Jens B Nielsen (J Nielsen, Jens Nielsen)

Loop profile ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 136

Top Venues

Nature communications

Proceedings of the National Academy of Sciences of the United States of America

Molecular systems biology

Biotechnology and bioengineering

This page only lists publications with an associated author ORCID identifier.

Publications

Jens B Nielsen
Autotrophic yeast. Nature communications 15 (1) (2024)
Johan Gustafsson, Jonathan L Robinson, Henrik Zetterberg, Jens B Nielsen
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (2024)
Ning Qin, Lingyun Li, Xiaozhen Wan, Xu Ji, Yu Chen, Chaokun Li, Ping Liu, Yijie Zhang, Weijie Yang, Junfeng Jiang, Jian-Ye Xia, Shuobo Shi, Tianwei Tan, Jens B Nielsen, Yun Chen, Zihe Liu
Increased CO 2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast. Nature communications 15 (1) (2024)
Johan Gustafsson, Jonathan L Robinson, Henrik Zetterberg, Jens B Nielsen
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (2024)
Johan Gustafsson, Jonathan L Robinson, Henrik Zetterberg, Jens B Nielsen
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (2024)
Ning Qin, Lingyun Li, Xiaozhen Wan, Xu Ji, Yu Chen, Chaokun Li, Ping Liu, Yijie Zhang, Weijie Yang, Junfeng Jiang, Jian-Ye Xia, Shuobo Shi, Tianwei Tan, Jens B Nielsen, Yun Chen, Zihe Liu
Increased CO 2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast. Nature communications 15 (1) (2024)
Johan Gustafsson, Jonathan L Robinson, Henrik Zetterberg, Jens B Nielsen
Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport. Proceedings of the National Academy of Sciences of the United States of America 121 (7) (2024)
Jens B Nielsen
Autotrophic yeast. Nature communications 15 (1) (2024)
Ning Qin, Lingyun Li, Xiaozhen Wan, Xu Ji, Yu Chen, Chaokun Li, Ping Liu, Yijie Zhang, Weijie Yang, Junfeng Jiang, Jian-Ye Xia, Shuobo Shi, Tianwei Tan, Jens B Nielsen, Yun Chen, Zihe Liu
Increased CO 2 fixation enables high carbon-yield production of 3-hydroxypropionic acid in yeast. Nature communications 15 (1) (2024)
Jens B Nielsen
Autotrophic yeast. Nature communications 15 (1) (2024)
Dimitra Lappa, Abraham S Meijnikman, Kimberly A Krautkramer, Lisa M Olsson, Ömrüm Aydin, Anne-Sophie Van Rijswijk, Yair I Z Acherman, Maurits L De Brauw, Valentina Tremaroli, Louise E Olofsson, Annika Lundqvist, Siv A Hjorth, Boyang Ji, Victor E A Gerdes, Albert K Groen, Thue W Schwartz, Max Nieuwdorp, Fredrik Bäckhed, Jens B Nielsen
Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery. PloS one 18 (3) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Zhiyong Cui, Yutao Zhong, Zhijie Sun, Zhennan Jiang, Jingyu Deng, Qian Wang, Jens B Nielsen, Jin Hou, Qingsheng Qi
Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica. Nature communications 14 (1) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Dimitra Lappa, Abraham S Meijnikman, Kimberly A Krautkramer, Lisa M Olsson, Ömrüm Aydin, Anne-Sophie Van Rijswijk, Yair I Z Acherman, Maurits L De Brauw, Valentina Tremaroli, Louise E Olofsson, Annika Lundqvist, Siv A Hjorth, Boyang Ji, Victor E A Gerdes, Albert K Groen, Thue W Schwartz, Max Nieuwdorp, Fredrik Bäckhed, Jens B Nielsen
Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery. PloS one 18 (3) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Dimitra Lappa, Abraham S Meijnikman, Kimberly A Krautkramer, Lisa M Olsson, Ömrüm Aydin, Anne-Sophie Van Rijswijk, Yair I Z Acherman, Maurits L De Brauw, Valentina Tremaroli, Louise E Olofsson, Annika Lundqvist, Siv A Hjorth, Boyang Ji, Victor E A Gerdes, Albert K Groen, Thue W Schwartz, Max Nieuwdorp, Fredrik Bäckhed, Jens B Nielsen
Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery. PloS one 18 (3) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Francesco Gatto, Sinisa Bratulic, Eric Jonasch, Angelo Limeta, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Sven Lundstam, Jens B Nielsen, Ulrika Stierner
Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study. JCO precision oncology 7 (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Francesco Gatto, Sinisa Bratulic, Eric Jonasch, Angelo Limeta, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Sven Lundstam, Jens B Nielsen, Ulrika Stierner
Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study. JCO precision oncology 7 (2023)
Dimitra Lappa, Abraham S Meijnikman, Kimberly A Krautkramer, Lisa M Olsson, Ömrüm Aydin, Anne-Sophie Van Rijswijk, Yair I Z Acherman, Maurits L De Brauw, Valentina Tremaroli, Louise E Olofsson, Annika Lundqvist, Siv A Hjorth, Boyang Ji, Victor E A Gerdes, Albert K Groen, Thue W Schwartz, Max Nieuwdorp, Fredrik Bäckhed, Jens B Nielsen
Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery. PloS one 18 (3) (2023)
Zhiyong Cui, Yutao Zhong, Zhijie Sun, Zhennan Jiang, Jingyu Deng, Qian Wang, Jens B Nielsen, Jin Hou, Qingsheng Qi
Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica. Nature communications 14 (1) (2023)
Min Chen, Tingting Xie, Huan Li, Yingping Zhuang, Jianye Xia, Jens B Nielsen
Yeast increases glycolytic flux to support higher growth rates accompanied by decreased metabolite regulation and lower protein phosphorylation. Proceedings of the National Academy of Sciences of the United States of America 120 (25) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir, Rebecka Jörnsten, Eduard Johannes Kerkhoven, Jonathan L Robinson, Jens B Nielsen
Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America 120 (6) (2023)
Jens B Nielsen
Engineering yeast to produce plant-derived anti-obesity agent. Nature chemistry (2023)
Francesco Gatto, Sinisa Bratulic, Eric Jonasch, Angelo Limeta, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Sven Lundstam, Jens B Nielsen, Ulrika Stierner
Plasma and Urine Free Glycosaminoglycans as Monitoring and Predictive Biomarkers in Metastatic Renal Cell Carcinoma: A Prospective Cohort Study. JCO precision oncology 7 (2023)
Zhiyong Cui, Yutao Zhong, Zhijie Sun, Zhennan Jiang, Jingyu Deng, Qian Wang, Jens B Nielsen, Jin Hou, Qingsheng Qi
Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica. Nature communications 14 (1) (2023)
Hongzhong Lu, Feiran Li, Le Yuan, Iván Domenzain, Rosemary Yu, Hao Wang, Gang Li, Yu Chen, Boyang Ji, Eduard Johannes Kerkhoven, Jens B Nielsen
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Molecular systems biology 17 (10) (2022)
Yu Chen, Feiran Li, Jens B Nielsen
Genome-scale modeling of yeast metabolism: retrospectives and perspectives. FEMS yeast research 22 (1) (2022)
Yu Chen, Jens B Nielsen
Yeast has evolved to minimize protein resource cost for synthesizing amino acids. Proceedings of the National Academy of Sciences of the United States of America 119 (4) (2022)
Feiran Li, Yu Chen, Qi Qi, Yanyan Wang, Le Yuan, Mingtao Huang, Ibrahim E Elsemman, Amir Feizi, Eduard Johannes Kerkhoven, Jens B Nielsen
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints. Nature communications 13 (1) (2022)
Sinisa Bratulic, Angelo Limeta, Saeed Dabestani, Helgi Birgisson, Gunilla Enblad, Karin Stålberg, Göran Hesselager, Michael Häggman, Martin Höglund, Oscar E Simonson, Peter Stålberg, Henrik Lindman, Anna Bång-Rudenstam, Matias Ekstrand, Gunjan Kumar, Ilaria Cavarretta, Massimo Alfano, Francesco Pellegrino, Thomas Mandel-Clausen, Ali Salanti, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Mads Daugaard, Mattias Belting, Sven Lundstam, Ulrika Stierner, Jan Nyman, Bengt Bergman, Per-Henrik D Edqvist, Max Levin, Alessia d'Arma, Henrik Kjölhede, Eric Jonasch, Jens B Nielsen, Francesco Gatto
