Publications

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2020
 

The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements

Browne, Patrick Denis ; Kot, Witold ; Jørgensen, Tue Sparholt ; Hansen, Lars Hestbjerg
part of: Horizontal Gene Transfer, pages: 253-264, 2020

Type: Book chapter

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1007/978-1-4939-9877-7_18

 

Yeast systems biology in understanding principles of physiology underlying complex human diseases

Yu, Rosemary ; Nielsen, Jens
in: Current Opinion in Biotechnology, vol: 63, pages: 63-69

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1016/j.copbio.2019.11.021

2019
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A high-throughput platform to select for regulators of crispr-cas associated activity

Vazquez-Uribe, Ruben ; Van Der Helm, Eric ; Sommer, Morten Otto Alexander ; Lee, Sang Woo
Patent no.: WO2019185750, Date: 2019-03-27

Type: Patent

Status: Published     |    Year: 2019

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Inhibitors of crispr-cas associated activity

Vazquez-Uribe, Ruben ; Van Der Helm, Eric ; Sommer, Morten Otto Alexander ; Misiakou, Maria-Anna ; Lee, Sang Woo
Patent no.: WO2019185751, Date: 2019-03-27

Type: Patent

Status: Published     |    Year: 2019

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Glycosylation of proteins

Voldborg, Bjørn ; Kol, Stefan ; Hansen, Anders ; Kildegaard, Helene
Patent no.: WO2019105770, Date: 2017-11-28

Type: Patent

Status: Published     |    Year: 2019

 

Synthetic Biology of Yeast

Liu, Zihe ; Zhang, Yueping ; Nielsen, Jens
in: Biochemistry, vol: 58, issue: 11, pages: 1511-1520

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.biochem.8b01236

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Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression

Wei, Yongjun ; Ji, Boyang ; Siewers, Verena ; Xu, Deyang ; Halkier, Barbara Ann ; Nielsen, Jens
in: Applied Microbiology and Biotechnology, vol: 103, issue: 9, pages: 3727-3736

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s00253-019-09720-3

 

3.53 Synthetic Biology: An Overview

de Carvalho, Ângela ; Garcia Vanegas, Katherina ; Pereira, Filipa ; Theobald, Sebastian ; Takos, Adam
part of: Comprehensive Biotechnology 3rd Edition, pages: 659-670, 2019, Pergamon Press

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019

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A carbohydrate-binding family 48 module enables feruloyl esterase action on polymeric arabinoxylan

Holck, Jesper ; Fredslund, Folmer ; Møller, Marie Sofie ; Brask, Jesper ; Krogh, Kristian B. R. M. ; Lange, Lene ; Welner, Ditte Hededam ; Svensson, Birte ; Meyer, Anne S. ; Wilkens, Casper
in: Journal of Biological Chemistry, vol: 294, issue: 46, pages: 17339-17353

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1074/jbc.RA119.009523

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Accelerated H-2 Evolution during Microbial Electrosynthesis with Sporomusa ovata

Tremblay, Pier-Luc ; Faraghiparapari, Neda ; Zhang, Tian
in: Catalysts, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3390/catal9020166

 

A comprehensive metabolic map for production of bio-based chemicals

Lee, Sang Yup ; Kim, Hyun Uk ; Chae, Tong Un ; Cho, Jae Sung ; Kim, Je Woong ; Shin, Jae Ho ; Kim, Dong In ; Ko, Yoo Sung ; Jang, Woo Dae ; Jang, Yu Sin
in: Nature Catalysis, vol: 2, issue: 1, pages: 18-33

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41929-018-0212-4

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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong ; Li, Feiran ; Sánchez, Benjamín J ; Zhu, Zhengming ; Li, Gang ; Domenzain, Iván ; Marcišauskas, Simonas ; Anton, Petre Mihail ; Lappa, Dimitra ; Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus ; Kerkhoven, Eduard J ; Nielsen, Jens
in: Nature Communications, vol: 10, issue: 1, pages: 3586

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-11581-3

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A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules

