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Adaptive immunity in prokaryotes: how Bacteria do not forgive and do not forget their enemies

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Publications

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

Author(s): Patrick A. de Jonge, F. A. Bastiaan von Meijenfeldt, Laura E. van Rooijen, Stan J. J. Brouns, Bas E. Dutilh
Published in: Viruses, 11/12, 2019, Page(s) 1085, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v11121085

An educational guide for nanopore sequencing in the classroom

Author(s): Alex N. Salazar, Franklin L. Nobrega, Christine Anyansi, Cristian Aparicio-Maldonado, Ana Rita Costa, Anna C. Haagsma, Anwar Hiralal, Ahmed Mahfouz, Rebecca E. McKenzie, Teunke van Rossum, Stan J. J. Brouns, Thomas Abeel
Published in: PLOS Computational Biology, 16/1, 2020, Page(s) e1007314, ISSN 1553-7358
Publisher: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1007314

Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism

Author(s): Jochem N.A. Vink, Koen J.A. Martens, Marnix Vlot, Rebecca E. McKenzie, Cristóbal Almendros, Boris Estrada Bonilla, Daan J.W. Brocken, Johannes Hohlbein, Stan J.J. Brouns
Published in: Molecular Cell, 77/1, 2020, Page(s) 39-50.e10, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2019.10.021

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

Author(s): Patrick A. de Jonge, F.A. Bastiaan von Meijenfeldt, Ana Rita Costa, Franklin L. Nobrega, Stan J.J. Brouns, Bas E. Dutilh
Published in: iScience, 23/9, 2020, Page(s) 101439, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2020.101439

Harnessing type I CRISPR–Cas systems for genome engineering in human cells

Author(s): Peter Cameron, Mary M. Coons, Sanne E. Klompe, Alexandra M. Lied, Stephen C. Smith, Bastien Vidal, Paul D. Donohoue, Tomer Rotstein, Bryan W. Kohrs, David B. Nyer, Rachel Kennedy, Lynda M. Banh, Carolyn Williams, Mckenzi S. Toh, Matthew J. Irby, Leslie S. Edwards, Chun-Han Lin, Arthur L. G. Owen, Tim Künne, John van der Oost, Stan J. J. Brouns, Euan M. Slorach, Chris K. Fuller, Scott Gradia, Stev
Published in: Nature Biotechnology, 37/12, 2019, Page(s) 1471-1477, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-019-0310-0

Conserved motifs in the CRISPR leader sequence control spacer acquisition levels in Type I-D CRISPR-Cas systems

Author(s): Sebastian N Kieper, Cristóbal Almendros, Stan J J Brouns
Published in: FEMS Microbiology Letters, 366/11, 2019, ISSN 1574-6968
Publisher: Oxford University Press
DOI: 10.1093/femsle/fnz129

Systematic analysis of Type I‐E Escherichia coli CRISPR‐Cas PAM sequences ability to promote interference and primed adaptation

Author(s): Olga Musharova, Vasily Sitnik, Marnix Vlot, Ekaterina Savitskaya, Kirill A. Datsenko, Andrey Krivoy, Ivan Fedorov, Ekaterina Semenova, Stan J. J. Brouns, Konstantin Severinov
Published in: Molecular Microbiology, 111/6, 2019, Page(s) 1558-1570, ISSN 0950-382X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mmi.14237

Molecular and Evolutionary Determinants of Bacteriophage Host Range

Author(s): Patrick A. de Jonge, Franklin L. Nobrega, Stan J.J. Brouns, Bas E. Dutilh
Published in: Trends in Microbiology, 27/1, 2019, Page(s) 51-63, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2018.08.006

Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages

Author(s): Ana Rita Costa, Stan J. J. Brouns, Franklin L. Nobrega
Published in: Genome Announcements, 6/26, 2018, ISSN 2169-8287
Publisher: American Society for Microbiology Journals
DOI: 10.1128/genomea.00586-18

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

Author(s): Marnix Vlot, Joep Houkes, Silke J A Lochs, Daan C Swarts, Peiyuan Zheng, Tim Kunne, Prarthana Mohanraju, Carolin Anders, Martin Jinek, John van der Oost, Mark J Dickman, Stan J J Brouns
Published in: Nucleic Acids Research, 46/2, 2017, Page(s) 873-885, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkx1264