Noninvasive detection of any-stage cancer using free glycosaminoglycans. Proceedings of the National Academy of Sciences of the United States of America 119 (50) (2022)
Fariba Roshanzamir, Jonathan L Robinson, Daniel Cook, Mohammad Hossein Karimi-Jafari, Jens B Nielsen
Metastatic triple negative breast cancer adapts its metabolism to destination tissues while retaining key metabolic signatures. Proceedings of the National Academy of Sciences of the United States of America 119 (35) (2022)
Jan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K Speicher, Christoph S Börlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt Dubhashi, Verena Siewers, Florian David, Jens B Nielsen, Aleksej Zelezniak
Controlling gene expression with deep generative design of regulatory DNA. Nature communications 13 (1) (2022)
Jens B Nielsen, Markus J Herrgård, Bobby Soni
The BioInnovation Institute as a catalyst for European life science startup creation. Nature biotechnology 40 (8) (2022)
Peishun Li, Boyang Ji, Hao Luo, Daniel Sundh, Mattias Lorentzon, Jens B Nielsen
One-year supplementation with Lactobacillus reuteri ATCC PTA 6475 counteracts a degradation of gut microbiota in older women with low bone mineral density. NPJ biofilms and microbiomes 8 (1) (2022)
Ibrahim E Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia-Albornoz, Victoria Harman, Stephen W Holman, Johan H van Heerden, Frank J Bruggeman, Markus M M Bisschops, Nikolaus Sonnenschein, Simon J Hubbard, Robert J Beynon, Pascale Daran-Lapujade, Jens B Nielsen, Bas Teusink
Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nature communications 13 (1) (2022)
Carl Malina, Rosemary Yu, Johan Björkeroth, Eduard Johannes Kerkhoven, Jens B Nielsen
Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast. Proceedings of the National Academy of Sciences of the United States of America 118 (51) (2022)
Tingting Xie, Min Chen, Jens B Nielsen, Jianye Xia
Multi-omics analyses of the transition to the Crabtree effect in S. cerevisiae reveals a key role for the citric acid shuttle. FEMS yeast research 22 (1) (2022)
Sebastien Fromentin, Sofia Kirke Forslund-Startceva, Kanta Chechi, Judith Aron-Wisnewsky, Rima Chakaroun, Trine Nielsen, Valentina Tremaroli, Boyang Ji, Edi Prifti, Antonis Myridakis, Julien Chilloux, Petros Andrikopoulos, Yong Fan, Michael T Olanipekun, Renato Jc Alves, Solia Adiouch, Noam Bar, Yeela Talmor-Barkan, Eugeni Belda, Robert Caesar, Luis Pedro Coelho, Gwen Falony, Soraya Fellahi, Pilar Galan, Nathalie Galleron, Gerard Helft, Lesley Hoyles, Richard Isnard, Emmanuelle Le Chatelier, Hanna Julienne, Lisa M Olsson, Helle Krogh Pedersen, Nicolas Pons, Benoit Quinquis, Christine Rouault, Hugo Roume, Joe-Elie Salem, Thomas Sebastian Benedikt Schmidt, Sara Vieira-Silva, Peishun Li, Maria Zimmermann-Kogadeeva, Christian Lewinter, Nadja B Sønderskov, Tue Haldor Hansen, Dominique Gauguier, Jens Peter Gøtze, Lars Valeur Køber, Ran Kornowski, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Serge Hercberg, Ivica Letunic, Fredrik Bäckhed, Jean-Michel Oppert, Jens B Nielsen, Jeroen Raes, Peer Bork, Michael Stumvoll, Eran Segal, Karine Clement, Marc Emmanuel Dumas, Stanislav Dusko Ehrlich, Oluf Pedersen
Microbiome and metabolome features of the cardiometabolic disease spectrum. Nature medicine 28 (2) (2022)
Xinyi Tan, Jens B Nielsen
