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Research Output 1996 2020

2017

Improved CRISPR-Cas9 genome editing tool

Louwen, R. & van der Oost, J., 14 Sep 2017, Patent No. WO2017155408, Priority date 11 Mar 2016

Research output: PatentOther research output

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Proteins
Gene Editing

Improved CRISPR-Cpf1 genome editing tool 

van der Oost, J., van Baarlen, P. & Louwen, R., 14 Sep 2017, Patent No. WO2017155407, Priority date 11 Mar 2016

Research output: PatentOther research output

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Proteins
Gene Editing
7 Citations (Scopus)

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms

Claassens, N. J., Siliakus, M. F., Spaans, S. K., Creutzburg, S. C. A., Nijsse, B., Schaap, P. J., Quax, T. E. F. & Van Der Oost, J., 2017, In : PLoS ONE. 12, 9, e0184355.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
codons
Codon
membrane proteins
Escherichia coli
Membrane Proteins
3 Citations (Scopus)

Monascus ruber as cell factory for lactic acid production at low pH

Weusthuis, R. A., Mars, A. E., Springer, J., Wolbert, E. J. H., van der Wal, H., de Vrije, T. G., Levisson, M., Leprince, A., Houweling-Tan, B., Moers, A., Hendriks, S. N. A., Mendes, O., Griekspoor, Y., Werten, M. W. T., Schaap, P. J., van der Oost, J. & Eggink, G., 2017, In : Metabolic Engineering. 42, p. 66-73

Research output: Contribution to journalArticleAcademicpeer-review

Monascus
Lactic acid
Industrial plants
Lactic Acid
Glucose
240 Citations (Scopus)

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., Degennaro, E. M., Winblad, N., Choudhury, S. R., Abudayyeh, O. O., Wu, W. Y. & van der Oost, J., 2017, In : Nature Biotechnology. 35, 1, p. 31-34

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Genes
Brain
Cells
5 Citations (Scopus)

Streptococcus caviae sp. nov., isolated from Guinea pig faecal samples

Palakawong Na Ayudthaya, S., Hilderink, L. J., van der Oost, J., de Vos, W. M. & Plugge, C. M., 2017, In : International Journal of Systematic and Evolutionary Microbiology. 67, 5, p. 1551-1556

Research output: Contribution to journalArticleAcademicpeer-review

Streptococcus
Poaceae
pig
guinea pigs
Guinea Pigs
90 Citations (Scopus)

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a

Swarts, D. C., van der Oost, J. & Jinek, M., 2017, In : Molecular Cell. 66, 2, p. 221-233.e4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Seeds
DNA
DNA Cleavage
2016
4 Citations (Scopus)

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T

Bosma, E. F., Koehorst, J. J., van Hijum, S. A. F. T., Renckens, B., Vriesendorp, B., van de Weijer, T., Schaap, P. J., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2016, In : Standards in Genomic Sciences. 11, 11 p., 52.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Nucleic Acid Databases
formate C-acetyltransferase
Bacillus
Acetates
Phosphate Acetyltransferase
22 Citations (Scopus)

CRISPR-Cas9 gene editing: Delivery aspects and therapeutic potential

Oude Blenke, E., Evers, M. J. W., Mastrobattista, E. & van der Oost, J., 2016, In : Journal of Controlled Release. 244, p. 139-148

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Associated Proteins
Therapeutics
Nobel Prize
Inborn Genetic Diseases
218 Citations (Scopus)

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

Mohanraju, P., Makarova, K. S., Zetsche, B., Zhang, F., Koonin, E. V. & van der Oost, J., 2016, In : Science. 353, 6299, 14 p., aad5147.

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Adaptive Immunity
Parasites
Genome
50 Citations (Scopus)

Harnessing the power of microbial autotrophy

Claassens, N. J., Machado de Sousa, D., Martins dos Santos, V., de Vos, W. M. & van der Oost, J., 2016, In : Nature Reviews Microbiology. 14, p. 692-706

Research output: Contribution to journalArticleAcademicpeer-review

Autotrophic Processes
Light
Semiconductors
Genetic Engineering
Biofuels
135 Citations (Scopus)

Healthy human gut phageome

Manrique, P., Bolduc, B., Walk, S. T., van der Oost, J., de Vos, W. M. & Young, M. J., 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 37, p. 10400-10405

