conventional laboratory evolution

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

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

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

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

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

Finding directionality and gene-disease predictions in disease associations

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

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

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

Applications of computational modeling in metabolic engineering of yeast

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

Stratification of Hepatocellular Carcinoma Patients Based on Acetate Utilization

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

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

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

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

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

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

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

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

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

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

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

Advancing metabolic engineering through systems biology of industrial microorganisms

Zongijie Dai, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 36, p. 8-15
Review article
2015

Production of natural products through metabolic engineering of Saccharomyces cerevisiae

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

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

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

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

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

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

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

Glucose repression in Saccharomyces cerevisiae

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

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

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

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

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

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
Review article
2015

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

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

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

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

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

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

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

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

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

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

FEMS yeast research: the yeast community journal

Jens B Nielsen
FEMS Yeast Research. Vol. 15 (2)
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2015

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

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

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-
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2015

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

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

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

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

Human metabolic atlas: an online resource for human metabolism

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

Cancer Metabolism: A Modeling Perspective

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

Enabling Technologies to Advance Microbial Isoprenoid Production

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

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), p. 1-16
Journal article
2015

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

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

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

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

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

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

Editorial

Jens B Nielsen, Ramon Gonzalez
Journal of Industrial Microbiology and Biotechnology. Vol. 42 (3), p. 315-316
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2015

Unlocking the potential of fungi: the QuantFung project

Z. Buttel, R. Diaz, B. Dirnberger et al
Fungal Biol Biotechnol. Vol. 2, p. 6-
Journal article
2014

Most influential FEMS publications

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

Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii

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

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

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

Defining the human gallbladder proteome by transcriptomics and affinity proteomics

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

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

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

Bridging the gaps in systems biology

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

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

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

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

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

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

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

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

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

Altered sterol composition renders yeast thermotolerant

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

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

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

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

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

Maintaining a strong yeast research community

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

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

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

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

Jens B Nielsen, Sergio Velasco, Intawat Nookaew
Comprehensive Biomedical Physics. Vol. 6, p. 165-173
Book chapter
2014

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

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

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

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

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

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

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

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

Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast

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

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

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

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

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

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

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

Systems biology: Developments and applications

Rahul Kumar, Petri-Jaan Lahtvee, Jens B Nielsen
Molecular Mechanisms in Yeast Carbon Metabolism, p. 83-96
Book chapter
2014

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

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

Kinetic models in industrial biotechnology - Improving cell factory performance

Joachim Almquist, Marija Cvijovic, V. Hatzimanikatis et al
Metabolic Engineering. Vol. 24, p. 38-60
Review article
2014

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

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

Development of a yeast cell factory for production of aromatic products

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

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

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

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

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

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

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

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

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

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics

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

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

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

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

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

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

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

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

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

Engineering synergy in biotechnology

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

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

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

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
Review article
2013

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

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

FANTOM: Functional and taxonomic analysis of metagenomes

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

Yeast as a platform cell factory in future biorefineries

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

Genome-Scale Modeling of the Protein Secretory Machinery in Yeast

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

Assessing the human gut microbiota in metabolic diseases.

Fredrik Karlsson, Valentina Tremaroli, Jens B Nielsen et al
Diabetes. Vol. 62 (10), p. 3341-9
Review article
2013

Metabolic engineering of yeast for production of fuels and chemicals

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

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

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

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

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

From the Chief Editor

Jens B Nielsen
FEMS Yeast Research. Vol. 13 (1), p. 1-1
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2013

The role of biofuels in the future energy supply

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

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

Adil Mardinoglu, Francesco Gatto, Jens B Nielsen
Biotechnology journal. Vol. 8 (9), p. 985-996
Review article
2013

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

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

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

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

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

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

Application of genome-scale metabolic models in metabolic engineering

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

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
Review article
2013

Specific growth rate and substrate dependent polyhydroxybutyrate production in Saccharomyces cerevisiae

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

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
Journal of Clinical Endocrinology and Metabolism. Vol. 98 (2), p. E370-E378
Journal article
2013

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

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

Correlation of cell growth and heterologous protein production by Saccharomyces cerevisiae

