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.

Source: orcid.org
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Showing 650 publications

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
2022

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

Yijin Zhao, Kaiwen Meng, Jinyu Fu et al
Folia Microbiologica. Vol. In Press
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

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

Xinyi Tan, Jens B Nielsen
Chemical Society Reviews. Vol. In Press
Review 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

Innovation trends in industrial biotechnology

Jens B Nielsen, Christian Brix Tillegreen, Dina Petranovic Nielsen
Trends in Biotechnology. Vol. In Press
Review 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
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

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

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

Feiran Li, Le Yuan, Hongzhong Lu et al
NATURE CATALYSIS. Vol. In Press
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

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

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

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

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

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

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

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

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

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

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

GotEnzymes: an extensive database of enzyme parameter predictions

Feiran Li, Yu Chen, Petre Mihail Anton et al
Nucleic Acids Research. Vol. In Press
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

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

Harnessing synthetic biology for mushroom farming

Gen Zou, Jens B Nielsen, Yongjun Wei
Trends in Biotechnology. Vol. In Press
Other text in scientific journal
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

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

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

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

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

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. In Press
Journal article
2022

Cellular limitation of enzymatic capacity explains glutamine addiction in cancers

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

Microbiome-derived ethanol in nonalcoholic fatty liver disease

A. S. Meijnikman, Mark Davids, H. Herrema et al
Nature Medicine. Vol. In Press
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

Metabolic reconfiguration enables synthetic reductive metabolism in yeast

Tao Yu, Quanli Liu, Xiang Wang et al
Nature Metabolism. Vol. In Press
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
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

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

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

A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance

Tyler Doughty, Rosemary Brown, Fang Chao et al
BMC Genomics. Vol. 22 (1)
Journal article
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

Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion

Yanyan Wang, Xiaowei Li, Xin Chen et al
Microbial Cell Factories. Vol. 20 (1)
Journal article
2021

INetModels 2.0: An interactive visualization and database of multi-omics data

Muhammad Arif, C. Zhang, Xiangyu Li et al
Nucleic Acids Research. Vol. 49 (W1), p. W271-W276
Journal article
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

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 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 Yu, Egor Vorontsov, C. Sihlbom et al
eLife. Vol. 10
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

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

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

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

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

Benjamín José Sánchez, Petri-Jaan Lahtvee, Kate Campbell et al
Proteomics. Vol. 21 (6)
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

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

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

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

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

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

Zihe Liu, Zhenquan Lin, Jens B Nielsen
Synthetic and Systems Biotechnology. Vol. 6 (1), p. 20-22
Journal article
2021

Strategies and challenges with the microbial conversion of methanol to high-value chemicals

Chunjun Zhan, Xiaowei Li, Yankun Yang et al
Biotechnology and Bioengineering. Vol. 118 (10), p. 3655-3668
Review 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

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

Combinatorial, additive and dose-dependent drug–microbiome associations

Sofia K. Forslund, Rima Chakaroun, Maria Zimmermann-Kogadeeva et al
Nature. Vol. 600 (7889), p. 500-505
Journal article
2021

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Linnea Österberg, Iván Domenzain Del Castillo Cerecer, Julia Münch et al
PLoS Computational Biology. Vol. 17 (4)
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

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

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

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

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

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

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Gang Li, Yating Hu, Jan Zrimec et al
Nature Communications. Vol. 12 (1)
Journal article
2021

A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic liver disease

Hong Yang, Muhammad Arif, Meng Yuan et al
ISCIENCE. Vol. 24 (11)
Journal article
2021

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Saleh Alseekh, Asaph Aharoni, Yariv Brotman et al
Nature Methods. Vol. 18 (7), p. 747-756
Review article
2021

CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention

Jun Geng, Boyang Ji, Gang Li et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (13)
Journal article
2021

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

Carl Malina, Francesca Di Bartolomeo, Eduard Kerkhoven et al
ISCIENCE. Vol. 24 (11)
Journal article
2021

Addressing the heterogeneity in liver diseases using biological networks

Simon Lam, Stephen Doran, Hatice Hilal Yuksel et al
Briefings in Bioinformatics. Vol. 22 (2), p. 1751-1766
Review 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

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

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

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

The yeastGemMap: A process diagram to assist yeast systems-metabolic studies

Luis Caspeta-Guadarrama, Eduard Kerkhoven, Alfredo Martinez et al
Biotechnology and Bioengineering. Vol. 118 (12), p. 4800-4814
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

