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1

Evolution and classification of the CRISPR–Cas systems

Makarova, Kira S., Haft, Daniel H., Barrangou, Rodolphe, Brouns, Stan J. J., Charpentier, Emmanuelle, Horvath, Philippe, Moineau, Sylvain, Mojica, Francisco J. M., Wolf, Yuri I., Yakunin, Alexander F.

Journal:

Nature Reviews Microbiology

Year:

2011

Language:

english

File:

PDF, 726 KB

english, 2011

2

The CRISPRs, They Are A-Changin': How Prokaryotes Generate Adaptive Immunity

Westra, Edze R., Swarts, Daan C., Staals, Raymond H.J., Jore, Matthijs M., Brouns, Stan J.J., van der Oost, John

Journal:

Annual Review of Genetics

Year:

2012

Language:

english

File:

PDF, 859 KB

english, 2012

3

Targeting mechanisms of tailed bacteriophages

Nobrega, Franklin L., Vlot, Marnix, de Jonge, Patrick A., Dreesens, Lisa L., Beaumont, Hubertus J. E., Lavigne, Rob, Dutilh, Bas E., Brouns, Stan J. J.

Journal:

Nature Reviews Microbiology

Year:

2018

Language:

english

File:

PDF, 25.42 MB

english, 2018

4

Structures of the RNA-guided surveillance complex from a bacterial immune system

Wiedenheft, Blake, Lander, Gabriel C., Zhou, Kaihong, Jore, Matthijs M., Brouns, Stan J. J., van der Oost, John, Doudna, Jennifer A., Nogales, Eva

Journal:

Year:

2011

Language:

english

File:

PDF, 1.28 MB

english, 2011

5

Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes

Al-Attar, Sinan, Westra, Edze R., van der Oost, John, Brouns, Stan J.J.

Journal:

Biological Chemistry

Year:

2011

Language:

english

File:

PDF, 319 KB

english, 2011

6

Archaeal MBF1 binds to 30S and 70S ribosomes via its helix–turn–helix domain

Blombach, Fabian, Launay, Helene, Snijders, Ambrosius P. L., Zorraquino, Violeta, Wu, Hao, de Koning, Bart, Brouns, Stan J. J., Ettema, Thijs J. G., Camilloni, Carlo, Cavalli, Andrea, Vendruscolo, Mic

Journal:

Biochemical Journal

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

7

An updated evolutionary classification of CRISPR–Cas systems

Makarova, Kira S., Wolf, Yuri I., Alkhnbashi, Omer S., Costa, Fabrizio, Shah, Shiraz A., Saunders, Sita J., Barrangou, Rodolphe, Brouns, Stan J. J., Charpentier, Emmanuelle, Haft, Daniel H., Horvath,

Journal:

Nature Reviews Microbiology

Year:

2015

Language:

english

File:

PDF, 531 KB

english, 2015

8

CRISPR sabotage

van der Oost, John, Brouns, Stan J. J.

Journal:

Year:

2015

Language:

english

File:

PDF, 472 KB

english, 2015

9

CRISPR-Cas: Adapting to change

Jackson, Simon A., McKenzie, Rebecca E., Fagerlund, Robert D., Kieper, Sebastian N., Fineran, Peter C., Brouns, Stan J. J.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

10

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

Makarova, Kira S., Wolf, Yuri I., Iranzo, Jaime, Shmakov, Sergey A., Alkhnbashi, Omer S., Brouns, Stan J. J., Charpentier, Emmanuelle, Cheng, David, Haft, Daniel H., Horvath, Philippe, Moineau, Sylvai

Journal:

Nature Reviews Microbiology

Year:

2019

File:

PDF, 2.42 MB

2019

11

Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

Ambrosius P. L. Snijders, Jasper Walther, Stefan Peter, Iris Kinnman, Marjon G. J. de Vos, Harmen J. G. van de Werken, Stan J. J. Brouns, John van der Oost, Phillip C. Wright

Journal:

Year:

2006

Language:

english

File:

PDF, 431 KB

english, 2006

12

Structure of the ribosome associating GTPase HflX

Hao Wu, Lei Sun, Fabian Blombach, Stan J.J. Brouns, Ambrosius P. L. Snijders, Kristina Lorenzen, Robert H. H. van den Heuvel, Albert J. R. Heck, Sheng Fu, Xuemei Li, Xuejun C. Zhang, Zihe Rao, John va

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 876 KB

english, 2010

13

Laboratory evolution ofPyrococcus furiosusalcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures

Ronnie Machielsen, Nicole G. H. Leferink, Annemarie Hendriks, Stan J. J. Brouns, Hans-Georg Hennemann, Thomas Dauβmann, John van der Oost

Journal:

Year:

2008

Language:

english

File:

PDF, 325 KB

english, 2008

14

CRISPR-based adaptive and heritable immunity in prokaryotes

John van der Oost, Matthijs M. Jore, Edze R. Westra, Magnus Lundgren, Stan J.J. Brouns

Journal:

Trends in Biochemical Sciences

Year:

2009

Language:

english

File:

PDF, 462 KB

english, 2009

15

The rise and fall of CRISPRs – dynamics of spacer acquisition and loss

Edze R. Westra, Stan J. J. Brouns

Journal:

Molecular Microbiology

Year:

2012

Language:

english

File:

PDF, 72 KB

english, 2012

16

Cascade-mediated binding and bending of negatively supercoiled DNA

Westra, Edze R., Nilges, Benedikt, van Erp, Paul B. G., van der Oost, John, Dame, Remus T., Brouns, Stan J. J.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.20 MB

english, 2012

17

RNAi: Prokaryotes Get in on the Act

John van der Oost, Stan J.J. Brouns

Journal:

Year:

2009

Language:

english

File:

PDF, 377 KB

english, 2009

18

The Structures of Inhibitor Complexes of Pyrococcus furiosus Phosphoglucose Isomerase Provide Insights into Substrate Binding and Catalysis

John M. Berrisford, Jasper Akerboom, Stan Brouns, Svetlana E. Sedelnikova, Andrew P. Turnbull, John van der Oost, Laurent Salmon, Renaud Hardré, Iain A. Murray, G. Michael Blackburn, David W. Rice, Pa

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 433 KB

english, 2004

19

Evidence Supporting a cis-enediol-based Mechanism for Pyrococcus furiosus Phosphoglucose Isomerase

John M. Berrisford, Andrea M. Hounslow, Jasper Akerboom, Wilfred R. Hagen, Stan J.J. Brouns, John van der Oost, Iain A. Murray, G. Michael Blackburn, Jonathan P. Waltho, David W. Rice, Patrick J. Bake

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 780 KB

english, 2006

20

Crystal Structure and Biochemical Properties of the d-Arabinose Dehydrogenase from Sulfolobus solfataricus

Stan J.J. Brouns, Andrew P. Turnbull, Hanneke L.D.M. Willemen, Jasper Akerboom, John van der Oost

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.97 MB

english, 2007

21

Structural Insight into Substrate Binding and Catalysis of a Novel 2-Keto-3-deoxy-d-arabinonate Dehydratase Illustrates Common Mechanistic Features of the FAH Superfamily

Stan J.J. Brouns, Thomas R.M. Barends, Petra Worm, Jasper Akerboom, Andrew P. Turnbull, Laurent Salmon, John van der Oost

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 2.38 MB

english, 2008

22

CRISPR-Cas systems preferentially target the leading regions of MOB F conjugative plasmids

Westra, Edze R., Staals, Raymond H.J., Gort, Gerrit, Høgh, Søren, Neumann, Sarah, de la Cruz, Fernando, Fineran, Peter C., Brouns, Stan J.J.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.44 MB

english, 2013

23

Planting the seed: target recognition of short guide RNAs

Künne, Tim, Swarts, Daan C., Brouns, Stan J.J.