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

Economic and environmental impacts of microbial biodiesel

Luis Caspeta-Guadarrama, Jens B Nielsen
Nature Biotechnology. Vol. 31 (9), p. 789-793
Other text in scientific journal
2013

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

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

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

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

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

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

Mapping Condition-Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae

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

A community-driven global reconstruction of human metabolism

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

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

Wanwipa Vongsangnak, Jens B Nielsen
Microbial Production of Food Ingredients, Enzymes and Nutraceuticals, p. 19-41
Book chapter
2013

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

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

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

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

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

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

Production of biopharmaceutical proteins by yeast Advances through metabolic engineering

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

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

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

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

S. L. Sjostrom, Y. Bai, Mingtao Huang et al
17th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2013. Vol. 2, p. 1270-1272
Paper in proceeding
2013

Advanced biofuel production by the yeast Saccharomyces cerevisiae

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

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

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

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

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

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

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

Heat shock response improves heterologous protein secretion in Saccharomyces cerevisiae

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

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

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

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

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

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
Review article
2013

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

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

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

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

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

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

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

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

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

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

Different expression systems for production of recombinant proteins in Saccharomyces cerevisiae

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Rasmus Ågren, Sergio Velasco, Adil Mardinoglu et al
PLoS Computational Biology. Vol. 8 (5)
Journal article
2012

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

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

Symptomatic atherosclerosis is associated with an altered gut metagenome

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

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

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

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

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

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

Pramote Chumnanpuen, Christian Brackmann, Subir Kumar Nandy et al
Biotechnology journal. Vol. 7 (5), p. 594-601
Journal article
2012

Applied systems biology - vanillin production in Saccharomyces cerevisiae

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

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

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

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

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

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

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

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

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

Genome-scale metabolic representation of Amycolatopsis balhimycina

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

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

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

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

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

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

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

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

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

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

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

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

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

Aspergilli: Systems biology and industrial applications

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

Systems biology: the 'new biotechnology' Editorial overview

Jens B Nielsen, S. Y. Lee
Current Opinion in Biotechnology. Vol. 23 (4), p. 583-584
Other text in scientific journal
2012

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

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

Mapping the polysaccharide degradation potential of Aspergillus niger

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

Translational and systems medicine Introduction

Jens B Nielsen
Journal of Internal Medicine. Vol. 271 (2), p. 108-110
Other text in scientific journal
2012

Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae

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

Systems medicine and metabolic modelling

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

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

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

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

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

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

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

Metabolic engineering, synthetic biology and systems biology

Jens B Nielsen, J. Pronk
FEMS Yeast Research. Vol. 12 (2), p. 103-103
Other text in scientific journal
2012

Recovery of phenotypes obtained by adaptive evolution through inverse metabolic engineering

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

Metabolic engineering of recombinant protein secretion by Saccharomyces cerevisiae

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

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

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

Bridging omics technologies with synthetic biology in yeast industrial biotechnology

Antonio Roldao, Il-Kwon Kim, Jens B Nielsen
Systems Metabolic Engineering. Vol. 9789400745346, p. 271-327
Book chapter
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. Vol. 69 (16), p. 2671-2690
Review article
2011

The Influence of Microgravity on Invasive Growth in Saccharomyces cerevisiae

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

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

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

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

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

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

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

Genome-scale metabolic models of Saccharomyces cerevisiae

Intawat Nookaew, Roberto Olivares Hernandez, S. Bhumiratana et al
Methods in Molecular Biology. Vol. 759, p. 445-463
Book chapter
2011

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

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

Prospects for microbial biodiesel production

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

Synergies between synthetic biology and metabolic engineering

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

Fermentation kinetics: Central and modern concepts

Jens B Nielsen
Fermentation Microbiology and Biotechnology, Third Edition, p. 37-76
Book chapter
2011

Versatile Enzyme Expression and Characterization System for Aspergillus nidulans, with the Penicillium brevicompactum Polyketide Synthase Gene from the Mycophenolic Acid Gene Cluster as a Test Case