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation

Author(s): Sebastian N. Kieper, Cristóbal Almendros, Juliane Behler, Rebecca E. McKenzie, Franklin L. Nobrega, Anna C. Haagsma, Jochem N.A. Vink, Wolfgang R. Hess, Stan J.J. Brouns
Published in: Cell Reports, 22/13, 2018, Page(s) 3377-3384, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.02.103

Complete Genome Sequence of the Escherichia coli Phage Ayreon

Author(s): Marnix Vlot, Franklin L. Nobrega, Che F. A. Wong, Yue Liu, Stan J. J. Brouns
Published in: Genome Announcements, 6/2, 2018, ISSN 2169-8287
Publisher: American Society for Microbiology Journals
DOI: 10.1128/genomea.01354-17

Repetitive DNA Reeling by the Cascade-Cas3 Complex in Nucleotide Unwinding Steps

Author(s): Luuk Loeff, Stan J.J. Brouns, Chirlmin Joo
Published in: Molecular Cell, 70/3, 2018, Page(s) 385-394.e3, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2018.03.031

Role of nucleotide identity in effective CRISPR target escape mutations

Author(s): Tim Künne, Yifan Zhu, Fausia da Silva, Nico Konstantinides, Rebecca E McKenzie, Ryan N Jackson, Stan JJ Brouns
Published in: Nucleic Acids Research, 46/19, 2018, Page(s) 10395-10404, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky687

CRISPR-Cas: Adapting to change

Author(s): Simon A. Jackson, Rebecca E. McKenzie, Robert D. Fagerlund, Sebastian N. Kieper, Peter C. Fineran, Stan J. J. Brouns
Published in: Science, 356/6333, 2017, Page(s) eaal5056, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aal5056

Molecular and Evolutionary Determinants of Bacteriophage Host Range

Author(s): Patrick A. de Jonge, Franklin L. Nobrega, Stan J.J. Brouns, Bas E. Dutilh
Published in: Trends in Microbiology, 2018, ISSN 0966-842X
Publisher: Elsevier BV
DOI: 10.1016/j.tim.2018.08.006

Targeting mechanisms of tailed bacteriophages

Author(s): Franklin L. Nobrega, Marnix Vlot, Patrick A. de Jonge, Lisa L. Dreesens, Hubertus J. E. Beaumont, Rob Lavigne, Bas E. Dutilh, Stan J. J. Brouns
Published in: Nature Reviews Microbiology, 16, 2018, Page(s) 760 - 773, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/s41579-018-0070-8

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Author(s): Tim Künne, Sebastian N. Kieper, Jasper W. Bannenberg, Anne I.M. Vogel, Willem R. Miellet, Misha Klein, Martin Depken, Maria Suarez-Diez, Stan J.J. Brouns
Published in: Molecular Cell, 63/5, 2016, Page(s) 852-864, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2016.07.011

An updated evolutionary classification of CRISPR–Cas systems

Author(s): Kira S. Makarova, Yuri I. Wolf, Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Sita J. Saunders, Rodolphe Barrangou, Stan J. J. Brouns, Emmanuelle Charpentier, Daniel H. Haft, Philippe Horvath, Sylvain Moineau, Francisco J. M. Mojica, Rebecca M. Terns, Michael P. Terns, Malcolm F. White, Alexander F. Yakunin, Roger A. Garrett, John van der Oost, Rolf Backofen, Eugene V. Koonin
Published in: Nature Reviews Microbiology, 13/11, 2015, Page(s) 722-736, ISSN 1740-1526
Publisher: Nature Publishing Group
DOI: 10.1038/nrmicro3569

CRISPR interference and priming varies with individual spacer sequences

Author(s): Chaoyou Xue, Arun S. Seetharam, Olga Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew J. Severin, Dipali G. Sashital
Published in: Nucleic Acids Research, 43/22, 2015, Page(s) 10831-10847, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkv1259

Using CAPTURE to detect spacer acquisition in native CRISPR arrays

Author(s): Rebecca E. McKenzie, Cristóbal Almendros, Jochem N. A. Vink, Stan J. J. Brouns
Published in: Nature Protocols, 14/3, 2019, Page(s) 976-990, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-018-0123-5

Cas4–Cas1 fusions drive efficient PAM selection and control CRISPR adaptation

Author(s): Cristóbal Almendros, Franklin L Nobrega, Rebecca E McKenzie, Stan J J Brouns
Published in: Nucleic Acids Research, 47/10, 2019, Page(s) 5223-5230, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz217

CRISPR sabotage

Author(s): John van der Oost, Stan J. J. Brouns
Published in: Genome Biology, 16/1, 2015, Page(s) 1-3, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-015-0820-0