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Research Output 1996 2020

2014
5 Citations (Scopus)

Phage Display of Engineered Binding Proteins

Levisson, M., Spruijt, R. B., Winkel, I. N., Kengen, S. W. M. & van der Oost, J., 2014, In : Methods in molecular biology. 1129, p. 211-229

Research output: Contribution to journalArticleAcademicpeer-review

Bacteriophage M13
Bacteriophages
Carrier Proteins
Proteins
Costs and Cost Analysis
2 Citations (Scopus)

Prokaryotic Argonautes – variations on the RNA interference theme

van der Oost, J., Swarts, D. C. & Jore, M. M., 2014, In : Microbial Cell. 1, 5, p. 158-159

Research output: Contribution to journalArticleAcademicpeer-review

Purification and Sequencing of DNA Guides from Prokaryotic Argonaute

Swarts, D. C., Westra, E. R., Brouns, S. J. J. & van der Oost, J., 2014, In : Bio-protocol. 4, 22

Research output: Contribution to journalComment/Letter to the editorAcademic

Purification
Molecules
DNA
Nucleic Acids
Amplification
130 Citations (Scopus)

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

Staals, R. H. J., Zhu, Y., Taylor, D. W., Kornfeld, J. E., Sharma, K., Barendregt, A., Koehorst, J. J., Vlot, M., Neupane, N., Varossieau, K., Sakamoto, K., Suzuki, T., Schaap, P. J., Urlaub, H., Heck, A. J. R., Nogales, E., Doudna, J. A., Shinkai, A. & van der Oost, J., 2014, In : Molecular Cell. 56, 4, p. 518-530

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Thermus thermophilus
RNA
CRISPR-Cas Systems
Complementary RNA
78 Citations (Scopus)

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

Sheng, G., Zhao, H., Wang, J., Rao, Y., Tian, W., Swarts, D. C., van der Oost, J., Patel, D. J. & Wang, Y., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 2, p. 652-657

Research output: Contribution to journalArticleAcademicpeer-review

DNA
Ribonuclease H
Nucleophiles
Seed
Cations
2 Citations (Scopus)

Substrate Specificity and Stereoselectivity of Two Sulfolobus 2-Keto-3-deoxygluconate Aldolases towards Azido-Substituted Aldehydes

Schurink, M., Wolterink-van Loo, S., van der Oost, J., Sonke, T. & Franssen, M. C. R., 2014, In : ChemCatChem. 6, 4, p. 1073-1081

Research output: Contribution to journalArticleAcademicpeer-review

aldolase
Stereoselectivity
Aldehydes
aldehydes
Enzymes
142 Citations (Scopus)

The evolutionary journey of Argonaute proteins

Swarts, D. C., Makarova, K., Wang, Y., Nakanishi, K., Ketting, R. F., Koonin, E. V., Patel, D. J. & van der Oost, J., 2014, In : Nature Structural and Molecular Biology. 21, 9, p. 743-753

Research output: Contribution to journalArticleAcademicpeer-review

Argonaute Proteins
RNA Interference
Carrier Proteins
87 Citations (Scopus)

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

Louwen, R., Staals, R. H. J., Endtz, H. P., van Baarlen, P. & van der Oost, J., 2014, In : Microbiology and Molecular Biology Reviews. 78, 1, p. 74-88

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Virulence
Bacteria
Archaeal Genome
Interspersed Repetitive Sequences
318 Citations (Scopus)

Unravelling the structural and mechanistic basis of CRISPR-Cas systems

van der Oost, J., Westra, E. R., Jackson, R. N. & Wiedenheft, B., 2014, In : Nature Reviews Microbiology. 12, 7, p. 479-492

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Archaea
Adaptive Immunity
Guide RNA
2013
2 Citations (Scopus)

A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide

Ruigrok, V. J. B., Westra, E. R., Brouns, S. J. J., Escudé, C., Smidt, H. & van der Oost, J., 2013, In : Nucleic acids research. 41, 10, e111.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Superhelical DNA
Oligonucleotides
Plasmids
DNA
Lac Repressors
11 Citations (Scopus)