The integration of bio-catalysis and electrocatalysis to produce fuels and chemicals from carbon dioxide. Chemical Society reviews 51 (11) (2022)
Mujdat Zeybel, Ozlem Altay, Muhammad Arif, Xiangyu Li, Hong Yang, Claudia Fredolini, Murat Akyildiz, Burcin Saglam, Mehmet Gökhan Gönenli, Dilek Ural, Woonghee Kim, Jochen M Schwenk, Cheng Zhang, Saeed Shoaie, Jens B Nielsen, Mathias Uhlén, Jan Borén, Adil Mardinglu
Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients. Molecular systems biology 17 (10) (2022)
Feiran Li, Yu Chen, Mihail Anton, Jens B Nielsen
GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic acids research (2022)
Neelu Begum, Sunjae Lee, Theo John Portlock, Aize Pellon, Shervin Dokht Sadeghi Nasab, Jens B Nielsen, Mathias Uhlen, David L Moyes, Saeed Shoaie
Integrative functional analysis uncovers metabolic differences between Candida species. Communications biology 5 (1) (2022)
Olena P Ishchuk, Iván Domenzain, Benjamín J Sánchez, Facundo Muñiz-Paredes, José Luis Martinez, Jens B Nielsen, Dina Petranovic
Genome-scale modeling drives 70-fold improvement of intracellular heme production in Saccharomyces cerevisiae . Proceedings of the National Academy of Sciences of the United States of America 119 (30) (2022)
Iván Domenzain, Benjamín J Sánchez, Petre Mihail Anton, Eduard Johannes Kerkhoven, Aarón Millán-Oropeza, Céline Henry, Verena Siewers, John P Morrissey, Nikolaus Sonnenschein, Jens B Nielsen
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0. Nature communications 13 (1) (2022)
Gang Li, Filip Buric, Jan Zrimec, Sandra Viknander, Jens B Nielsen, Aleksej Zelezniak, Martin K M Engqvist
Learning deep representations of enzyme thermal adaptation. Protein science : a publication of the Protein Society 31 (12) (2022)
Jian-Ye Xia, Benjamin J Sánchez, Yu Chen, Kate Campbell, Sergo Kasvandik, Jens B Nielsen
Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation. Nature communications 13 (1) (2022)
Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Buğra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oğuzhan Subaş, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens B Nielsen, Mathias Uhlen, Adil Mardinglu
iNetModels 2.0: an interactive visualization and database of multi-omics data. Nucleic acids research 49 (W1) (2021)
Zhenquan Lin, Kang Xu, Guang Cai, Yangqingxue Liu, Yi Li, Zhihao Zhang, Jens B Nielsen, Shuobo Shi, Zihe Liu
Characterization of cross-species transcription and splicing from Penicillium to S. cerevisiae. Journal of industrial microbiology & biotechnology (2021)
Sofia Kirke Forslund-Startceva, Rima Chakaroun, Maria Zimmermann-Kogadeeva, Lajos Markó, Judith Aron-Wisnewsky, Trine Nielsen, Lucas Moitinho-Silva, Thomas S B Schmidt, Gwen Falony, Sara Vieira-Silva, Solia Adriouch, Renato Jc Alves, Karen Assmann, Jean-Philippe Bastard, Till Birkner, Robert Caesar, Julien Chilloux, Luis Pedro Coelho, Leopold Fezeu, Nathalie Galleron, Gerard Helft, Richard Isnard, Boyang Ji, Michael Kuhn, Emmanuelle Le Chatelier, Antonis Myridakis, Lisa M Olsson, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Joe-Elie Salem, Nataliya Sokolovska, Valentina Tremaroli, Mireia Valles-Colomer, Christian Lewinter, Nadja B Sønderskov, Helle Krogh Pedersen, Tue Haldor Hansen, null null, Jens Peter Gøtze, Lars Valeur Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Serge Hercberg, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Fredrik Bäckhed, Stanislav Dusko Ehrlich, Marc Emmanuel Dumas, Jeroen Raes, Oluf Pedersen, Karine Clement, Michael Stumvoll, Peer Bork
Combinatorial, additive and dose-dependent drug-microbiome associations. Nature (2021)