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Yu Chen, Eunice van Pelt-KleinJan, Berdien van Olst et al
Molecular Systems Biology. Vol. 17 (4)
Journal article
2021

Fatty acid synthesis is required for breast cancer brain metastasis

Gino B. Ferraro, Ahmed Ali, Alba Luengo et al
Nature Cancer. Vol. 2 (4), p. 414-428
Journal article
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

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Hongzhong Lu, Feiran Li, Le Yuan et al
Molecular Systems Biology. Vol. 17 (10)
Journal article
2020

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

John Hellgren, Alexei Godina, Jens B Nielsen et al
Metabolic Engineering. Vol. 62, p. 150-160
Journal article
2020

A systems biology approach for studying neurodegenerative diseases

Simon Lam, Abdulahad Bayraktar, C. Zhang et al
Drug Discovery Today. Vol. 25 (7), p. 1146-1159
Review article
2020

Current Status of COVID-19 Therapies and Drug Repositioning Applications

Ozlem Altay, Elyas Mohammadi, Simon Lam et al
iScience. Vol. 23 (7)
Review article
2020

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

Yiming Zhang, Mo Su, Ning Qin et al
Microbial Cell Factories. Vol. 19 (1)
Journal article
2020

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

Angelo Limeta, Boyang Ji, Max Levin et al
JCI Insight. Vol. 5 (23)
Journal article
2020

Current state of aromatics production using yeast: achievements and challenges

Quanli Liu, Yi Liu, Yun Chen et al
Current Opinion in Biotechnology. Vol. 65, p. 65-74
Review article
2020

Rewiring carbon flux in Escherichia coli using a bifunctional molecular switch

Jianshen Hou, Cong Gao, Liang Guo et al
Metabolic Engineering. Vol. 61, p. 47-57
Journal article
2020

Evolution from adherent to suspension: systems biology of HEK293 cell line development

Magdalena Malm, Rasool Saghaleyni, Magnus Lundqvist et al
Scientific Reports. Vol. 10 (1)
Journal article
2020

An atlas of human metabolism

Jonathan Robinson, Pinar Kocabas, Hao Wang et al
Science signaling. Vol. 13 (624)
Journal article
2020

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

Christoph Sebastian Börlin, Jens B Nielsen, Verena Siewers
FEMS Microbiology Letters. Vol. 367 (13)
Journal article
2020

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

Johan Gustafsson, Jonathan Robinson, Juan Salvador Inda Diaz et al
PLoS ONE. Vol. 15 (12 December)
Journal article
2020

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

Nachon Raethong, Hao Wang, Jens B Nielsen et al
Computational and Structural Biotechnology Journal. Vol. 18, p. 1-8
Journal article
2020

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

Francesca Di Bartolomeo, Carl Malina, Kate Campbell et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (13), p. 7524-7535
Journal article
2020

Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media

Johan Björkeroth, Kate Campbell, Carl Malina et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (35), p. 21804-21812
Journal article
2020

Building blocks are synthesized on demand during the yeast cell cycle

Kate Campbell, Jakub Westholm, Sergo Kasvandik et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (14), p. 7575-7583
Journal article
2020

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

Zihe Liu, Kai Wang, Yun Chen et al
NATURE CATALYSIS. Vol. 3 (3), p. 274-288
Review article
2020

Pan-cancer analysis of the metabolic reaction network

Francesco Gatto, Raphael Ferreira, Jens B Nielsen
Metabolic Engineering. Vol. 57, p. 51-62
Journal article
2020

Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts

Tyler Doughty, Iván Domenzain Del Castillo Cerecer, Aaron Millan-Oropeza et al
Nature Communications. Vol. 11 (1)
Journal article
2020

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

Sara Vieira-Silva, Gwen Falony, Eugeni Belda et al
Nature. Vol. 581 (7808), p. 310-315
Journal article
2020

MEMOTE for standardized genome-scale metabolic model testing

Christian Lieven, Moritz E. Beber, Brett G. Olivier et al
Nature Biotechnology. Vol. 38 (3), p. 272-276
Other text in scientific journal
2020

The role of peroxisomes in xylose alcoholic fermentation in the engineered Saccharomyces cerevisiae

Ljubov Dzanaeva, Barbara Kruk, Justyna Ruchala et al
Cell Biology International. Vol. 44 (8), p. 1606-1615
Journal article
2020