A novel bacterial enzyme with D-glucuronyl C5-epimerase activity

Raedts, J. G. J., Lundgren, M., Kengen, S. W. M., Li, J. P. & van der Oost, J., 2013, In : Journal of Biological Chemistry. 288, 34, p. 24332-24339

Research output: Contribution to journalArticleAcademicpeer-review

4 alpha-glucanotransferase
Racemases and Epimerases
Iduronic Acid
Glycosaminoglycans
Polysaccharides
79 Citations (Scopus)

A novel link between Campylobacter jejuni bacteriophage defence, virulence and Guillain-Barré syndrome

Louwen, R., Horst-Kreft, D., de Boer, A. G., van der Graaf, L., de Knegt, G., Hamersma, M., Heikema, A. P., Timms, A. R., Jacobs, B. C., Wagenaar, J. A., Endtz, H. P., van der Oost, J., Wells, J., Nieuwenhuis, E. E. S., van Vliet, A. H., Willemsen, P. T. J., van Baarlen, P. & van Belkum, A., 2013, In : European Journal of Clinical Microbiology and Infectious Diseases. 32, 2, p. 207-226

Research output: Contribution to journalArticleAcademicpeer-review

Campylobacter jejuni
Bacteriophages
Virulence
Gangliosides
Computational Biology
13 Citations (Scopus)

A thermophile under pressure: Transcriptional analysis of the response of Caldicellulosiruptor saccharolyticus to different H2 partial pressures

Bielen, A. A. M., Verhaart, M. R. A., Vanfossen, A. L., Blumer-Schuette, S. E., Stams, A. J. M., van der Oost, J., Kelly, R. M. & Kengen, S. W. M., 2013, In : International Journal of Hydrogen Energy. 38, 4, p. 1837-1849

Research output: Contribution to journalArticleAcademicpeer-review

thermophiles
lactates
fermentation
dehydrogenases
Transcription
24 Citations (Scopus)

Biohydrogen Production by the Thermophilic Bacterium Caldicellulosiruptor saccharolyticus: Current Status and Perspectives

Bielen, A. A. M., Verhaart, M. R. A., van der Oost, J. & Kengen, S. W. M., 2013, In : Life. 3, 1, p. 52-85

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Caldicellulosiruptor saccharolyticus
thermophilic bacterium
thermophilic bacteria
hydrogen production
bacteria
5 Citations (Scopus)

crRNA biogenesis

Charpentier, E., van der Oost, J. & White, M., 2013, CRISPR-Cas Systems. Barrangou, R., O. J. V. D. (ed.). Berlin-Heidelberg: Springer Verlag, p. 115-144

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

endoribonucleases
RNA
double-stranded RNA
nucleic acids
proteins
36 Citations (Scopus)

Differential translation tunes uneven production of operon-encoded proteins

Quax, T. E. F., Wolf, Y. I., Koehorst, J. J., Wurtzel, O., van der Oost, R., Ran, W., Blombach, F., Makarova, K. S., Brouns, S. J. J., Forster, A. C., Wagner, E. G. H., Sorek, R., Koonin, E. V. & van der Oost, J., 2013, In : Cell Reports. 4, 5, p. 938-944

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Operon
Genes
Gene Expression
Proteins
Archaea
43 Citations (Scopus)

Massive activation of archaeal defense genes during viral infection

Quax, T. E. F., Voet, M., Sismeiro, O., Dillies, M. A., Jagla, B., Coppée, J. Y., Sezonov, G., Forterre, P., van der Oost, J., Lavigne, R. & Prangishvili, D., 2013, In : Journal of Virology. 87, 15, p. 8419-8428

Research output: Contribution to journalArticleAcademicpeer-review

Sulfolobus virus SIRV-2
Rudiviridae
Archaeal Genes
Virus Diseases
Clustered Regularly Interspaced Short Palindromic Repeats

Modified cascade ribonucleoproteins and uses thereof 

Brouns, S. J. J. & van der Oost, J., 4 Jul 2013, Patent No. WO2013098244, Priority date 30 Dec 2011