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacteriophages
Metagenomics
Microbiota
7 Citations (Scopus)

Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy

Volpers, M., Claassens, N. J., Noor, E., van der Oost, J., de Vos, W. M., Kengen, S. W. M. & Martins dos Santos, V., 2016, In : PLoS ONE. 11, 6, e0157851.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Autotrophic Processes
Carbon Cycle
autotrophs
Computer Simulation
Calvin cycle
11 Citations (Scopus)

Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost

Daas, T., van de Weijer, T., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2016, In : Biotechnology for Biofuels. 9, 210.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Xylans
Lactic acid
compost
Lactic Acid
Bacteria
56 Citations (Scopus)

Next Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit

Mougiakos, I., Bosma, E. F., de Vos, W. M., van Kranenburg, R. & van der Oost, J., 2016, In : Trends in Biotechnology. 34, 7, p. 575-587

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Cas Systems
Genes
Bacteria
Chemical Phenomena

Nuclease-mediated genome editing

van der Oost, J., 20 Oct 2016, Patent No. WO2016166340, Priority date 16 Apr 2015

Research output: PatentOther research output

Open Access
Nucleic Acids
Peptides
Synthetic Biology
Synthetic Genes
Genetic Techniques

Riboswitch-controlled screening and selection of desired biocatalysts 

Creutzburg, S. C. A. & van der Oost, J., 20 Oct 2016, Patent No. WO2016166303, Priority date 16 Apr 2015

Research output: PatentOther research output

Open Access
Riboswitch
Enzymes
RNA Splicing
Bacterial Genomes
Reading Frames

Riboswitch inducible gene expression

Creutzburg, S. C. A. & van der Oost, J., 20 Oct 2016, Patent No. WO2016166310, Priority date 16 Apr 2015

Research output: PatentOther research output

Open Access
Riboswitch
Gene Expression
Enzymes
Reading Frames
Reporter Genes
8 Citations (Scopus)

Structural and biochemical characterisation of Archaeoglobus fulgidus esterase reveals a bound CoA molecule in the vicinity of the active site

Sayer, C., Finnigan, W., Isupov, M. N., Levisson, M., Kengen, S. W. M., van der Oost, J., Harmer, N. J. & Littlechild, J. A., 10 May 2016, In : Scientific Reports. 6, 25542.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Esterases
Coenzyme A
Molecules
Enzymes
Pantetheine

Thermostable Cas9 nucleases

van der Oost, J., Daas, M. J. A., Kengen, S. W. M. & de Vos, W. M., 15 Dec 2016, Patent No. WO2016198361, Priority date 12 Jun 2015

Research output: PatentOther research output

Open Access
Micrococcal Nuclease
Genetic Engineering
Nucleic Acids
DNA Cleavage
Peptides
2015
14 Citations (Scopus)

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

Sharma, K., Hrle, A., Kramer, K., Sachsenberg, T., Staals, R. H. J., Randau, L., Marchfelder, A., van der Oost, J., Kohlbacher, O., Conti, E. & Urlaub, H., 2015, In : Methods : a companion to Methods in enzymology. 89, p. 138-148

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Mass spectrometry
Mass Spectrometry
RNA
Proteins
803 Citations (Scopus)

An updated evolutionary classification of CRISPR-Cas systems

Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Brouns, S. J. J. & Van Der Oost, J., 2015, In : Nature Reviews Microbiology. 13, 11, p. 722-736

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Archaea
Immune System
Bacteria
56 Citations (Scopus)

Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

Swarts, D. C., Hegge, J. W., Hinojo, I., Shiimori, M., Ellis, M. A., Dumrongkulraksa, J., Terns, R. M., Terns, M. P. & Van Der Oost, J., 2015, In : Nucleic acids research. 43, 10, p. 5120-5129

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Pyrococcus furiosus
Deoxyribonucleases
Archaea
DNA
Guide RNA
13 Citations (Scopus)

Bacteriophage exclusion, a new defense system

Barrangou, R. & van der Oost, J., 2015, In : The EMBO Journal. 34, 2, p. 134-135

Research output: Contribution to journalArticleAcademicpeer-review

Bacteriophages
Clustered Regularly Interspaced Short Palindromic Repeats
Bacterial Genomes
Genes
DNA Restriction-Modification Enzymes
1 Citation (Scopus)