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

MEMOSys: Bioinformatics platform for genome-scale metabolic models

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

BIOFUELS Chimeric synthetic pathways

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

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

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

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

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

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

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

Industrial systems biology

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

Transcriptional control of metabolic fluxes

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

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

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

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

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

Opportunities for yeast metabolic engineering: Lessons from synthetic biology

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

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

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

Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae

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

Molecular Basis for Mycophenolic Acid Biosynthesis in Penicillium brevicompactum

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

Prospects for systems biology and modeling of the gut microbiome

Fredrik Karlsson, Intawat Nookaew, Dina Petranovic Nielsen et al
Trends in Biotechnology. Vol. 29 (6), p. 251-258
Journal article
2011

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

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

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

Marija Cvijovic, Sergio Velasco, Jens B Nielsen
Microbial Biotechnology. Vol. 4 (5), p. 572-584
Journal article
2010

BioMet Toolbox: genome-wide analysis of metabolism

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

Systems Biology of lipid metabolism: From yeast to human

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

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

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

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

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

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

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

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

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

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: e12781-11
Journal article
2010

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

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

Systems biology of microorganisms

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

Industrial Systems Biology

José Manuel Otero, Jens B Nielsen
Industrial Biotechnology: Sustainable Growth and Economic Success, p. 79-147
Book chapter
2010

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

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

Use of genome-scale metabolic models for understanding microbial physiology

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

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

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

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

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

Transcriptional progression of atrophic gastritis development in humans

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

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

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

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

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

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

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

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

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

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

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

Toward Design-based Engineering of Industrial Microbes

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

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

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

Systems Biology of Industrial Microorganisms

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

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

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

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

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

Industrial Systems Biology

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

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

Roberto Olivares Hernandez, R. Usaite, Jens B Nielsen
Biotechnology and Bioengineering. Vol. 107 (5), p. 865-875
Journal article
2010

Systems biology of energy homeostasis in yeast

Jie Zhang, Goutham Vemuri, Jens B Nielsen
Current Opinion in Microbiology. Vol. 13 (3), p. 382-388
Journal article
2009

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3

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

Systemic analysis of the response of Aspergillus niger to ambient pH

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

Genome-wide analysis of maltose utilization and regulation in aspergilli

Wanwipa Vongsangnak, Margarita Salazar Pena, Kim Hansen et al
Microbiology. Vol. 155 (12), p. 3893-3902
Journal article
2009

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

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

Yeast as a Prototype for Systems Biology

Goutham Vemuri, Jens B Nielsen
Systems Biology and Synthetic Biology, p. 287-353
Book chapter
2009

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

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

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

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

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

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

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

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

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

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

Random sampling of metabolic networks

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

Systems biology of lipid metabolism: From yeast to human

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

Structure and flux analysis of metabolic networks

K. R. Patil, P. M. Bapat, Jens B Nielsen
The Metabolic Pathway Engineering Handbook: Fundamentals, p. 17 1-17 18
Book chapter
2009

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

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

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

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

Physiological characterisation of acuB deletion in Aspergillus niger

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

Developing appropriate hosts for metabolic engineering (Section V. - Introduction)

Jens B Nielsen
The Metabolic Pathway Engineering Handbook: Fundamentals, p. V1-V8
Book chapter
2009

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

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

Current status of systems biology in Aspergilli

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

Nutritional Systems Biology: Definitions and Approaches

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

Qualification of flux control in metabolic pathways

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

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

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

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

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

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

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

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

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

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

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

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

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

Recombinant bacterial hemoglobin alters metabolism of Aspergillus niger

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

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

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

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

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

Metabolic engineering of streptomyces

I. Borodina, Anna Eliasson, Jens B Nielsen
The Metabolic Pathway Engineering Handbook: Fundamentals, p. 24-1-24-30
Book chapter
2009

Vintage paper - Introduction

Jens B Nielsen
Biotechnology and Bioengineering. Vol. 103 (1), p. 1-59
Journal article
2008

A trispecies Aspergillus microarray: Comparative transcriptomics of three Aspergillus species

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

Analysis of Aspergillus nidulans metabolism at the genome-scale

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

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

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

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

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

Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae

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

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

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

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

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

Systems biology: Is the hope worth the hype

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

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

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

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

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

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

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

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

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

Penicillium chrysogenum is involved in regulation of b-lactam production

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

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

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

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

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

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

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

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

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

Metabolomics. Topics in Current Genetics

Jens B Nielsen
Springer Verlag, Heidelberg. Vol. 18
Journal article
2008

Characterization of Global Yeast Quantitative Proteome Data Generated from the Wild-Type and Glucose Repression Saccharomyces cerevisiae Strains: The comparison of two Quantitative Methods