Research output: PatentOther research output

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Ribonucleoproteins
CRISPR-Associated Proteins
Nucleic Acids
Antiviral Agents
33 Citations (Scopus)

Molecular biology - New tool for genome surgery

van der Oost, J., 2013, In : Science. 339, 6121, p. 768-770

Research output: Contribution to journalEditorialAcademicpeer-review

Deoxyribonucleases
Molecular Biology
Genome
Mutation
Genetic Therapy
17 Citations (Scopus)

Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms

Claassens, N. J. H. P., Volpers, M., Martins Dos Santos, V. A. P., van der Oost, J. & de Vos, W. M., 2013, In : Trends in Biotechnology. 31, 11, p. 633-642

Research output: Contribution to journalArticleAcademicpeer-review

Rhodopsin
Microorganisms
Protons
Light
Microbial Rhodopsins
27 Citations (Scopus)

Reporter-based screening and selection of enzymes

van Rossum, T., Kengen, S. W. M. & van der Oost, J., 2013, In : FEBS Journal. 280, 13, p. 2979-2996

Research output: Contribution to journalArticleAcademicpeer-review

Screening
Enzymes
Riboswitch
High-Throughput Screening Assays
Catalytic RNA
9 Citations (Scopus)

RNA-mediated Adaptive Immunity in Bacteria and Archaea

Barrangou, R. & van der Oost, J., 2013, CRISPR-Cas Systems. Berlin-Heidelberg: Springer Verlag, 299 p.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

127 Citations (Scopus)

Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus

Staals, R. H. J., Agari, Y., Maki-Yonekura, S., Zhu, Y., Taylor, D. W., van Duijn, E., Barendregt, A., Vlot, M., Koehorst, J. J., Sakamoto, K., Masuda, A., Dohmae, N., Schaap, P. J., Doudna, J. A., Heck, A., Yonekura, K., van der Oost, J. & Shinkai, A., 2013, In : Molecular Cell. 52, 1, p. 135-145

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Thermus thermophilus
RNA
Protein Subunits

Sustainable Production of Bio-Based Chemicals by Extremophiles

Bosma, E. F., van der Oost, J., de Vos, W. M. & van Kranenburg, R., 2013, In : Current Biotechnology. 2, 4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Fermentation
Saccharification
Clostridium
Biotechnology
Solubility
2012
25 Citations (Scopus)

Cascade-mediated binding and bending of negatively supercoiled DNA

Westra, E. R., Nilges, B., Erp, P. B., van der Oost, J., Dame, R. T. & Brouns, S. J. J., 2012, In : RNA Biology. 9, 9, p. 1134-1138

Research output: Contribution to journalEditorialAcademicpeer-review

Superhelical DNA
DNA
Clustered Regularly Interspaced Short Palindromic Repeats
Ribonucleoproteins
Conserved Sequence
24 Citations (Scopus)

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Ruigrok, V. J. B., Levisson, M., Hekelaar, J., Smidt, H., Dijkstra, B. W. & van der Oost, J., 2012, In : International Journal of Molecular Sciences. 13, 8, p. 10537-10552

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
X ray crystallography
X Ray Crystallography
crystallography
proteins
Proteins
290 Citations (Scopus)

CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3

Westra, E. R., Erp, P. B. G., Künne, T., Wong, S. P., Staals, R. H. J., Seegers, C. L. C., Bollen, S., Jore, M. M., Semenova, E., Severinov, K., de Vos, W. M., Dame, R. T., de Vries, R., Brouns, S. J. J. & van der Oost, J., 2012, In : Molecular Cell. 46, 5, p. 595-605

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Superhelical DNA
Immunity
CRISPR-Cas Systems
DNA
30 Citations (Scopus)

Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima

Levisson, M., Han, G. W., Deller, M. C., Hendriks, S. N. A., van der Oost, J. & Kengen, S. W. M., 2012, In : Proteins : Structure, Function, and Bioinformatics. 80, 6, p. 1545-1559

Research output: Contribution to journalArticleAcademicpeer-review

Thermotoga maritima
Esterases
Xylans
acetylxylan esterase
Serine
18 Citations (Scopus)