Beat their swords into ploughshares

van der Oost, J., 2015, In : Microbial Biotechnology. 8, 1, p. 34-35

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biotechnology
97 Citations (Scopus)

Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity

Charpentier, E., Richter, H., van der Oost, J. & White, M. F., 2015, In : FEMS Microbiology Reviews. 39, 3, p. 428-441

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Adaptive Immunity
CRISPR-Associated Proteins
RNA
207 Citations (Scopus)

Codon Bias as a Means to Fine-Tune Gene Expression

Quax, T. E. F., Claassens, N. J. H. P., Söll, D. & van der Oost, J., 2015, In : Molecular Cell. 59, 2, p. 149-161

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Codon
Gene Expression
Synthetic Biology
Genetic Code
Proteins
1195 Citations (Scopus)

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Zetsche, B., Gootenberg, JS., Abudayyeh, OO., Slaymaker, IM., Makarova, KS., Essletzbichler, P., Volz, SE., Joung, J., van der Oost, J., Regev, A., Koonin, EV. & Zhang, F., 2015, In : Cell. 163, 3, p. 759-771

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Endonucleases
RNA
Acidaminococcus
2 Citations (Scopus)

CRISPR sabotage

van der Oost, J. & Brouns, S. J. J., 2015, In : Genome Biology. 16, 1, 248.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
coevolution
CRISPR-Cas Systems
virus
Viruses
18 Citations (Scopus)

Effects of Argonaute on Gene Expression in Thermus thermophilus

Swarts, D. C., Koehorst, J. J., Westra, E. R., Schaap, P. J. & van der Oost, J., 2015, In : PLoS ONE. 10, 4, 13 p., e0124880.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Thermus thermophilus
Gene expression
plasmids
Plasmids
Gene Expression
10 Citations (Scopus)

Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains

Bosma, E. F., van de Weijer, A. H. P., Vlist, L., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2015, In : Microbial Cell Factories. 14, 12 p., 99.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Deletion
Bacilli
Bacillus
Metabolic engineering
Metabolic Engineering
9 Citations (Scopus)

Formation of the ether lipids archaetidylglycerol and archaetidylethanolamine in Escherichia coli

Caforio, A., Jain, S., Fodran, P., Siliakus, M., Minnaard, A. J., Van Der Oost, J. & Driessen, A. J. M., 2015, In : Biochemical Journal. 470, 3, p. 343-355 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Ether
Escherichia coli
Cytidine Diphosphate
Lipids
Biosynthesis
17 Citations (Scopus)

Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans

Kruse, T., van de Pas, B. A., Atteia, A., Krab, K., Hagen, W. R., Goodwin, L., Chain, P., Boeren, S., Maphosa, F., Schraa, G., de Vos, W. M., van der Oost, J., Smidt, H. & Stams, A. J. M., 2015, In : Journal of Bacteriology. 197, 5, p. 893-904

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
formic acid
Desulfitobacterium
Proteomics
Fumarates
Electrons
17 Citations (Scopus)

Isolation and Screening of Thermophilic Bacilli from Compost for Electrotransformation and Fermentation: Characterization of Bacillus smithii ET 138 as a New Biocatalyst

Bosma, E. F., van de Weijer, A. H. P., Daas, M. J. A., van der Oost, J., de Vos, W. M. & van Kranenburg, R., 2015, In : Applied and Environmental Microbiology. 81, 5, p. 1874-1883

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacillus smithii
accessibility
compost
Bacillus
composts
81 Citations (Scopus)

NADPH-generating systems in bacteria and archaea

Spaans, S. K., Weusthuis, R. A., van der Oost, J. & Kengen, S. W. M., 2015, In : Frontiers in Microbiology. 6, 47 p., 742.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Archaea
NADP
Bacteria
Regeneration
Isocitrate Dehydrogenase
60 Citations (Scopus)

Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

Taylor, D. W., Zhu, Y., Staals, R. H. J., Kornfeld, J. E., Shinkai, A., van der Oost, J., Nogales, E. & Doudna, J. A., 2015, In : Science. 348, 6234, p. 581-585

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Cryoelectron Microscopy
Adaptive Immunity
Nucleic Acids

Systematic optimization of coding sequence for functional protein expression

van der Oost, J., 9 Apr 2015, Patent No. WO2015048989, Priority date 2 Oct 2013

Research output: PatentOther research output

Open Access
Codon
Proteins
22 Citations (Scopus)