Saleh Alseekh, Asaph Aharoni, Yariv Brotman, Kevin Contrepois, John Charles D'Auria, Jan Ewald, Jennifer C Ewald, Paul D Fraser, Patrick Giavalisco, Robert D Hall, Matthias Heinemann, Hannes Link, Jie Luo, Steffen Neumann, Jens B Nielsen, Leonardo Perez de Souza, Takashi Hashimoto, Uwe Sauer, Frank C Schroeder, Stefan Schuster, Gary E Siuzdak, Aleksandra Skirycz, Lloyd W Sumner, Michael Paul Snyder, Huiru Tang, Takayuki Tohge, Yulan Wang, Weiwei Wen, Si Wu, Guo-Wang Xu, Nicola Zamboni, Alisdair Robert Fernie
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. Nature methods 18 (7) (2021)
Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens B Nielsen, Jonathan L Robinson
Machine learning-based investigation of the cancer protein secretory pathway. PLoS computational biology 17 (4) (2021)
Yu Chen, Feiran Li, Jiwei Mao, Yun Chen, Jens B Nielsen
Yeast optimizes metal utilization based on metabolic network and enzyme kinetics. Proceedings of the National Academy of Sciences of the United States of America 118 (12) (2021)
Tyler W Doughty, Rosemary Yu, Lucy Fang-I Chao, Zhongjun Qin, Verena Siewers, Jens B Nielsen
A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance. BMC genomics 22 (1) (2021)
Yu Chen, Jens B Nielsen
In vitro turnover numbers do not reflect in vivo activities of yeast enzymes. Proceedings of the National Academy of Sciences of the United States of America 118 (32) (2021)
Gang Li, Yating Hu, Jan Zrimec, Hao Luo, Hao Wang, Aleksej Zelezniak, Boyang Ji, Jens B Nielsen
Bayesian genome scale modelling identifies thermal determinants of yeast metabolism. Nature communications 12 (1) (2021)
Cheng Zhang, Elias Bjornson, Muhammad Arif, Abdellah Tebani, Alen Lovric, Rui Benfeitas, Mehmet Ozcan, Kajetan Juszczak, Woonghee Kim, Jung Tae Kim, Gholamreza Bidkhori, Marcus Ståhlman, Per-Olof Bergh, Martin Adiels, Hasan Turkez, Marja-Riitta Taskinen, Jim Bosley, Hanns-Ulrich Marschall, Jens B Nielsen, Mathias Uhlen, Jan Borén, Adil Mardinglu
The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease. Molecular systems biology 16 (4) (2021)
Yu Chen, Eunice van Pelt-KleinJan, Berdien van Olst, Sieze Douwenga, Sjef Boeren, Herwig Bachmann, Douwe Molenaar, Jens B Nielsen, Bas Teusink
Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments. Molecular systems biology 17 (4) (2021)
Benjamín J Sánchez, Petri-Jaan Lahtvee, Kate Campbell, Sergo Kasvandik, Rosemary Yu, Iván Domenzain, Aleksej Zelezniak, Jens B Nielsen
Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae. Proteomics 21 (6) (2021)
Linnea Österberg, Iván Domenzain, Julia Münch, Jens B Nielsen, Stefan Hohmann, Marija Cvijovic
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PLoS computational biology 17 (4) (2021)
Quanli Liu, Yi Liu, Gang Li, Otto Savolainen, Yun Chen, Jens B Nielsen
De novo biosynthesis of bioactive isoflavonoids by engineered yeast cell factories. Nature communications 12 (1) (2021)
Sonja Blasche, Yongkyu Kim, Ruben A T Mars, Daniel Machado, Maria Maansson, Eleni Kafkia, Alessio Milanese, Georg Zeller, Bas Teusink, Jens B Nielsen, Vladimir Benes, Rute Neves, Uwe Sauer, Kiran Raosaheb Patil
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community. Nature microbiology 6 (2) (2021)
Rosemary Yu, Egor Vorontsov, Carina Sihlbom, Jens B Nielsen
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast. eLife 10 (2021)
Yijin Zhao, Yueping Zhang, Jens B Nielsen, Zihe Liu
Production of β-carotene in Saccharomyces cerevisiae through altering yeast lipid metabolism. Biotechnology and bioengineering 118 (5) (2021)
Jens B Nielsen
Professor John Villadsen, PhD, Dr. techn., Dr. h. c. mult (12.6.1936-22.7.2021). Biotechnology and bioengineering 119 (1) (2021)