Kinetic and Stoichiometric Characterisation of Streptavidin-Binding Aptamers

Ruigrok, V. J. B., van Duijn, E., Barendregt, A., Dyer, K., Tainer, J. A., Stoltenburg, R., Strehlitz, B., Levisson, M., Smidt, H. & van der Oost, J., 2012, In : ChemBioChem. 13, 6, p. 829-836

Research output: Contribution to journalArticleAcademicpeer-review

Streptavidin
Kinetics
Binders
Surface Plasmon Resonance
Surface plasmon resonance
61 Citations (Scopus)

Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in CRISPR-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa

van Duijn, E., Barbu, I. M., Barendregt, A., Jore, M. M., Wiedenheft, B., Lundgren, M., Westra, E. R., Brouns, S. J. J., Doudna, J. A., van der Oost, J. & Heck, A. J. R., 2012, In : Molecular and Cellular Proteomics. 11, p. 1430-1441

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Associated Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Pseudomonas aeruginosa
Escherichia coli
Mass spectrometry

Process for polylactic acid production using Monascus

Weusthuis, R. A., Wolbert, E. J. H., Springer, J., van der Oost, J. & Eggink, G., 3 May 2012, Patent No. WO2012055997, Priority date 28 Oct 2010

Research output: PatentOther research output

Open Access
polylactic acid
Monascus
polymerization
lactic acid
fermentation
46 Citations (Scopus)

RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements

Jore, M. M., Brouns, S. J. J. & van der Oost, J., 2012, In : Cold Spring Harbor Perspectives in Biology. 4, 6, a003657.

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Interspersed Repetitive Sequences
CRISPR-Cas Systems
Plasmids
RNA
185 Citations (Scopus)

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

Westra, E. R., Swarts, D. C., Staals, R. H. J., Jore, M. M., Brouns, S. J. J. & van der Oost, J., 2012, In : Annual Review of Genetics. 46, p. 311-339

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Adaptive Immunity
DNA
Bacteria
Escherichia coli K12
10 Citations (Scopus)

Thermal Stabilization of an Endoglucanase by Cyclization

van Lieshout, J. F. T., Gutierrez, O., Vroom, W., Planas, A., de Vos, W. M., van der Oost, J. & Koutsopoulos, S., 2012, In : Applied Biochemistry and Biotechnology. 167, 7, p. 2039-2053

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Cellulase
Cyclization
Thermodynamic stability
Stabilization
Protein Stability

Use of Monascus in organic acid production

Weusthuis, R. A., Wolbert, E. J. H., Springer, J., van der Oost, J. & Eggink, G., 3 May 2012, Patent No. WO2012055998, Priority date 28 Oct 2010

Research output: PatentOther research output

Open Access
Monascus
organic acids and salts
methodology
69 Citations (Scopus)

Virus-like particle nanoreactors: programmed en capsulation of the thermostable CelB glycosidase inside the P22 capsid

Patterson, D. P., Schwarz, B., El-Boubbou, K., van der Oost, J., Prevelige, P. E. & Douglas, T., 2012, In : Soft Matter. 8, 39, p. 10158-10166

Research output: Contribution to journalArticleAcademicpeer-review

Nanoreactors
Glycoside Hydrolases
viruses
Viruses
Enzyme activity
2011

Afweer bacteriën ontrafeld

van der Oost, J., 2011, In : Resource: nieuwssite voor studenten en medewerkers van Wageningen UR.

Research output: Contribution to journalArticlePopular

Open Access
110 Citations (Scopus)

Alternative affinity tools: more attractive than antibodies?

Ruigrok, V. J. B., Levisson, M., Eppink, M. H. M., Smidt, H. & van der Oost, J., 2011, In : Biochemical Journal. 436, 1, p. 1-13

Research output: Contribution to journalArticleAcademicpeer-review

Antibodies
Nucleic Acids
Carrier Proteins
Drug delivery
Purification
12 Citations (Scopus)

An HflX-type GTPase from Sulfolobus solfataricus binds to the 50S ribosomal subunit in all nucleotide-bound states

Blombach, F., Swarts, D. C. & van der Oost, J., 2011, In : Journal of Bacteriology. 193, 11, p. 2861-2867

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sulfolobus solfataricus
Ribosome Subunits
GTP Phosphohydrolases
Nucleotides
Archaea

Archaea: de ontdekking van een nieuwe vorm van leven

van der Oost, J., 2011, Microcanon. wat je beslist moet weten over microbiologie. Smit, H., Reijders, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, p. Hfst. 3 246 p.