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

C. Zhang, Elias Björnson, Muhammad Arif et al
Molecular Systems Biology. Vol. 16 (4)
Journal article
2020

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

Daniel John Cook, Jonatan Kallus, Rebecka Jörnsten et al
Cancer Medicine. Vol. 9 (10), p. 3551-3562
Journal article
2020

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

Mehmet Ozcan, Ozlem Altay, Simon Lam et al
ADVANCED BIOSYSTEMS. Vol. 4 (6)
Review article
2020

Editorial: yeast synthetic biology

Jin Hou, Jens B Nielsen
FEMS Yeast Research. Vol. 20 (6)
Other text in scientific journal
2020

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

Xiangyu Li, Beste Turanli, Kajetan Juszczak et al
Heliyon. Vol. 6 (2)
Journal article
2020

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

J. Zhang, Søren D. Petersen, Tijana Radivojevic et al
Nature Communications. Vol. 11 (1)
Journal article
2020

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

Sakda Khoomrung, Intawat Nookaew, Partho Sen et al
Journal of Proteome Research. Vol. 19 (1), p. 269-278
Journal article
2020

Metabolic Engineering of Saccharomyces cerevisiae for Rosmarinic Acid Production

Mahsa Babaei, Gheorghe M. Borja Zamfir, Xiao Chen et al
ACS Synthetic Biology. Vol. 9 (8), p. 1978-1988
Journal article
2020

Different routes of protein folding contribute to improved protein production in saccharomyces cerevisiae

Qi Qi, Feiran Li, Rosemary Yu et al
mBio. Vol. 11 (6), p. 1-12
Journal article
2020

Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production

Yi Liu, Quanli Liu, Anastasia Krivoruchko et al
Nature Chemical Biology. Vol. 16 (2), p. 197-205
Journal article
2020

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

Marie Palmnäs, Carl Brunius, Lin Shi et al
Advances in nutrition (Bethesda, Md.). Vol. 11 (3), p. 524-532
Review article
2020

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

Elyas Mohammadi, Rui Benfeitas, Hasan Turkez et al
Cancers. Vol. 12 (9), p. 1-24
Review article
2020

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Stefania Vaga, Sunjae Lee, Boyang Ji et al
Scientific Reports. Vol. 10 (1)
Journal article
2020

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

Antonio Molinaro, Pierre Bel Lassen, Marcus Henricsson et al
Nature Communications. Vol. 11 (1)
Journal article
2020

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

Ning Qin, Lingyun Li, Xu Ji et al
ACS Synthetic Biology. Vol. 9 (12), p. 3236-3244
Journal article
2020

Advances in Metabolic Engineering of Saccharomyces cerevisiae for Cocoa Butter Equivalent Production

Mengge Wang, Yongjun Wei, Boyang Ji et al
Frontiers in Bioengineering and Biotechnology. Vol. 8
Review article
2020

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

Jahir M. Gutierrez, Amir Feizi, Shangzhong Li et al
Nature Communications. Vol. 11 (1)
Journal article
2020

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Jan Zrimec, Christoph Sebastian Börlin, Filip Buric et al
Nature Communications. Vol. 11 (1)
Journal article
2020

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

Tao Yu, Kate Campbell, Rui Pereira et al
Nature Communications. Vol. 11 (1)
Journal article
2020

Comprehensive understanding of Saccharomyces cerevisiae phenotypes with whole-cell model WM_S288C

Chao Ye, Nan Xu, Cong Gao et al
Biotechnology and Bioengineering. Vol. 117 (5), p. 1562-1574
Journal article
2020

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

Yating Hu, Zhu Zhiwei, David Gradischnig et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (37), p. 22974-22983
Journal article
2020

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

K. S. Pedersen, Francesco Gatto, Bo Zerahn et al
iScience. Vol. 23 (4)
Journal article
2020

Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution

Rui Pereira, Elsayed Mohamed, Mohammad Radi et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (45), p. 27954-27961
Journal article
2020

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis

Avlant Nilsson, J. R. Haanstra, Martin Engqvist et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 117 (19), p. 10294-10304
Journal article
2020

Sources of variation in cell-type RNA-Seq profiles

Johan Gustafsson, Felix Held, Jonathan Robinson et al
PLoS ONE. Vol. 15 (9), p. e0239495-
Journal article
2020

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
Review article
2020

Multidimensional engineering of Saccharomyces cerevisiae for efficient synthesis of medium-chain fatty acids