Jun Geng, Boyang Ji, Gang Li, Felipe López-Isunza, Jens B Nielsen
CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention. Proceedings of the National Academy of Sciences of the United States of America 118 (13) (2021)
David Bergenholm, Yasaman Dabirian, Raphael Ferreira, Verena Siewers, Florian David, Jens B Nielsen
Rational gRNA design based on transcription factor binding data. Synthetic biology (Oxford, England) 6 (1) (2021)
Hao Wang, Jonathan L Robinson, Pinar Kocabas, Johan Gustafsson, Petre Mihail Anton, Pierre-Etienne Cholley, Shan Huang, Johan Gobom, L Thomas Svensson, Mattias Uhlen, Henrik Zetterberg, Jens B Nielsen
Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proceedings of the National Academy of Sciences of the United States of America 118 (30) (2021)
Hongzhong Lu, Feiran Li, Benjamín J Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard Johannes Kerkhoven, Jens B Nielsen
Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature communications 11 (1) (2020)
Tyler W Doughty, Iván Domenzain, Aaron Millan-Oropeza, Noemi Montini, Philip A de Groot, Rui Pereira, Jens B Nielsen, Céline Henry, Jean-Marc G Daran, Verena Siewers, John P Morrissey
Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. Nature communications 11 (1) (2020)
Qi Qi, Feiran Li, Rosemary Yu, Martin K M Engqvist, Verena Siewers, Johannes Fuchs, Jens B Nielsen
Different Routes of Protein Folding Contribute to Improved Protein Production in Saccharomyces cerevisiae. mBio 11 (6) (2020)
Alyaa M Abdel-Haleem, Vaishnavi Ravikumar, Boyang Ji, Katsuhiko Mineta, Xin Gao, Jens B Nielsen, Takashi Gojobori, Ivan Mijakovic
Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. mSystems 5 (5) (2020)
Rui Pereira, Elsayed T Mohamed, Mohammad S Radi, Markus J Herrgård, Adam M Feist, Jens B Nielsen, Yun Chen
Elucidating aromatic acid tolerance at low pH in Saccharomyces cerevisiae using adaptive laboratory evolution. Proceedings of the National Academy of Sciences of the United States of America 117 (45) (2020)
Yating Hu, Zhiwei Zhu, David Gradischnig, Margit Winkler, Jens B Nielsen, Verena Siewers
Engineering carboxylic acid reductase for selective synthesis of medium-chain fatty alcohols in yeast. Proceedings of the National Academy of Sciences of the United States of America 117 (37) (2020)
Rosemary Yu, Kate Campbell, Rui Pereira, Johan Björkeroth, Qi Qi, Egor Vorontsov, Carina Sihlbom, Jens B Nielsen
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. Nature communications 11 (1) (2020)
Jan Zrimec, Christoph S Börlin, Filip Buric, Azam Sheikh Muhammad, Rhongzen Chen, Verena Siewers, Vilhelm Verendel, Jens B Nielsen, Mats Töpel, Aleksej Zelezniak
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nature communications 11 (1) (2020)
Francesca Di Bartolomeo, Carl Malina, Kate Campbell, Maurizio Mormino, Johannes Fuchs, Egor Vorontsov, Claes M Gustafsson, Jens B Nielsen
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. Proceedings of the National Academy of Sciences of the United States of America 117 (13) (2020)
Antonio Molinaro, Pierre Bel Lassen, Marcus Henricsson, Hao Wu, Solia Adriouch, Eugeni Belda, Rima Chakaroun, Trine Nielsen, Per-Olof Bergh, Christine Rouault, Sébastien André, Florian Marquet, Fabrizio Andreelli, Joe-Elie Salem, Karen Assmann, Jean-Philippe Bastard, Sofia Forslund, Emmanuelle Le Chatelier, Gwen Falony, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Sara Vieira-Silva, Tue Haldor Hansen, Helle Krogh Pedersen, Christian Lewinter, Nadja B Sønderskov, null null, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Pilar Galan, Marc Emmanuel Dumas, Jeroen Raes, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Peer Bork, Stanislav Dusko Ehrlich, Michael Stumvoll, Oluf Pedersen, Judith Aron-Wisnewsky, Karine Clement, Fredrik Bäckhed
