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Integrating a novel layer of synthetic biology tools in Pseudomonas, inspired by bacterial viruses

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Publications

SEVAtile: a standardised DNA assembly method optimised for Pseudomonas.

Author(s): Eveline-Marie Lammens; M. Boon; Dennis Grimon; Yves Briers; Rob Lavigne
Published in: Microbial biotechnology, 2021, ISSN 1751-7915
Publisher: Society for Applied Microbiology and John Wiley & Sons Ltd
DOI: 10.1111/1751-7915.13922

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

Author(s): Eveline-Marie Lammens, Pablo Ivan Nikel, Rob Lavigne
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19124-x

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

Author(s): Leena Putzeys; Maarten Boon; Eveline-Marie Lammens; Konstantin Kuznedelov; Konstantin Severinov; Rob Lavigne
Published in: Computational and Structural Biotechnology Journal, 20010370, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.05.034

SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas

Author(s): Lucas Coppens, Rob Lavigne
Published in: BMC Bioinformatics, 21/1, 2020, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-020-03730-z

‘Drc’, a structurally novel ssDNA-binding transcriptionregulator of N4-related bacterial viruses

Author(s): Maarten Boon, Elke De Zitter, Jeroen De Smet, Jeroen Wagemans, Marleen Voet, Lisa Friederike Pennemann, Thomas Schalk, Konstantin Kuznedelov, Konstantin Severinov, Luc Van Meervelt, Marc De Maeyer, Rob Lavigne
Published in: Nucleic Acids Research, 48/1, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1048

SAPPHIRE.CNN: Implementation of dRNA-seq-driven, species-specific promoter prediction using convolutional neural networks

Author(s): Lucas Coppens; Laura Wicke; Rob Lavigne
Published in: Computational and Structural Biotechnology Journal, 20010370, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.09.006

Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ

Author(s): Laura Wicke, Falk Ponath, Lucas Coppens, Milan Gerovac, Rob Lavigne, Jörg Vogel
Published in: RNA Biology, 2020, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2020.1827785

A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions

Author(s): Milan Gerovac, Laura Wicke, Kotaro Chihara, Cornelius Schneider, Rob Lavigne, Jörg Vogel
Published in: mBio, 12/1, 2021, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.03454-20

Bacteriophages as drivers of bacterial virulence and their potential for biotechnological exploitation

Author(s): Kaat Schroven, Abram Aertsen, Rob Lavigne
Published in: FEMS Microbiology Reviews, 45/1, 2020, ISSN 1574-6976
Publisher: FEMS microbiology reviews
DOI: 10.1093/femsre/fuaa041

Deconstructing the Phage–Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies

Author(s): Annegrete Visnapuu; Marie Van der Gucht; Jeroen Wagemans; Rob Lavigne
Published in: Viruses, 19994915, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14051057

Differential transcription profiling of the phage LUZ19 infection process in different growth media

Author(s): Ana Brandão, Diana P. Pires, Lucas Coppens, Marleen Voet, Rob Lavigne, Joana Azeredo
Published in: RNA Biology, 2021, Page(s) 1-13, ISSN 1547-6286
Publisher: Landes Bioscience
DOI: 10.1080/15476286.2020.1870844