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List of works by Peter J. Schaap

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

scientific article

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth-associated genes

scientific article published on 16 March 2021

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

scientific article

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

scientific article published on 26 June 2014

A protocol for adding knowledge to Wikidata, a case report

scientific article published on 07 April 2020

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses ⬇️

January 2021 scholarly article

An endo-1,4-beta-xylanase-encoding gene from Agaricus bisporus is regulated by compost-specific factors

scientific article published on March 1998

An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation

scientific article

An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

scientific article

An iterative workflow for mining the human intestinal metaproteome

scientific article

Aspergillus niger Secretes Citrate to Increase Iron Bioavailability.

scientific article published on 2 August 2017

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

scientific article published on 01 April 2019

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters.

scientific article published on 17 September 2015

Assembly and Comparison of Ca. Neoehrlichia mikurensis Genomes

scientific article published in 2022

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

scientific article published on 14 September 2015

Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics.

scientific article published in March 2009

Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

scientific article published in 2023

Characterisation of Aspergillus niger prolyl aminopeptidase

scientific article published on 15 January 2005

Characterisation of the Aspergillus niger dapB gene, which encodes a novel fungal type IV dipeptidyl aminopeptidase

scientific article

Cloning and characterization of two rhamnogalacturonan hydrolase genes from Aspergillus niger.

scientific article published on July 1997

Cloning and expression of candidate allergens from Culicoides obsoletus for diagnosis of insect bite hypersensitivity in horses.

scientific article

Cloning of a prolidase gene from Aspergillus nidulans and characterisation of its product

scientific article published on 9 March 2002

Cloning, sequence and expression of the gene coding for rhamnogalacturonase ofAspergillus aculeatus; a novel pectinolytic enzyme ⬇️

scientific article published on October 1, 1995

Comparative genomics highlights symbiotic capacities and high metabolic flexibility of the marine genus Pseudovibrio

scientific article published on 8 January 2018

Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice

scientific article published on 23 June 2015

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

scientific article

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

scientific article published on 30 March 2017

Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data

scientific article (publication date: 6 December 2016)

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut.

scientific article published on 5 January 2017

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T))

scientific article published on 11 December 2012

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

scientific article published on 24 August 2016

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

scientific article

Concurrent Haloalkanoate Degradation and Chlorate Reduction by Pseudomonas chloritidismutans AW-1T.

scientific article

Consistency, Inconsistency and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome Scale Metabolic Modelling

scientific article published on 27 December 2018

Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling

scientific article published on 06 February 2019

CorNet: Assigning function to networks of co-evolving residues by automated literature mining

scientific article

Correlated mutation analyses on super-family alignments reveal functionally important residues

scientific article published in August 2009

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach

scientific article published on 19 February 2018

Description of Trichococcus ilyis sp. nov. by combined physiological and in silico genome hybridization analyses

scientific article

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

scientific article published on 17 August 2019

Different temporal and spatial expression of two hydrophobin-encoding genes of the edible mushroom Agaricus bisporus

scientific article published in May 1999

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcus furiosus Phosphoglucose Isomerase

scientific article published on 31 May 2019

Draft Genome Sequence of the Oleaginous Green Alga Tetradesmus obliquus UTEX 393.

scientific article published on 19 January 2017

Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S.

scientific article

Effects of Argonaute on Gene Expression in Thermus thermophilus

scientific article published on 22 April 2015

FAIR data station for lightweight metadata management and validation of omics studies

scientific article published in 2022

Forward Genetics by Genome Sequencing Uncovers the Central Role of the Locus in Hydrogen Peroxide Induced Glucose Oxidase Expression

article

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline

scientific article published on 12 January 2016

Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans

scientific article published in March 2014

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.).