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature communications 11 (1) (2020)
Antonio Molinaro, Pierre Bel Lassen, Marcus Henricsson, Hao Wu, Solia Adriouch, Eugeni Belda, Rima Chakaroun, Trine Nielsen, Per-Olof Bergh, Christine Rouault, Sébastien André, Florian Marquet, Fabrizio Andreelli, Joe-Elie Salem, Karen Assmann, Jean-Philippe Bastard, Sofia Forslund, Emmanuelle Le Chatelier, Gwen Falony, Nicolas Pons, Edi Prifti, Benoit Quinquis, Hugo Roume, Sara Vieira-Silva, Tue Haldor Hansen, Helle Krogh Pedersen, Christian Lewinter, Nadja B Sønderskov, null null, Lars Køber, Henrik Vestergaard, Torben Hansen, Jean-Daniel Zucker, Pilar Galan, Marc Emmanuel Dumas, Jeroen Raes, Jean-Michel Oppert, Ivica Letunic, Jens B Nielsen, Peer Bork, Stanislav Dusko Ehrlich, Michael Stumvoll, Oluf Pedersen, Judith Aron-Wisnewsky, Karine Clement, Fredrik Bäckhed
Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nature communications 11 (1) (2020)
Jonathan L Robinson, Pinar Kocabas, Hao Wang, Pierre-Etienne Cholley, Daniel J Cook, Avlant Nilsson, Petre Mihail Anton, Raphael Ferreira, Iván Domenzain, Virinchi Billa, Angelo Limeta, Alex Hedin, Johan Gustafsson, Eduard Johannes Kerkhoven, L Thomas Svensson, Bernhard O Palsson, Adil Mardinglu, Lena Hansson, Mathias Uhlen, Jens B Nielsen
An atlas of human metabolism. Science signaling 13 (624) (2020)
Avlant Nilsson, Jurgen R Haanstra, Martin K M Engqvist, Albert Gerding, Barbara M Bakker, Ursula Klingmüller, Bas Teusink, Jens B Nielsen
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. Proceedings of the National Academy of Sciences of the United States of America 117 (19) (2020)
Jahir M Gutierrez, Amir Feizi, Shangzhong Li, Thomas B Kallehauge, Hooman Hefzi, Lise M Grav, Daniel Ley, Deniz Baycin Hizal, Michael J Betenbaugh, Bjorn Voldborg, Helene Faustrup Kildegaard, Gyun Min Lee, Bernhard O Palsson, Jens B Nielsen, Nathan E Lewis
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion. Nature communications 11 (1) (2020)
Christian Lieven, Moritz Emanuel Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary A King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinglu, Gregory L Medlock, Jonathan M Monk, Jens B Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran Raosaheb Patil, Mark G Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
MEMOTE for standardized genome-scale metabolic model testing. Nature biotechnology 38 (3) (2020)
Meng Zhao, Yu Zhao, Mingdong Yao, Hala Iqbal, Qi Hu, Hong Liu, Bin Qiao, Chun Li, Christine A S Skovbjerg, Jens Christian Nielsen, Jens B Nielsen, Rasmus J N Frandsen, Ying-Jin Yuan, Jef D Boeke
Pathway engineering in yeast for synthesizing the complex polyketide bikaverin. Nature communications 11 (1) (2020)
Sara Vieira-Silva, Gwen Falony, Eugeni Belda, Trine Nielsen, Judith Aron-Wisnewsky, Rima Chakaroun, Sofia K Forslund, Karen Assmann, Mireia Valles-Colomer, Thi Thuy Duyen Nguyen, Sebastian Proost, Edi Prifti, Valentina Tremaroli, Nicolas Pons, Emmanuelle Le Chatelier, Fabrizio Andreelli, Jean-Phillippe Bastard, Luis Pedro Coelho, Nathalie Galleron, Tue H Hansen, Jean-Sébastien Hulot, Christian Lewinter, Helle K Pedersen, Benoit Quinquis, Christine Rouault, Hugo Roume, Joe-Elie Salem, Nadja B Sønderskov, Sothea Touch, null null, Marc Emmanuel Dumas, Stanislav Dusko Ehrlich, Pilar Galan, Jens P Gøtze, Torben Hansen, Jens Juul Holst, Lars Køber, Ivica Letunic, Jens B Nielsen, Jean-Michel Oppert, Michael Stumvoll, Henrik Vestergaard, Jean-Daniel Zucker, Peer Bork, Oluf Pedersen, Fredrik Bäckhed, Karine Clement, Jeroen Raes
