Publications - DTU Biosustain

A Hitchhiker’s guide to CRISPR editing tools in bacteria

Krink, Nicolas ; Nikel, Pablo Iván ; Beisel, Chase L.
in: EMBO Reports, vol: 25, pages: 1694 - 1699

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1038/s44319-024-00086-w

Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system

Pause, Laura ; Weimer, Anna ; Wirth, Nicolas T. ; Nguyen, Anh Vu ; Lenz, Claudius ; Kohlstedt, Michael ; Wittmann, Christoph ; Nikel, Pablo I. ; Lai, Bin ; Krömer, Jens O.
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1111/1751-7915.14375

A novel strategy for extraction of intracellular poly(3-hydroxybutyrate) from engineered Pseudomonas putida using deep eutectic solvents: Comparison with traditional biobased organic solvents

Didion, Yannick Patrice ; Vargas, Maria Victoria Gracia Alvan ; Tjaslma, Tjalling Gijsbert ; Woodley, John ; Nikel, Pablo Ivan ; Malankowska, Magdalena ; Su, Ziran ; Pinelo, Manuel
in: Separation and Purification Technology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1016/j.seppur.2024.126465

Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16

Vinacour, Matias ; Moiana, Mauro ; Forné, Ignasi ; Jung, Kirsten ; Bertea, Micaela ; Valdayo, Patricia M. Calero ; Nikel, Pablo I. ; Imhof, Axel ; Palumbo, Miranda C. ; Fernández Do Porto, Dario ; Ruiz, Jimena A.
in: Applied and Environmental Microbiology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1128/aem.00630-23

How many Mutations are needed to Evolve the Chemical Makeup of a Synthetic Cell?

Lefèvre-Morand, Rodrigue Yves Louis ; Nikel, Pablo Iván ; Acevedo-Rocha, Carlos G.
in: ChemBioChem

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1002/cbic.202300829

The pAblo·pCasso self-curing vector toolset for unconstrained cytidine and adenine base-editing in Gram-negative bacteria

Kozaeva, Ekaterina ; Nielsen, Zacharias S. ; Nieto-Domínguez, Manuel ; Nikel, Pablo I.
in: Nucleic Acids Research, vol: 52, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1093/nar/gkad1236

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 ; Pacheco Pastor, Felix ; Maury, Jerome ; Hanke, René ; Herrgård, Markus J ; Wulff, Tune ; Jakociunas, Tadas ; Nielsen, Lars Keld ; McCloskey, Douglas
in: n p j Systems Biology and Applications, vol: 9

Type: Journal article (Peer reviewed)

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

An expanded CRISPR–Cas9-assisted recombineering toolkit for engineering genetically intractable Pseudomonas aeruginosa isolates

Pankratz, Debbie ; Gomez, Nicolas Oswaldo ; Nielsen, Agnes ; Mustafayeva, Ayten ; Gür, Melisa ; Arce-Rodriguez, Fabián ; Nikel, Pablo Ivan ; Häussler, Susanne ; Arce-Rodriguez, Alejandro
in: Nature Protocols, vol: 18, pages: 3253–3288

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1038/s41596-023-00882-z

A SEVA-based, CRISPR-Cas3-assisted genome engineering approach for Pseudomonas with efficient vector curing

Lammens, Eveline-Marie ; Volke, Daniel Christophe ; Schroven, Kaat ; Voet, Marleen ; Kerremans, Alison ; Lavigne, Rob ; Hendrix, Hanne
in: Microbiology Spectrum, vol: 11, issue: 6

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1128/spectrum.02707-23

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, vol: 74, pages: 1-15

Type: Journal article (Peer reviewed)

Status: Published | Year: 2023 | DOI: https://doi.org/10.1016/j.nbt.2023.01.002