The chromosome copy number of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1

Spaans, S. K., van der Oost, J. & Kengen, S. W. M., 2015, In : Extremophiles. 19, 4, p. 741-750

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Thermococcus
Euryarchaeota
Polyploidy
Archaea
Chromosomes
2014
6 Citations (Scopus)

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

Blombach, F., Launay, H., Snijders, A. P., Zorraquino, V., Wu, H., de Koning, B., Brouns, S. J. J., Ettema, T. J., Camilloni, C., Cavalli, A., Vendruscolo, M., Dickman, M. J., Cabrita, L. D., La Teana, A., Benelli, D., Londei, P., Christodoulou, J. & van der Oost, J., 2014, In : Biochemical Journal. 462, 2, p. 373-384

Research output: Contribution to journalArticleAcademicpeer-review

Archaeal Proteins
Ribosomes
Ribosome Subunits
Proteins
Transcription
10 Citations (Scopus)

Biocatalytic asymmetric phosphorylation of mevalonate

Matsumi, R., Hellriegel, C., Schoenenberger, B., Milesi, T., van der Oost, J. & Wohlgemuth, R., 2014, In : RSC Advances : An international journal to further the chemical sciences. 4, 25, p. 12989-12994

Research output: Contribution to journalArticleAcademicpeer-review

mevalonate kinase
Mevalonic Acid
Phosphorylation
Phosphates
Biocatalysts
130 Citations (Scopus)

Crystal structure of the CRISPR RNA–guided surveillance complex from Escherichia coli

Jackson, R. N., Golden, S. M., Erp, P. B., Carter, J., Westra, E. R., Brouns, S. J. J., van der Oost, J., Terwilliger, T. C., Read, R. J. & Wiedenheft, B., 2014, In : Science. 345, 6203, p. 1473-1479

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Escherichia coli
Antiviral Agents
Nucleotides
RNA
15 Citations (Scopus)

DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications

Falcicchio, P., Wolterink-van Loo, S., Franssen, M. C. R. & van der Oost, J., 2014, In : Extremophiles. 18, 1, p. 1-13

Research output: Contribution to journalArticleAcademicpeer-review

Aldehyde-Lyases
Biochemistry
Carbon
Dihydroxyacetone Phosphate
Synthetic Chemistry Techniques

DNA-guided DNA interference by a prokaryotic Argonaute

van der Oost, J. & Swarts, D. C., 27 Nov 2014, Patent No. WO2014189628, Priority date 11 Apr 2013

Research output: PatentOther research output

Open Access
Nucleic Acids
DNA
Amino Acids
Chemical analysis
156 Citations (Scopus)

DNA-guided DNA interference by a prokaryotic Argonaute

Swarts, D. C., Jore, M. M., Westra, E. R., Zhu, Y., Janssen, J. H., Snijders, A. P., Wang, Y., Patel, D. J., Berenguer, J., Brouns, S. J. J. & van der Oost, J., 2014, In : Nature. 507, 7491, p. 258-261

Research output: Contribution to journalArticleAcademicpeer-review

RNA Interference
DNA
Argonaute Proteins
Guide RNA
RNA

Genetically engineered micro-organisms for production of fatty acids

Weusthuis, R. A., van der Oost, J. & Eggink, G., 30 Jan 2014, Patent No. WO2014016328, Priority date 25 Jul 2012

Research output: PatentOther research output

Open Access
fatty acid
micro-organism
method
16 Citations (Scopus)

Molecular Characterization of an NADPH-Dependent Acetoin Reductase/2,3-Butanediol Dehydrogenase from Clostridium beijerinckii NCIMB 8052

Raedts, J. G. J., Siemerink, M. A. J., Levisson, M., van der Oost, J. & Kengen, S. W. M., 2014, In : Applied and Environmental Microbiology. 80, 6, p. 2011-2020

Research output: Contribution to journalArticleAcademicpeer-review

butanediol dehydrogenase
Clostridium beijerinckii
butanediol
acetoin
NADP
40 Citations (Scopus)

Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3

Gong, B., Shin, M., Sun, J., Jung, C. H., Bolt, E. L., van der Oost, J. & Kim, J. S., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 46, p. 16359-16364

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Adenosine Triphosphate
Histidine
Aspartic Acid
Bacteria
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