Research output: Chapter in Book/Report/Conference proceedingChapterPopular

10 Citations (Scopus)

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

Blombach, F., Brouns, S. J. J. & van der Oost, J., 2011, In : Biochemical Society Transactions. 39, 1, p. 45-50

Research output: Contribution to journalArticleAcademicpeer-review

GTP Phosphohydrolases
Ribosomes
Ribosome Subunits
Archaea
Eukaryota
97 Citations (Scopus)

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

Al-Attar, S., Westra, E. R., van der Oost, J. & Brouns, S. J. J., 2011, In : Biological Chemistry. 392, 4, p. 277-289

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Antiviral Agents
DNA
Prokaryotic Cells
Immunologic Memory
53 Citations (Scopus)

D-2,3-Butanediol Production Due to Heterologous Expression of an Acetoin Reductase in Clostridium acetobutylicum

Siemerink, M. A. J., Kuit, W., Lopez Contreras, A. M., Eggink, G., van der Oost, J. & Kengen, S. W. M., 2011, In : Applied and Environmental Microbiology. 77, 8, p. 2582-2588

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
butanediol dehydrogenase
Clostridium acetobutylicum
butanediol
acetoin
Acetoin
1162 Citations (Scopus)

Evolution and classification of the CRISPR-Cas systems

Makarova, K. S., Brouns, S. J. J. & van der Oost, J., 2011, In : Nature Reviews Microbiology. 9, 6, p. 467-477

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Associated Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Archaea
Adaptive Immunity
Phylogeny

Extremofiele micro-organismen: some like it hot

Kengen, S. W. M. & van der Oost, J., 2011, Microcanon. Smit, H., Reijners, W., van Doorn, J., van der Oost, J. & Willemsen, P. (eds.). Diemen: NVVM, p. 28-31 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapterPopular

Open Access
17 Citations (Scopus)

Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences

Esser, D., Kouril, T., Zaparty, M., Sierocinski, P., van der Oost, J., Makarova, K. S. & Siebers, B., 2011, In : Extremophiles. 15, 6, p. 711-712

Research output: Contribution to journalArticleAcademicpeer-review

Sulfolobus solfataricus
Crenarchaeota
Sulfolobus
Genome
Molecular Sequence Annotation
1 Citation (Scopus)

Growth phase-dependent gene regulation in vivo in Sulfolobus solfataricus

DeYoung, M. & van der Oost, J., 2011, In : FEMS Microbiology Letters. 321, 2, p. 92-99

Research output: Contribution to journalArticleAcademicpeer-review

Sulfolobus solfataricus
rRNA Genes
Archaea
Sulfolobus
Growth
149 Citations (Scopus)

Initial mutations direct alternative pathways of protein evolution

Salverda, M. L. M., Dellus, E., Gorter, F. A., Debets, A. J. M., van der Oost, J., Hoekstra, R. F., Tawfik, D. S. & de Visser, J. A. G. M., 2011, In : Plos Genetics. 7, 3, 11 p., e1001321.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
epistasis
mutation
Mutation
protein
substitution
391 Citations (Scopus)

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

Semenova, E. V., Jore, M. M., Westra, E. R., van der Oost, J. & Brouns, S. J. J., 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 25, p. 10098-10103

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Seeds
RNA
Viruses
Mutation
75 Citations (Scopus)

Isoprenoid biosynthesis in Archaea - Biochemical and evolutionary implications

Matsumi, R., Atomi, H., Driessen, A. J. M. & van der Oost, J., 2011, In : Research in Microbiology. 162, 1, p. 39-52

Research output: Contribution to journalArticleAcademicpeer-review

Archaea
Terpenes
Membrane Lipids
Eukaryota
Bacteria