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature 581 (7808) (2020)
Kate Campbell, Jakub Orzechowski Westholm, Sergo Kasvandik, Francesca Di Bartolomeo, Maurizio Mormino, Jens B Nielsen
Building blocks are synthesized on demand during the yeast cell cycle. Proceedings of the National Academy of Sciences of the United States of America 117 (14) (2020)
Johan Björkeroth, Kate Campbell, Carl Malina, Rosemary Yu, Francesca Di Bartolomeo, Jens B Nielsen
Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media. Proceedings of the National Academy of Sciences of the United States of America 117 (35) (2020)
Hongzhong Lu, Feiran Li, Benjamín J Sánchez, Zhengming Zhu, Gang Li, Iván Domenzain, Simonas Marcišauskas, Petre Mihail Anton, Dimitra Lappa, Christian Lieven, Moritz Emanuel Beber, Nikolaus Sonnenschein, Eduard Johannes Kerkhoven, Jens B Nielsen
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature communications 10 (1) (2019)
Simonas Marcišauskas, Boyang Ji, Jens B Nielsen
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. BMC bioinformatics 20 (1) (2019)
Zihe Liu, Yueping Zhang, Jens B Nielsen
Synthetic Biology of Yeast. Biochemistry 58 (11) (2019)
T I Henriksen, L V Wigge, Jens B Nielsen, Bente Klarlund Pedersen, M Sandri, Camilla Scheele
Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes. Scientific reports 9 (1) (2019)
G Othoum, S Prigent, Abderahmane Derouiche, L Shi, A Bokhari, S Alamoudi, Salim Bougouffa, Xin Gao, Hoehndorf Robert, S T Arold, T Gojobori, Heribert Hirt, Feras F Lafi, Jens B Nielsen, Vladimir B Bajic, I Mijakovic, Magbubah Essack
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs). Scientific reports 9 (1) (2019)
Manish Kumar, Boyang Ji, Karsten Zengler, Jens B Nielsen
Modelling approaches for studying the microbiome. Nature microbiology 4 (8) (2019)
Jens Christian Nielsen, Sylvain Prigent, Sietske Grijseels, Mhairi Workman, Boyang Ji, Jens B Nielsen
Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. mSystems 4 (2) (2019)
Mathias Uhlen, Max J Karlsson, Andreas Hober, Anne-Sophie Svensson, Julia Scheffel, David Kotol, Wen Zhong, Abdellah Tebani, Linnéa Strandberg, Fredrik Edfors, Evelina Sjöstedt, Jan Mulder, Adil Mardinglu, Anna Berling, Siri Ekblad, Melanie Dannemeyer, Sara Kanje, Johan Rockberg, Magnus Lundqvist, Magdalena Malm, Anna-Luisa Volk, Peter Nilsson, Anna Månberg, Tea Dodig-Crnkovic, Elisa Pin, Martin Zwahlen, Per Oksvold, Kalle von Feilitzen, Ragna S Häussler, Mun-Gwan Hong, Cecilia Lindskog, Frederik Pontén, Borbala Katona, Jimmy Vuu, Emil Lindström, Jens B Nielsen, Jonathan L Robinson, Burcu Ayoglu, Diana Mahdessian, Devin P Sullivan, Peter J Thul, Frida Danielsson, Charlotte Stadler, Emma Lundberg, Göran Bergström, Anders Gummesson, Bjørn Gunnar Rude Voldborg, Hanna Tegel, Sophia Hober, Björn Forsström, Jochen M Schwenk, Linn Fagerberg, Åsa Sivertsson
The human secretome. Science signaling 12 (609) (2019)
Parizad Babaei, Saeed Shoaie, Boyang Ji, Jens B Nielsen
Challenges in modeling the human gut microbiome. Nature biotechnology 36 (8) (2019)
Gheorghe M Borja, Angelica Rodriguez, Kate Campbell, Irina Borodina, Yun Chen, Jens B Nielsen
Metabolic engineering and transcriptomic analysis of Saccharomyces cerevisiae producing p-coumaric acid from xylose. Microbial cell factories 18 (1) (2019)

Jens B Nielsen.css-eqlu8i{font-size:small;padding-left:4px;} (J Nielsen, Jens Nielsen)

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Jens B Nielsen (J Nielsen, Jens Nielsen)