Zhu Zhiwei, Yating Hu, Paulo Teixeira et al
Nature Catalysis. Vol. 3 (1), p. 64-74
Journal article
2020

Pathway engineering in yeast for synthesizing the complex polyketide bikaverin

Meng Zhao, Yu Zhao, Mingdong Yao et al
Nature Communications. Vol. 11 (1)
Journal article
2020

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

Zhenquan Lin, Jens B Nielsen, Zihe Liu
Frontiers in Bioengineering and Biotechnology. Vol. 8
Review article
2019

Yeast Systems Biology: Model Organism and Cell Factory

Jens B Nielsen
Biotechnology journal. Vol. 14 (9)
Review article
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
Journal article
2019

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)
Journal article
2019

Big data in yeast systems biology

Tao Yu, Jens B Nielsen
FEMS Yeast Research. Vol. 19 (7)
Review article
2019

Modelling approaches for studying the microbiome

Manish Kumar, Boyang Ji, Karsten Zengler et al
Nature Microbiology. Vol. 4 (8), p. 1253-1267
Review article
2019

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
Journal article
2019

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)
Journal article
2019

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
Journal article
2019

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
Journal article
2019

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)
Journal article
2019

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)
Journal article
2019

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
Journal article
2019

The human secretome

Mathias Uhlen, Max J. Karlsson, Andreas Hober et al
Science signaling. Vol. 12 (609)
Journal article
2019

Metagenomic analysis of bile salt biotransformation in the human gut microbiome

Promi Das, Simonas Marcisauskas, Boyang Ji et al
BMC Genomics. Vol. 20 (1)
Journal article
2019

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
Journal article
2019

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)
Journal article
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)
Journal article
2019

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
Journal article
2019

Tackling Cancer with Yeast-Based Technologies

Raphael Ferreira, Angelo Limeta, Jens B Nielsen
Trends in Biotechnology. Vol. 37 (6), p. 592-603
Review article
2019

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, p. 329-345
Book chapter
2019

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
Journal article
2019

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
Journal article
2019

Complex I is bypassed during high intensity exercise

Avlant Nilsson, Elias Björnson, Mikael Flockhart et al
Nature Communications. Vol. 10 (1)
Journal article
2019

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)
Journal article
2019

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)
Journal article
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)
Journal article
2019

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
Journal article
2019

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
Journal article
2019

Recent trends in metabolic engineering of microbial chemical factories

Yi Liu, Jens B Nielsen
Current Opinion in Biotechnology. Vol. 60, p. 188-197
Review article
2019

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)
Journal article
2019

Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model

Simonas Marcisauskas, Boyang Ji, Jens B Nielsen
BMC Bioinformatics. Vol. 20 (1)
Journal article
2019

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
2019

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)
Journal article
2019

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
Review article
2019

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)
Journal article
2019

METABOLISM: A stress-coping strategy for yeast cells

Jens B Nielsen
Nature. Vol. 572 (7768), p. 184-185
Other text in scientific journal
2019

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
Journal article
2019

A bioinformatic pipeline to analyze ChIP-exo datasets

Christoph Sebastian Börlin, David Bergenholm, Petter Holland et al
Biology Methods and Protocols. Vol. 4 (1)
Journal article
2019

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
Journal article
2019

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)
Journal article
2019

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)
Journal article
2019

Cell factory engineering for improved production of natural products

Jens B Nielsen
Natural Product Reports. Vol. 36 (9), p. 1233-1236
Review article
2019

The pan-genome of Saccharomyces cerevisiae

Gang Li, Boyang Ji, Jens B Nielsen
FEMS Yeast Research. Vol. 19 (7)
Journal article
2019

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
Journal article
2019

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)
Journal article
2019

Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Promi Das, Parizad Babaei, Jens B Nielsen
BMC Genomics. Vol. 20 (1)
Journal 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 secretion in microorganisms: the theory of metabolic overflow put to the test

Farhana R. Pinu, Ninna Granucci, James Daniell et al
Metabolomics. Vol. 14 (4)
Review article
2018

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
Journal article
2018

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
Journal article
2018

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)
Journal article
2018

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)
Journal article
2018

Regulation of yeast-to-hyphae transition in Yarrowia lipolytica

Kyle R. Pomraning, Erin L. Bredeweg, Eduard Kerkhoven et al
mSphere. Vol. 3 (6)
Journal article
2018

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang, Simonas Marcisauskas, Benjamin José Sanchez Barja et al
PLoS Computational Biology. Vol. 14 (10), p. e1006541-
Journal article
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

