Jens B Nielsen

Full Professor at Systems and Synthetic Biology

Jens Nielsen is Professor of Quantitative Systems Biology.

Jens Nielsen has an MSc degree in Chemical Engineering and a PhD degree (1989) in Biochemical Engineering from the Danish Technical University (DTU), and after that established his independent research group and was appointed full Professor there in 1998. He was Fulbright visiting professor at MIT in 1995-1996. At DTU he founded and directed Center for Microbial Biotechnology. In 2008 he was recruited as Professor and Director to Chalmers University of Technology, Sweden, where he is directing a research group of more than 50 people. At Chalmers he established the Area of Advance Life Science Engineering, a cross departmental strategic research initiative and was founding Head of the Department of Biology and Biological Engineering, which now encompass more than 200 people. Jens Nielsen is also a co-founder of the Novo Nordisk Foundation Center for Biosustainability that now have more than 300 people affiliated, for which he served as Chief Science Officer in the period 2013-2018. In 2019 Jens Nielsen was appointed as CEO of the BioInnovation Institute in Denmark, which is a new institute that will foster translational research and support new spin-out companies in life sciences. Jens Nielsen has supervised more than 100 PhD students and more than 75 post doctoral researchers. He has published so far more than 700 papers that have been cited more than 65,000 times (current H-factor 118), and co-authored more than 40 books. He was identified as a highly cited researcher in 2015-2018. He is inventor of more than 50 patents and he has founded several biotech companies. He has received numerous Danish and international awards including the Nature Mentor Award, the ENI Award, the Eric and Sheila Samson Prime Minister Prize, the Novozymes Prize, and the Gold Medal from the Royal Swedish Academy of Engineering Sciences. He is member of several academies, including the National Academy of Engineering and National Academy of Science in USA, the Royal Swedish Academy of Science, the Royal Danish Academy of Science and Letters, the Royal Swedish Academy of Engineering Sciences and the American Academy of Microbiology. He is a founding president of the International Metabolic Engineering Society.

More information about publications and the other details:
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Source: chalmers.se
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Showing 702 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

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

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
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
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

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

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

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

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

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DSAVE: Detection of misclassified cells in single-cell RNA-Seq data

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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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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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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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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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Improvement in the Current Therapies for Hepatocellular Carcinoma Using a Systems Medicine Approach

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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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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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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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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)

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Scientific Reports. Vol. 9 (1)
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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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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
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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
Other text in scientific journal
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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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2019

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
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Predictive models of eukaryotic transcriptional regulation reveals changes in transcription factor roles and promoter usage between metabolic conditions

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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
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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
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Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree negative

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AMB Express. Vol. 8 (1)
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Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production

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Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

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Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

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Metabolic Network-Based Identification and Prioritization o f Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma

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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

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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

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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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An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans

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Cell Metabolism. Vol. 27 (3), p. 559-571.e5
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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

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Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors

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2018

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
Journal article
2018

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

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

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

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

Metabolic engineering of yeast for fermentative production of flavonoids

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

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

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
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

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

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

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

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
Other text in scientific journal
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
Other text in scientific journal
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