User profiles for P. J. Schaap

PJ Schaap

Associate professor, Systems and Synthetic Biology, Wageningen University, The …
Verified email at wur.nl
Cited by 8858

[HTML][HTML] Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

…, DB Archer, PS Dyer, G Hofmann, PJ Schaap… - Nature …, 2007 - nature.com
The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for
the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-…

[HTML][HTML] A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities

…, M Visser, VT Sedano-Núñez, PJ Schaap… - … et Biophysica Acta (BBA …, 2014 - Elsevier
In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed
and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and …

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

MR Andersen, MP Salazar, PJ Schaap… - Genome …, 2011 - genome.cshlp.org
The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found
globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic …

MEMOTE for standardized genome-scale metabolic model testing

…, A Richelle, I Rocha, BJ Sánchez, PJ Schaap… - Nature …, 2020 - nature.com
To the Editor—Reconstructing metabolic reaction networks enables the development of
testable hypotheses of an organism’s metabolism under different conditions 1. State-of-the-art …

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

…, T Suzuki, N Dohmae, S Yokoyama, PJ Schaap… - Molecular cell, 2014 - cell.com
CRISPR-Cas is a prokaryotic adaptive immune system that provides sequence-specific
defense against foreign nucleic acids. Here we report the structure and function of the effector …

Green genes: bioinformatics and systems-biology innovations drive algal biotechnology

…, VAPM dos Santos, AG Smith, PJ Schaap - Trends in …, 2014 - cell.com
Many species of microalgae produce hydrocarbons, polysaccharides, and other valuable
products in significant amounts. However, large-scale production of algal products is not yet …

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

…, K Sakamoto, A Masuda, N Dohmae, PJ Schaap… - Molecular cell, 2013 - cell.com
The CRISPR-Cas system is a prokaryotic host defense system against genetic elements. The
Type III-B CRISPR-Cas system of the bacterium Thermus thermophilus, the TtCmr complex…

Designing eukaryotic gene expression regulation using machine learning

…, ADJ van Dijk, MK Julsing, PJ Schaap… - Trends in …, 2020 - cell.com
Controlling the expression of genes is one of the key challenges of synthetic biology. Until
recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their …

[HTML][HTML] NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

…, C Giatsis, D Sipkema, EG Zoetendal, PJ Schaap… - …, 2016 - ncbi.nlm.nih.gov
Background: Massive high-throughput sequencing of short, hypervariable segments of the
16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing …

3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities

…, VAP Martins dos Santos, PJ Schaap - Proteins: Structure …, 2010 - Wiley Online Library
Ten years of experience with molecular class–specific information systems (MCSIS) such as
with the hand‐curated G protein–coupled receptor database (GPCRDB) or the …