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List of works by John van der Oost

"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus

scientific article

9 Functional Genomics of the Thermo-Acidophilic Archaeon Sulfolobus solfataricus

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

scientific article published on 9 April 2013

A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes

scientific article published on 17 September 2007

A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts

scientific article

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

scientific article

Alternative affinity tools: more attractive than antibodies?

scientific article published on May 2011

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

scientific article published on 8 April 2011

An updated evolutionary classification of CRISPR-Cas systems

scientific article

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

scientific article

Argonaute bypasses cellular obstacles without hindrance during target search

scientific article published on 26 September 2019

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

scientific article published on January 2011

Bacteriophage exclusion, a new defense system

scientific article published on 12 December 2014

Beat their swords into ploughshares

scientific article published on January 2015

Biochemical adaptations of two sugar kinases from the hyperthermophilic archaeon Pyrococcus furiosus

scientific article published on August 2002

Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases

scientific article

Biochemical characterization of the xylan hydrolysis profile of the extracellular endo-xylanase from Geobacillus thermodenitrificans T12.

scientific article

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

scientific article

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

scientific article published on 19 April 2012

CRISPR sabotage

scientific article

CRISPR-Cas ribonucleoprotein mediated homology-directed repair for efficient targeted genome editing in microalgae IMET1

scientific article published on 25 March 2019

CRISPR-Cas9 gene editing: Delivery aspects and therapeutic potential

scientific article published on 4 August 2016

CRISPR-based adaptive and heritable immunity in prokaryotes

scientific article published on 29 July 2009

Calcium-induced tertiary structure modifications of endo-beta-1,3-glucanase from Pyrococcus furiosus in 7.9 M guanidinium chloride

scientific article published on March 2005

Cascade-mediated binding and bending of negatively supercoiled DNA.

scientific article published on September 2012

Characterization and structural modeling of a new type of thermostable esterase from Thermotoga maritima

scientific journal article

Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense

scientific article published on April 2006

Characterization of aptamer-protein complexes by X-ray crystallography and alternative approaches

scientific article published on 22 August 2012

Characterization of plasmid pRT1 from Pyrococcus sp. strain JT1.

scientific article

Cloning and expression of islandisin, a new thermostable subtilisin from Fervidobacterium islandicum, in Escherichia coli

scientific article

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

scientific article published on 07 February 2011

Codon Bias as a Means to Fine-Tune Gene Expression

scientific article published on July 2015

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

scientific article published on 24 August 2016

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system

scientific article

CprK crystal structures reveal mechanism for transcriptional control of halorespiration

scientific article

Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain

scientific article

Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus

scientific article

Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus--structural basis of substrate recognition

scientific article

Crystal structure of fervidolysin from Fervidobacterium pennivorans, a keratinolytic enzyme related to subtilisin

scientific article

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

scientific article published on 29 October 2013

DNA-guided DNA interference by a prokaryotic Argonaute

scientific article published on 16 February 2014

Differential translation tunes uneven production of operon-encoded proteins

scientific article published on 5 September 2013

Discovering novel biology by in silico archaeology

scientific article

Divergent roles of CprK paralogues from Desulfitobacterium hafniense in activating gene expression

scientific article published in December 2008

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

scientific article

Effects of Argonaute on Gene Expression in Thermus thermophilus

scientific article published on 22 April 2015

Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9.

scientific article published on February 2017

Engineering a selectable marker for hyperthermophiles

scientific article published on 7 January 2005

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

scientific article

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

scientific article published on 19 December 2019

Fidelity in archaeal information processing

scientific article published on 05 September 2010

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae

scientific article published on 2 November 2017

Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form

scientific article published on 25 October 2006

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

scientific article

Functional study on GTP hydrolysis by the GTP-binding protein from Sulfolobus solfataricus, a member of the HflX family

scientific article

Genome editing by natural and engineered CRISPR-associated nucleases

scientific article published on 18 June 2018

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

scientific article

Guide-free Cas9 from pathogenic Campylobacter jejuni bacteria causes severe damage to DNA

scientific article published on 17 June 2020

Harnessing the power of microbial autotrophy

scientific article published on 26 September 2016

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

scientific article published on 18 November 2019

Healthy human gut phageome

scientific article published on 29 August 2016

Hot Transcriptomics ⬇️

scientific article published on February 7, 2011

Hydrogen production by hyperthermophilic and extremely thermophilic bacteria and archaea: mechanisms for reductant disposal