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

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

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

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, p. 74-93
Book chapter
2018

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
Review 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

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

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

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

Drug Repositioning for Effective Prostate Cancer Treatment

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

Engineering the protein secretory pathway of Saccharomyces cerevisiae enables improved protein production

Mingtao Huang, Guokun Wang, Jiufu Qin et al
Proceedings of the National Academy of Sciences of the United States of America. Vol. 115 (47), p. E11025-E11032
Journal article
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

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)
Journal 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

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
Journal article
2018

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)
Journal article
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

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

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

Global rewiring of cellular metabolism renders Saccharomyces cerevisiae Crabtree negative

Zongijie Dai, Mingtao Huang, Yun Chen et al
Nature Communications. Vol. 9 (1)
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

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

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)
Journal article
2018

High-throughput microfluidics for the screening of yeast libraries

Mingtao Huang, H. N. Joensson, Jens B Nielsen
Synthetic Metabolic Pathways, p. 307-317
Book chapter
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

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
2018

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)
Journal article
2018

Investigation of putative regulatory acetylation sites in Fas2p of Saccharomyces cerevisiae

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

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
Review 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

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
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

Editorial: Where is scientific publishing heading?

Jens B Nielsen
FEMS Yeast Research. Vol. 17 (7)
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

Systems Biology of Metabolism

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

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

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

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

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

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

Genome scale metabolic modeling of cancer

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

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

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 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

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

Engineering Robustness of Microbial Cell Factories

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

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

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

Expanding the product portfolio of fungal type I fatty acid synthases

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

Systematic inference of functional phosphorylation events in yeast metabolism

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

Transcriptional reprogramming in yeast using dCas9 and combinatorial gRNA strategies

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

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

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

Efficient protein production by yeast requires global tuning of metabolism

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

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

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

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

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

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

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

METABOLISM: Built on stable catalysts

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

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

Systems Biology

Jens B Nielsen, Stefan Hohmann
Book
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

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 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

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

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

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

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
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

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

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

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

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

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

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

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

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

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

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

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

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

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

Avlant Nilsson, Jens B Nielsen
Scientific Reports. Vol. 6
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

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

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

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

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

Engineering of synthetic, stress-responsive yeast promoters

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

Flux control through protein phosphorylation in yeast

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

Adaptation to different types of stress converge on mitochondrial metabolism

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

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

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

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

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

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

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

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 yeast for high-level production of stilbenoid antioxidants

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

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

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

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

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

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

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

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

K. R. Kildegaard, N. B. Jensen, K. Schneider et al
Microbial Cell Factories. Vol. 15 (1)
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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

New insight into the gut microbiome through metagenomics

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

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

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

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

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

Cancer Metabolism: A Modeling Perspective

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

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

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
2015

HCSD: The human cancer secretome database

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

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

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

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

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

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

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

Tissue-based map of the human proteome

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

Networking in metabolism and human disease

Leif Väremo, Jens B Nielsen
Oncotarget. Vol. 6 (18), p. 15708-15709
Other text in scientific journal
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

Editorial

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

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

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

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

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

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

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

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

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

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

A. Ebrahim, E. Almaas, E. Bauer et al
Molecular Systems Biology. Vol. 11 (10), p. Article Number: 831-
Other text in scientific journal
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

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

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

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

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

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

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

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

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

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

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

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

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

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

How to set up collaborations between academia and industrial biotech companies

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

Metabolic engineering strategies for microbial synthesis of oleochemicals

B. F. Pfleger, Michael Gossing, Jens B Nielsen
Metabolic Engineering. Vol. 29, p. 1-11
Other text in scientific journal
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

Human metabolic atlas: an online resource for human metabolism

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

Finding directionality and gene-disease predictions in disease associations

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

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

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

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

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

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

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

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

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

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

Glucose repression in Saccharomyces cerevisiae

Ömur Kayikci, Jens B Nielsen
FEMS Yeast Research. Vol. 15 (6)
Other text in scientific journal
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

FEMS yeast research: the yeast community journal

Jens B Nielsen
FEMS Yeast Research. Vol. 15 (2)
Other text in scientific journal
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

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

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

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

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
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

Most influential FEMS publications

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

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

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

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

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

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

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

Altered sterol composition renders yeast thermotolerant

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

Engineering synergy in biotechnology

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

Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast

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

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

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

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

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

Maintaining a strong yeast research community

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

Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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