Publications

Publikationer rss feed

2019
  PDF

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

  PDF

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

  PDF

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1074/jbc.RA119.009523

 

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13396

  PDF

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

  PDF

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

 

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

  PDF

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

  PDF

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

  PDF

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

 

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

  PDF

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

Li, Jun ; Rettedal, Elizabeth A ; van der Helm, Eric ; Ellabaan, Mostafa M Hashim ; Panagiotou, Gianni ; Sommer, Morten Otto Alexander
in: Genomics, Proteomics and Bioinformatics, vol: 17, issue: 1, pages: 39-51

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.gpb.2018.12.003

  PDF

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Blin, Kai ; Shaw, Simon ; Steinke, Katharina ; Villebro, Rasmus ; Ziemert, Nadine ; Lee, Sang Yup ; Medema, Marnix H ; Weber, Tilmann
in: Nucleic acids research, vol: 87, issue: W2, pages: W81-W87

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gkz310

  PDF

A rapid methods development workflow for high-throughput quantitative proteomic applications

Chen, Yan ; Vu, Jonathan ; Thompson, Mitchell G. ; Sharpless, William A. ; Chan, Leanne Jade G. ; Gin, Jennifer W. ; Keasling, Jay D. ; Adams, Paul D. ; Petzold, Christopher J.
in: PLOS ONE, vol: 14, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0211582

 

Are we there yet? How and when specific biotechnologies will improve human health

O'Day, Elizabeth ; Hosta-Rigau, Leticia ; Oyarzún, Diego A. ; Okano, Hideyuki ; de Lorenzo, Víctor ; von Kameke, Conrad ; Alsafar, Habiba ; Cao, Cong ; Chen, Guo-Qiang ; Ji, Weizhi ; Roberts, Richard J. ; Ronaghi, Mostafa ; Yeung, Karen ; Zhang, Feng ; Lee, Sang Yup
in: Biotechnology Journal, vol: 14, issue: 1, pages: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800195

 

A robotic platform to screen aqueous two-phase systems for overcoming inhibition in enzymatic reactions

Bussamra, Bianca Consorti ; Gomes, Joana Castro ; Freitas, Sindelia ; Mussatto, Solange I. ; da Costa, Aline Carvalho ; van der Wielen, Luuk ; Ottens, Marcel
in: Bioresource Technology, vol: 280, pages: 37-50

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biortech.2019.01.136

  PDF

A Systematic Investigation of the Malignant Functions and Diagnostic Potential of the Cancer Secretome

Robinson, Jonathan L. ; Feizi, Amir ; Uhlén, Mathias ; Nielsen, Jens
in: Cell Reports, vol: 26, issue: 10, pages: 2622-2635

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.celrep.2019.02.025

 

Automated "cells-To-Peptides" Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes

Chen, Yan ; Guenther, Joel M. ; Gin, Jennifer W. ; Chan, Leanne Jade G. ; Costello, Zak ; Ogorzalek, Tadeusz L. ; Tran, Huu M. ; Blake-Hedges, Jacquelyn M. ; Keasling, Jay D. ; Adams, Paul D. ; García Martín, Héctor ; Hillson, Nathan J. ; Petzold, Christopher J.
in: Journal of Proteome Research, vol: 18, issue: 10, pages: 3752-3761

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.jproteome.9b00455

 

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Yang, Jason H ; Wright, Sarah N ; Hamblin, Meagan ; McCloskey, Douglas ; Alcantar, Miguel A ; Schrübbers, Lars ; Lopatkin, Allison J ; Satish, Sangeeta ; Nili, Amir ; Palsson, Bernhard O ; Walker, Graham C ; Collins, James J
in: CELL, vol: 177, issue: 6, pages: 1649-1661.e9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cell.2019.04.016

 

BCAT1 and BCAT2 disruption in CHO cells has cell line-dependent effects

Pereira, Sara ; Ley, Daniel ; Schubert, Mikkel ; Grav, Lise Marie ; Kildegaard, Helene Faustrup ; Andersen, Mikael Rørdam
in: Journal of Biotechnology, vol: 306, pages: 24-31

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.jbiotec.2019.08.017