scientific article

Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism

scientific article

Identification of a novel alpha-galactosidase from the hyperthermophilic archaeon Sulfolobus solfataricus

scientific article published on April 2006

Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Crenarchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea

scientific article published on 14 October 2009

Identification of modules in Aspergillus niger by gene co-expression network analysis

scientific article published on 27 March 2010

Identification of the Missing Links in Prokaryotic Pentose Oxidation Pathways

scientific article published in Journal of Biological Chemistry

Improving low-temperature activity of Sulfolobus acidocaldarius 2-keto-3-deoxygluconate aldolase

scientific article

Initial Mutations Direct Alternative Pathways of Protein Evolution ⬇️

scientific article published on March 3, 2011

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

scientific article

Isolation and screening of thermophilic bacilli from compost for electrotransformation and fermentation: characterization of Bacillus smithii ET 138 as a new biocatalyst

scientific article

Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost

scientific article published on 06 October 2016

Isoprenoid biosynthesis in Archaea – Biochemical and evolutionary implications ⬇️

scientific article published on October 27, 2010

Kinetic and stoichiometric characterisation of streptavidin-binding aptamers

scientific article

Massive activation of archaeal defense genes during viral infection

scientific article published on 22 May 2013

Molecular and biochemical characterization of a distinct type of fructose-1,6-bisphosphatase from Pyrococcus furiosus

scientific article

Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima.

scientific article

Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator

scientific article

Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans

scientific article

Molecular characterization of phosphoglycerate mutase in archaea

scientific article

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

scientific article

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

scientific article published on 05 December 2016

Multiplex genome editing of microorganisms using CRISPR-Cas

scientific article published on 01 April 2019

NADPH-generating systems in bacteria and archaea

scientific article (publication date: 2015)

Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa

scientific article

Next Generation Prokaryotic Engineering: The CRISPR-Cas Toolkit

scientific article published on March 2016

Occurrence of L-iduronic acid and putative D-glucuronyl C5-epimerases in prokaryotes ⬇️

scientific article published on February 24, 2011

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

scientific article published on 01 November 2019

Phage display of engineered binding proteins

scientific article

Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms

scientific article published on 09 October 2013

Production and characterization of a thermostable alcohol dehydrogenase that belongs to the aldo-keto reductase superfamily

scientific article

Production by Clostridium acetobutylicum ATCC 824 of CelG, a cellulosomal glycoside hydrolase belonging to family 9.

scientific article

Prokaryotic Argonaute proteins: novel genome-editing tools?

scientific article

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

scientific article

Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans

scientific article

Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus

scientific article published on 28 February 2007

RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus

scientific article

RNAi: prokaryotes get in on the act.

scientific article

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

scientific article published in March 2006

Reporter-based screening and selection of enzymes

scientific article published on 29 April 2013

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

scientific article published on February 2009

Small CRISPR RNAs guide antiviral defense in prokaryotes

scientific article

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

scientific article

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

scientific article

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli

scientific article

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

scientific article

Structural features of a hyperthermostable endo-beta-1,3-glucanase in solution and adsorbed on "invisible" particles

scientific article published on 29 October 2004

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

scientific article

Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus

scientific article published in October 2013

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

scientific article

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

scientific article

Substrate specificity and mechanism from the structure of Pyrococcus furiosus galactokinase

scientific article

Substrate specificity engineering of beta-mannosidase and beta-glucosidase from Pyrococcus by exchange of unique active site residues

scientific article

The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity

scientific article

The Lrp family of transcriptional regulators

scientific article

The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut

scientific article published on 13 March 2019

The chromosome copy number of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1.

scientific article published on 8 May 2015

The evolutionary journey of Argonaute proteins

scientific article

The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation

scientific article

Thermal stabilization of an endoglucanase by cyclization

scientific article published on June 2012

Towards next-generation cell factories by rational genome-scale engineering

Transcription of the rod-shaped viruses SIRV1 and SIRV2 of the hyperthermophilic archaeon sulfolobus

scientific article published on November 2004

Type III-B CRISPR-Cas cascade of proteolytic cleavages

scientific article published on 01 February 2024

Unravelling the structural and mechanistic basis of CRISPR-Cas systems

scientific article

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

scientific article published on February 18, 2011

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