Publications - DTU Biosustain

An automated workflow for multi-omics screening of microbial model organisms

Donati, Stefano ; Mattanovich, Matthias ; Hjort, Pernille ; Baallal Jacobsen, Simo Abdessamad ; Blomquist, Sarah Dina ; Mangaard, Drude ; Gurdo, Nicolas ; Pastor, Felix Pacheco ; Maury, Jerome ; Hanke, Rene ; Herrgård, Markus J ; Wulff, Tune ; Jakociunas, Tadas ; Nielsen, Lars Keld ; McCloskey, Douglas
in: bioRxiv

Type: Journal article (Peer reviewed)

Status: Submitted | Year: 2023 | DOI: https://doi.org/10.1101/2022.07.18.500181

Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

Gurdo, Nicolás ; Volke, Daniel C. ; McCloskey, Douglas ; Nikel, Pablo Iván
in: New Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2023 | DOI: https://doi.org/10.1016/j.nbt.2023.01.002

Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism

Haas, Robert ; Nikel, Pablo I
in: Trends in Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2023 | DOI: https://doi.org/10.1016/j.tibtech.2022.06.004

Engineering of Pseudomonas putida for accelerated co-utilization of glucose and cellobiose yields aerobic overproduction of pyruvate explained by an upgraded metabolic model

Bujdoš, Dalimil ; Popelářová, Barbora ; Volke, Daniel C. ; Nikel, Pablo I. ; Sonnenschein, Nikolaus ; Dvořák, Pavel
in: Metabolic Engineering, vol: 75, pages: 29-46

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.ymben.2022.10.011

SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes

Martínez-García, Esteban ; Fraile, Sofía ; Algar, Elena ; Aparicio, Tomás ; Velázquez, Elena ; Calles, Belén ; Tas, Huseyin ; Blázquez, Blas ; Martín, Bruno ; Prieto, Clara ; Sánchez-Sampedro, Lucas ; Nørholm, Morten H. H. ; Volke, Daniel C. ; Wirth, Nicolas T. ; Dvořák, Pavel ; Alejaldre, Lorea ; Grozinger, Lewis ; Crowther, Matthew ; Goñi-Moreno, Angel ; Nikel, Pablo I ; Nogales, Juan ; de Lorenzo, Víctor
in: Nucleic Acids Research, vol: 51, issue: D1, pages: D1558–D1567

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1093/nar/gkac1059

A Nonconventional Archaeal Fluorinase Identified by in Silico Mining for Enhanced Fluorine Biocatalysis

Pardo, Isabel ; Bednar, David ; Calero, Patricia ; Volke, Daniel C. ; Damborský, Jiří ; Nikel, Pablo I.
in: ACS Catalysis, vol: 12, issue: 11, pages: 6570-6577

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1021/acscatal.2c01184

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes

Wirth, Nicolas T. ; Gurdo, Nicolás ; Krink, Nicolas ; Vidal-Verdú, Àngela ; Donati, Stefano ; Férnandez-Cabezón, Lorena ; Wulff, Tune ; Nikel, Pablo I.
in: Metabolic Engineering, vol: 74, pages: 83-97

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1016/j.ymben.2022.09.004

Bacterial cells and methods for production of 2-fluoro-cis,cis-muconate

Wirth, Nicolas Thilo ; Nikel, Pablo
Patent no.: WO2022003144, Date: 2021-04-26

Type: Patent

Status: Published | Year: 2022

CFD-kinetic Modelling for the Scale-up of P. putida Fed-batch Fermentations

Jamshidzadeh, Maryam ; Jensen, Jesper Wang ; Krühne, Ulrich ; Nikel, Pablo Ivan ; Junicke, Helena
Presented at: 7th Bioproscale symposium

Type: Conference abstract for conference

Status: Published | Year: 2022

Developing a CRISPR-assisted base-editing system for genome engineering of Pseudomonas chlororaphis

Yue, Sheng Jie ; Huang, Peng ; Li, Song ; Cai, Yu Yuan ; Wang, Wei ; Zhang, Xue Hong ; Nikel, Pablo I. ; Hu, Hong Bo
in: Microbial Biotechnology, vol: 15, issue: 9, pages: 2324-2336

Type: Journal article (Peer reviewed)

Status: Published | Year: 2022 | DOI: https://doi.org/10.1111/1751-7915.14075