scientific article

Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium

scientific article

Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T)

scientific article published on 15 April 2013

Genome and proteome analysis of Pseudomonas chloritidismutans AW-1T that grows on n-decane with chlorate or oxygen as electron acceptor

scientific article published on 20 April 2015

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

scientific article

Genome-Scale Model and Omics Analysis of Metabolic Capacities of Akkermansia muciniphila Reveal a Preferential Mucin-Degrading Lifestyle

scientific article published on 7 July 2017

Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species

scientific article published on 08 January 2020

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

scientific article published on 24 August 2013

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

scientific article published on 06 January 2021

Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

scientific article published in December 2020

Genome-scale metabolic modelling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

scientific article published on 9 July 2020

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine.

scientific article published on 11 September 2017

Genomic convergence between Akkermansia muciniphila in different mammalian hosts

scientific article published on 29 October 2021

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

scientific article published on 21 October 2014

Identification and functional characterization of novel xylose transporters from the cell factories Aspergillus niger and Trichoderma reesei

scientific article

Identification of a Novel L-rhamnose Uptake Transporter in the Filamentous Fungus Aspergillus niger

scientific article

Identification of a gatekeeper residue that prevents dehydrogenases from acting as oxidases.

scientific article

Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method

scientific article published in January 2008

Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni

scientific article published on 24 July 2017

Identification of regulatory mutants of Aspergillus aculeatus affected in rhamnogalacturonan hydrolase expression

scientific article published on 01 November 1996

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

scientific article published on 13 September 2017

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

scientific article published on 22 October 2019

In vivo and in vitro analysis of structure-function relationships in ribosomal protein L25 from Saccharomyces cerevisiae.

scientific article

Induction of glucose oxidase, catalase, and lactonase in Aspergillus niger

scientific article published on 01 November 1993

Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis

scientific article

Lignin degradation by Agaricus bisporus accounts for a 30% increase in bioavailable holocellulose during cultivation on compost

scientific article published on 01 April 2003

Lysine aminopeptidase of Aspergillus niger

scientific article published in August 2001

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains

scientific article published on 23 November 2021

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate

scientific article published on 10 June 2017

Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation.

scientific article published on 29 August 2013

Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas

scientific article published on 02 December 2019

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut.

scientific article

Model-driven design of a minimal medium for Akkermansia muciniphila confirms mucus adaptation

scientific article

Modeling Host-Pathogen Interaction to Elucidate the Metabolic Drug Response of Intracellular

scientific article published on 08 May 2019

Modeling the Metabolic State of Upon Infection

scholarly article by Rienk A Rienksma et al published 2018 in Frontiers in cellular and infection microbiology

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access.

scientific article published on 15 June 2018

Molecular characterization of the glnA gene encoding glutamine synthetase from the edible mushroom Agaricus bisporus ⬇️

scientific article published on September 1, 1997

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

scientific article published on 02 June 2017

Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress

scientific article published on 13 April 2018

Novel tools for extraction and validation of disease-related mutations applied to Fabry disease

scientific article published on 01 September 2010

Overexpression of the Aspergillus niger GatA transporter leads to preferential use of D-galacturonic acid over D-xylose

scientific article published on 23 August 2014

Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi.

scientific article published on 23 January 2007

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life.

scientific article published on 7 February 2017

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.

scientific article published on 15 August 2016

Proteomic Analysis of the Secretory Response of Aspergillus niger to D-Maltose and D-Xylose ⬇️

scientific article published on June 17, 2011

Proteomic analysis of nitrate-dependent acetone degradation by Alicycliphilus denitrificans strain BC.

scientific article published on 14 May 2015

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource

scientific article (publication date: 2015)

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

scientific article

Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story

scientific article

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

scientific article published on 05 April 2019

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

scientific article published on 23 November 2017

Shotgun proteomics of Aspergillus niger microsomes upon D-xylose induction.

scientific article published on 7 May 2010

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

scientific article published in October 2013

Studying microbial functionality within the gut ecosystem by systems biology

scientific article published on 6 March 2018

Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets

scientific article

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

scientific article published on 04 November 2019

The primary structure of a gene encoding yeast ribosomal protein L34.

scientific article published in December 1984

Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets

scientific article published on 24 February 2020

Unravelling the one-carbon metabolism of the acetogen Sporomusa strain An4 by genome and proteome analysis.

scientific article published on 3 July 2015

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