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

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

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

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

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

Promise and reality of systems biology in elucidating cellular behavior: Studying global regulation in yeast

Gregory Stephanopoulos, Joel F. Moxley, Maciek R. Antoniewicz et al
2008 AIChE Annual Meeting, AIChE 100; Philadelphia, PA; United States; 16 November 2008 through 21 November 2008
Paper in proceeding
2008

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

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

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Showing 31 research projects

2019–2021

Production of Benzylisoquinoline Alkaloids in Yeast

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

2 publications exist
2018–

Engineering a robust biocatalyst for sustainable biofuel production

Eduard Kerkhoven Systems and Synthetic Biology
Jens B Nielsen Systems and Synthetic Biology
Chalmers

2018–2021

Mätning av glykosaminoglykaner till cancerdiagnostik

Jens B Nielsen Systems and Synthetic Biology
Cancerfonden

2018–2021

Fat from wood: Optimizing the yeast Yarrowia lipolytica for defined composition food oil production from lignocellulosic hydrolysate

Jens B Nielsen Systems and Synthetic Biology
Joakim Norbeck Systems and Synthetic Biology
Formas

4 publications exist
2017–2020

Proof of concept: Glycosaminoglyucan profiling as a novel pan-cancer minimally invasive systems biomarker

Jens B Nielsen Systems and Synthetic Biology
Knut and Alice Wallenberg Foundation

2017–2022

Systembiologi av eukaryal proteinsekretion

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

2017–2020

Biobaserad produktion av diesel och jetbränsle

Jens B Nielsen Systems and Synthetic Biology
Swedish Energy Agency

2017–2019

Syntetisk biologi för biosyntes och produktion av naturliga produkter

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

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 (EC)

7 publications exist
2016–2020

Predictive and Accelerated Metabolic Engineering Network (PAcMEN)

Jens B Nielsen Systems and Synthetic Biology
European Commission (EC)

4 publications exist
2016–2022

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

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk Foundation

2 publications exist
2016–2020

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

Jens B Nielsen Systems and Synthetic Biology
European Commission (EC)

8 publications exist
2016–2017

Mapping the Transcription Factor Network of Yeast

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

2016–2019

Transkriptionsreglering i jäst på genomnivå

Jens B Nielsen Systems and Synthetic Biology
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

2015–2021

Biological Production Systems 2014

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

2 publications exist
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)

1 publication exists
2014–2016

Biopetrolia

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk 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)

André Kelkkanen Innovationskontor Väst
Jens B Nielsen Systems and Synthetic Biology
Region Västra Götaland

1 publication exists
2013–2017

Quantitative Biology for Fungal Secondary Metabolite Producers (QUANTFUNG)

Jens B Nielsen System Biology
European Commission (EC)

2013–2017

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

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

3 publications exist
2013–2015

MetaboGen

Jens B Nielsen Systems and Synthetic Biology
Novo Nordisk Foundation

2013–2017

Biobased production of diesel and jetfuel

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

2012–2017

Engineering the Secretory Pathway for Recombinant Protein Secretion in Saccharomyces cerevisiae

Mingtao Huang Systems and Synthetic Biology
Jens B Nielsen Systems and Synthetic Biology
Dina Petranovic Nielsen Systems and Synthetic Biology
Chalmers
Novo Nordisk Foundation
Knut and Alice Wallenberg Foundation

2012–2017

Metagenomics in Cardiometabolic Diseases (METACARDIS)

Jens B Nielsen System Biology
European Commission (EC)

8 publications exist
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)

2012–2015

Infrastructure for Systems Biology - Europe (ISBE)

Jens B Nielsen System Biology
European Commission (EC)

2012–2017

Biomarkers For Enhanced Vaccine Safety (BioVacSafe)

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

2012–2015

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

Jens B Nielsen System Biology
Torsten Söderbergs Stiftelse

2010–2014

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

Jens B Nielsen System Biology
European Commission (EC)

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