Liang, Mindong ; Li, Zilong ; Wang, Weishan ; Liu, Jiakun ; Liu, Leshi ; Zhu, Guoliang ; Karthik, Loganathan ; Wang, Man ; Wang, Ke Feng ; Wang, Zhong ; Yu, Jing ; Shuai, Yuting ; Yu, Jiaming ; Zhang, Lu ; Yang, Zhiheng ; Li, Chuan ; Zhang, Qian ; Shi, Tong ; Zhou, Liming ; Xie, Feng ; Dai, Huanqin ; Liu, Xueting ; Zhang, Jingyu ; Liu, Guang ; Zhuo, Ying ; Zhang, Buchang ; Liu, Chenli ; Li, Shanshan ; Xia, Xuekui ; Tong, Yaojun ; Liu, Yanwen ; Alterovitz, Gil ; Tan, Gao Yi ; Zhang, Li Xin
in: Nature Communications, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-11648-1

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Adapting to the airways: Metabolic requirements of Pseudomonas aeruginosa during the infection of cystic fibrosis patients

La Rosa, Ruggero ; Johansen, Helle Krogh ; Molin, Søren
in: Metabolites, vol: 9, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3390/metabo9100234

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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Anand, Amitesh ; Chen, Ke ; Yang, Laurence ; Sastry, Anand V. ; Olson, Connor A. ; Poudel, Saugat ; Seif, Yara ; Hefner, Ying ; Phaneuf, Patrick V. ; Xu, Sibei ; Szubin, Richard ; Feist, Adam ; Palsson, Bernhard
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 116, issue: 50, pages: 25287-25292

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1073/pnas.1909987116

 

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

Pereira, Rui ; Wei, Yongjun ; Mohamed, Elsayed Tharwat Tolba ; Radi, Mohammad ; Malina, Carl ; Herrgård, Markus J. ; Feist, Adam M. ; Nielsen, Jens ; Chen, Yun
in: Metabolic Engineering, vol: 56, pages: 130-141

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2019.09.008

 

A gender matching effect in learning with pedagogical agents in an immersive virtual reality science simulation

Makransky, Guido ; Wismer, Philip ; Mayer, Richard E.
in: Journal of Computer Assisted Learning, vol: 35, issue: 3, pages: 349-358

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/jcal.12335

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A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae

Zhang, Yueping ; Wang, Juan ; Wang, Zibai ; Zhang, Yiming ; Shi, Shuobo ; Nielsen, Jens ; Liu, Zihe
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-09005-3

 

A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts

de Rond, Tristan ; Gao, Jian ; Zargar, Amin ; de Raad, Markus ; Cunha, Jack ; Northen, Trent R. ; Keasling, Jay D.
in: ANGEWANDTE CHEMIE, vol: 58, issue: 30, pages: 10114-10119

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/anie.201901782

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Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

Phaneuf, Patrick V. ; Gosting, Dennis ; Palsson, Bernhard O. ; Feist, Adam M.
in: Nucleic acids research, vol: 47, issue: D1, pages: D1164-D1171

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky983

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A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory

Kristjansdottir, Thordis ; Bosma, Elleke Fenna ; Branco Dos Santos, Filipe ; Özdemir, Emre ; Herrgård, Markus J. ; França, Lucas ; Ferreira, Bruno ; Toftgaard Nielsen, Alex ; Gudmundsson, Steinn
in: Microbial Cell Factories, vol: 18, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1229-3

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Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

D'Arrigo, Isotta ; Cardoso, João G. R. ; Rennig, Maja ; Sonnenschein, Nikolaus ; Herrgård, Markus J. ; Long, Katherine S.
in: Environmental Microbiology Reports, vol: 11, issue: 2, pages: 87-97

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1758-2229.12704

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Antibacterial effect of boron nitride flakes with controlled orientation in polymer composites

Pandit, Santosh ; Gaska, Karolina ; Mokkapati, V. R.S.S. ; Forsberg, Sven ; Svensson, Magnus ; Kádár, Roland ; Mijakovic, Ivan
in: RSC Advances, vol: 9, issue: 57, pages: 33454-33459

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1039/c9ra06773f

 

Antibiotic Lethality Is Impacted by Nutrient Availabilities: New Insights from Machine Learning

Nielsen, Jens
in: CELL, vol: 177, issue: 6, pages: 1373-1374

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cell.2019.05.015