Journal:

Trends in Microbiology

Year:

2014

Language:

english

File:

PDF, 1.06 MB

english, 2014

24

DNA-guided DNA interference by a prokaryotic Argonaute

Swarts, Daan C., Jore, Matthijs M., Westra, Edze R., Zhu, Yifan, Janssen, Jorijn H., Snijders, Ambrosius P., Wang, Yanli, Patel, Dinshaw J., Berenguer, José, Brouns, Stan J. J., van der Oost, John

Journal:

Year:

2014

Language:

english

File:

PDF, 5.30 MB

english, 2014

25

Defense Against Viral Attack: Single-Molecule View on a Bacterial Adaptive Immune System

Blosser, Timothy, Westra, Edze, Loeff, Luuk, Dekker, Cees, Brouns, Stan, Joo, Chirlmin

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

26

Differential Translation Tunes Uneven Production of Operon-Encoded Proteins

Quax, Tessa E.F., Wolf, Yuri I., Koehorst, Jasper J., Wurtzel, Omri, van der Oost, Richard, Ran, Wenqi, Blombach, Fabian, Makarova, Kira S., Brouns, Stan J.J., Forster, Anthony C., Wagner, E. Gerhart

Journal:

Year:

2013

Language:

english

File:

PDF, 1.39 MB

english, 2013

27

Improving the Performance of a Quadrupole Time-of-Flight Instrument for Macromolecular Mass Spectrometry

van den Heuvel, Robert H. H., van Duijn, Esther, Mazon, Hortense, Synowsky, Silvia A., Lorenzen, Kristina, Versluis, Cees, Brouns, Stan J. J., Langridge, Dave, van der Oost, John, Hoyes, John, Heck, A

Journal:

Analytical Chemistry

Year:

2006

Language:

english

File:

PDF, 459 KB

english, 2006

28

CRISPRTarget

Biswas, Ambarish, Gagnon, Joshua N., Brouns, Stan J.J., Fineran, Peter C., Brown, Chris M.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.89 MB

english, 2013

29

Two Distinct DNA Binding Modes Guide Dual Roles of a CRISPR-Cas Protein Complex

Blosser, Timothy R., Loeff, Luuk, Westra, Edze R., Vlot, Marnix, Künne, Tim, Sobota, Małgorzata, Dekker, Cees, Brouns, Stan J.J., Joo, Chirlmin

Journal:

Year:

2015

Language:

english

File:

PDF, 2.57 MB

english, 2015

30

Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition

Westra, Edze R., Semenova, Ekaterina, Datsenko, Kirill A., Jackson, Ryan N., Wiedenheft, Blake, Severinov, Konstantin, Brouns, Stan J. J., Viollier, Patrick H.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.45 MB

english, 2013

31

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence

Ekaterina Semenova, Matthijs M. Jore, Kirill A. Datsenko, Anna Semenova, Edze R. Westra, Barry Wanner, John van der Oost, Stan J. J. Brouns and Konstantin Severinov

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.27 MB

english, 2011

32

CRISPR interference and priming varies with individual spacer sequences

Xue, Chaoyou, Seetharam, Arun S., Musharova, Olga, Severinov, Konstantin, J. Brouns, Stan J., Severin, Andrew J., Sashital, Dipali G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.11 MB

english, 2015

33

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Künne, Tim, Kieper, Sebastian N., Bannenberg, Jasper W., Vogel, Anne I.M., Miellet, Willem R., Klein, Misha, Depken, Martin, Suarez-Diez, Maria, Brouns, Stan J.J.

Journal:

Year:

2016

Language:

english

File:

PDF, 2.06 MB

english, 2016

34

Assembling the archaeal ribosome: roles for translation-factor-related GTPases

Blombach, Fabian, Brouns, Stan J.J., van der Oost, John

Journal:

Biochemical Society Transactions

Year:

2011

Language:

english

File:

PDF, 329 KB

english, 2011

35

DNA family shuffling of hyperthermostable β-glycosidases

KAPER, Thijs, BROUNS, Stan J.J., GEERLING, Ans C.M., VOS, Willem M. DE, VAN der OOST, John

Journal:

Biochemical Journal

Year:

2002

Language:

english

File:

PDF, 288 KB

english, 2002

36

Role of multiprotein bridging factor 1 in archaea: bridging the domains?

de Koning, Bart, Blombach, Fabian, Wu, Hao, Brouns, Stan J.J., van der Oost, John

Journal:

Biochemical Society Transactions

Year:

2009

Language:

english

File:

PDF, 335 KB

english, 2009

37

Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system

Staals, Raymond H. J., Jackson, Simon A., Biswas, Ambarish, Brouns, Stan J. J., Brown, Chris M., Fineran, Peter C.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 3.11 MB

english, 2016

38

Repetitive Loop Formation by the CRISPR-Cas3 Helicase

Loeff, Luuk, Brouns, Stan, Joo, Chirlmin

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 41 KB

english, 2017

39

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

Vlot, Marnix, Houkes, Joep, Lochs, Silke J.A., Swarts, Daan C., Zheng, Peiyuan, Kunne, Tim, Mohanraju, Prarthana, Anders, Carolin, Jinek, Martin, van der Oost, John, Dickman, Mark J., Brouns, Stan J.J

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 3.25 MB

english, 2017

40

Complete Genome Sequence of the Escherichia coli Phage Ayreon

Vlot, Marnix, Nobrega, Franklin L., Wong, Che F. A., Liu, Yue, Brouns, Stan J. J.

Journal:

Genome Announcements

Year:

2018

Language:

english

File:

PDF, 125 KB

english, 2018

41

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation

Kieper, Sebastian N., Almendros, Cristóbal, Behler, Juliane, McKenzie, Rebecca E., Nobrega, Franklin L., Haagsma, Anna C., Vink, Jochem N.A., Hess, Wolfgang R., Brouns, Stan J.J.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

42

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

Loeff, Luuk, Brouns, Stan J.J., Joo, Chirlmin

Journal:

Year:

2018

Language:

english

File:

PDF, 2.93 MB

english, 2018

43

Fidelity in Archaeal Information Processing

de Koning, Bart, Blombach, Fabian, Brouns, Stan J. J., van der Oost, John

Journal:

Year:

2010

Language:

english

File:

PDF, 3.04 MB

english, 2010

44

Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages

Costa, Ana Rita, Brouns, Stan J. J., Nobrega, Franklin L.

Journal:

Genome Announcements

Year:

2018

Language:

english

File:

PDF, 121 KB

english, 2018

45

Role of nucleotide identity in effective CRISPR target escape mutations

Künne, Tim, Zhu, Yifan, da Silva, Fausia, Konstantinides, Nico, McKenzie, Rebecca E, Jackson, Ryan N, Brouns, Stan JJ

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 3.50 MB

english, 2018

46

Molecular and Evolutionary Determinants of Bacteriophage Host Range

de Jonge, Patrick A., Nobrega, Franklin L., Brouns, Stan J.J., Dutilh, Bas E.

Journal:

Trends in Microbiology

Year:

2018

Language:

english

File:

PDF, 1.99 MB

english, 2018

47

Using CAPTURE to detect spacer acquisition in native CRISPR arrays

McKenzie, Rebecca E., Almendros, Cristóbal, Vink, Jochem N. A., Brouns, Stan J. J.

Journal:

Nature Protocols

Year:

2019

File:

PDF, 914 KB

2019

48

Using CAPTURE to detect spacer acquisition in native CRISPR arrays

McKenzie, Rebecca E., Almendros, Cristóbal, Vink, Jochem N. A., Brouns, Stan J. J.

Journal:

Nature Protocols

Year:

2019

Language:

english

File:

PDF, 914 KB

english, 2019

49

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

Musharova, Olga, Sitnik, Vasily, Vlot, Marnix, Savitskaya, Ekaterina, Datsenko, Kirill A., Krivoy, Andrey, Fedorov, Ivan, Semenova, Ekaterina, Brouns, Stan J.J., Severinov, Konstantin

Journal:

Molecular Microbiology

Year:

2019

File:

PDF, 1.06 MB

2019

50

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Edwards, Robert A., Vega, Alejandro A., Norman, Holly M., Ohaeri, Maria, Levi, Kyle, Dinsdale, Elizabeth A., Cinek, Ondrej, Aziz, Ramy K., McNair, Katelyn, Barr, Jeremy J., Bibby, Kyle, Brouns, Stan J

Journal:

Nature Microbiology

Year:

2019

Language:

english

File:

PDF, 1.73 MB

english, 2019