Publications

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2020
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Accelerated genome engineering of Pseudomonas putida by I-SceI-mediated recombination and CRISPR-Cas9 counterselection

Wirth, Nicolas ; Kozaeva, Ekaterina ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 233-249

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1111/1751-7915.13396

 

Addressing environmental sustainability of biochemicals

Ögmundarson, Ólafur ; Herrgård, Markus J. ; Forster, Jochen ; Hauschild, Michael Zwicky ; Fantke, Peter
in: Nature Sustainability

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41893-019-0442-8

 

Awakening dormant glycosyltransferases in CHO cells with CRISPRa

Julie la Cour Karottki, Karen ; Hefzi, Hooman ; Xiong, Kai ; Shamie, Isaac ; Hansen, Anders Holmgaard ; Li, Songyuan ; Pedersen, Lasse Ebdrup ; Li, Shangzhong ; Lee, Jae Seong ; Min Lee, Gyun ; Kildegaard, Helene Faustrup ; Lewis, Nathan E.
in: Biotechnology and Bioengineering, vol: 117, issue: 2, pages: 593-598

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1002/bit.27199

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Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Poblete-Castro, Ignacio ; Wittmann, Christoph ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 32-53

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1111/1751-7915.13400

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Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity

Kiesewalter, Heiko T. ; Lozano-Andrade, Carlos N. ; Maróti, Gergely ; Snyder, Dan ; Jørgensen, Tue Sparholt ; Weber, Tilmann ; Kovács, Ákos T.
in: Microbiology Resource Announcements, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1128/mra.01406-19

 

Dual-function chromogenic screening-based CRISPR/Cas9 genome editing system for actinomycetes

Wang, Qiushui ; Xie, Feng ; Tong, Yaojun ; Habisch, Rebecca ; Yang, Bowen ; Zhang, Lixin ; Müller, Rolf ; Fu, Chengzhang
in: Applied Microbiology and Biotechnology, vol: 104, pages: 225-239

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1007/s00253-019-10223-4

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Environmental hotspots of lactic acid production systems

Ögmundarson, Ólafur ; Sukumara, Sumesh ; Laurent, Alexis ; Fantke, Peter
in: GCB Bioenergy, vol: 12, issue: 1, pages: 19-38

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1111/gcbb.12652

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Evolution-guided engineering of small-molecule biosensors

Snoek, Tim ; Chaberski, Evan Kirk ; Ambri, Francesca ; Kol, Stefan ; Bjørn, Sara P ; Pang, Bo ; Barajas, Jesus F ; Welner, Ditte Hededam ; Jensen, Michael Krogh ; Keasling, Jay D.
in: Nucleic acids research, vol: 48, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1093/nar/gkz954

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Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida

Incha, Matthew R. ; Thompson, Mitchell G. ; Blake-Hedges, Jacquelyn M. ; Liu, Yuzhong ; Pearson, Allison N. ; Schmidt, Matthias ; Gin, Jennifer W. ; Petzold, Christopher J. ; Deutschbauer, Adam M. ; Keasling, Jay D.
in: Metabolic Engineering Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1016/j.mec.2019.e00119

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MIBiG 2.0: a repository for biosynthetic gene clusters of known function

Kautsar, Satria A ; Blin, Kai ; Shaw, Simon ; Navarro-Muñoz, Jorge C ; Terlouw, Barbara R ; van der Hooft, Justin J J ; van Santen, Jeffrey A ; Tracanna, Vittorio ; Suarez Duran, Hernando G ; Pascal Andreu, Victòria ; Selem-Mojica, Nelly ; Alanjary, Mohammad ; Robinson, Serina L ; Lund, George ; Epstein, Samuel C ; Sisto, Ashley C ; Charkoudian, Louise K ; Collemare, Jérôme ; Linington, Roger G ; Weber, Tilmann ; Medema, Marnix H
in: Nucleic acids research, vol: 48, pages: D454–D458

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1093/nar/gkz882

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

Raethong, Nachon ; Wang, Hao ; Nielsen, Jens ; Vongsangnak, Wanwipa
in: Computational and Structural Biotechnology Journal, vol: 18, pages: 1-8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1016/j.csbj.2019.11.003

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Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida

Volke, Daniel Christoph ; Turlin, Justine ; Mol, Viviënne ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 222-232

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1111/1751-7915.13383

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Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

Choi, Kyeong Rok ; Lee, Sang Yup
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 199-209

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1111/1751-7915.13374

 

Recent advances of metabolic engineering strategies in natural isoprenoid production using cell factories

Li, Meijie ; Hou, Feifei ; Wu, Tong ; Jiang, Xinglin ; Li, Fuli ; Liu, Haobao ; Xian, Mo ; Zhang, Haibo
in: Natural Product Reports

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2020     |    DOI: https://doi.org/10.1039/c9np00016j

 

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