PJ Schaap
PJ Schaap
Associate professor, Systems and Synthetic Biology, Wageningen University, The Netherlands
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Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
HJ Pel, JH de Winde, DB Archer, PS Dyer, G Hofmann, PJ Schaap, ...
Nature biotechnology 25 (2), 221-231, 2007
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
MR Andersen, MP Salazar, PJ Schaap, PJI van de Vondervoort, D Culley, ...
Genome research 21 (6), 885-897, 2011
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus
RHJ Staals, Y Zhu, DW Taylor, JE Kornfeld, K Sharma, A Barendregt, ...
Molecular cell 56 (4), 518-530, 2014
Structure and activity of the RNA-targeting Type III-B CRISPR-Cas complex of Thermus thermophilus
RHJ Staals, Y Agari, S Maki-Yonekura, Y Zhu, DW Taylor, E Van Duijn, ...
Molecular cell 52 (1), 135-145, 2013
NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes
J Ramiro-Garcia, GDA Hermes, C Giatsis, D Sipkema, EG Zoetendal, ...
F1000Research 5, 2016
Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle
N Ottman, M Davids, M Suarez-Diez, S Boeren, PJ Schaap, ...
Applied and environmental microbiology 83 (18), e01014-17, 2017
3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities
RK Kuipers, HJ Joosten, WJH Van Berkel, NGH Leferink, E Rooijen, ...
Proteins: Structure, Function, and Bioinformatics 78 (9), 2101-2113, 2010
Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics
ES Martens-Uzunova, PJ Schaap
Fungal Genetics and Biology 46 (1), S170-S179, 2009
TheAgaricus bisporus hypAgene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development
PWJ De Groot, PJ Schaap, ASM Sonnenberg, J Visser, ...
Journal of molecular biology 257 (5), 1008-1018, 1996
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
MM Leimena, J Ramiro-Garcia, M Davids, B van den Bogert, H Smidt, ...
BMC genomics 14, 1-14, 2013
Oxaloacetate hydrolase, the C–C bond lyase of oxalate secreting fungi
Y Han, HJ Joosten, W Niu, Z Zhao, PS Mariano, M McCalman, J Van Kan, ...
Journal of Biological Chemistry 282 (13), 9581-9590, 2007
An iterative workflow for mining the human intestinal metaproteome
K Rooijers, C Kolmeder, C Juste, J Doré, M De Been, S Boeren, P Galan, ...
BMC genomics 12, 1-11, 2011
Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation
NAL Flahaut, A Wiersma, B van de Bunt, DE Martens, PJ Schaap, ...
Applied microbiology and biotechnology 97, 8729-8739, 2013
Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing
RA Rienksma, M Suarez-Diez, HJ Mollenkopf, GM Dolganov, A Dorhoi, ...
BMC genomics 16, 1-15, 2015
Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
J Gerritsen, B Hornung, B Renckens, SAFT van Hijum, VAPM Dos Santos, ...
PeerJ 5, e3698, 2017
A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities
P Worm, JJ Koehorst, M Visser, VT Sedano-Núñez, PJ Schaap, ...
Biochimica et Biophysica Acta (BBA)-Bioenergetics 1837 (12), 2004-2016, 2014
NG-Tax 2.0: a semantic framework for high-throughput amplicon analysis
W Poncheewin, GDA Hermes, JCJ Van Dam, JJ Koehorst, H Smidt, ...
Frontiers in Genetics 10, 458455, 2020
Identification of a Gatekeeper Residue That Prevents Dehydrogenases from Acting as Oxidases*♦
NGH Leferink, MW Fraaije, HJ Joosten, PJ Schaap, A Mattevi, ...
Journal of Biological Chemistry 284 (7), 4392-4397, 2009
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
M Braaksma, ES Martens-Uzunova, PJ Punt, PJ Schaap
BMC genomics 11, 1-11, 2010
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