1993 …2020

Research output per year

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Research Output

2020

Designing Eukaryotic Gene Expression Regulation Using Machine Learning

de Jongh, R. P. H., van Dijk, A. D. J., Julsing, M. K., Schaap, P. J. & de Ridder, D., Feb 2020, In : Trends in Biotechnology. 38, 2, p. 191-201

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

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

Strepis, N., Naranjo, H. D., Meier-Kolthoff, J., Göker, M., Shapiro, N., Kyrpides, N., Klenk, H. P., Schaap, P. J., Stams, A. J. M. & Sousa, D. Z., 8 Jan 2020, In : BMC Genomics. 21, 1, 24.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., Hatzimanikatis, V. & 49 others, van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D. Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B. J., Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M. & Zhang, C., 1 Mar 2020, In : Nature Biotechnology. 38, 3, p. 272-276 5 p.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
1 Citation (Scopus)
Open Access

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

Suarez-Diez, M., Porras, S., Laguna-Teno, F., Schaap, P. J. & Tamayo-Ramos, J. A., 24 Feb 2020, In : Scientific Reports. 10, 1, 3232.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2019

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

Odoni, D. I., Vazquez-Vilar, M., van Gaal, M. P., Schonewille, T., Martins Dos Santos, V. A. P., Tamayo-Ramos, J. A., Suarez-Diez, M. & Schaap, P. J., 1 Apr 2019, In : FEMS Microbiology Letters. 366, 7, fnz071.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Consistency, inconsistency, and ambiguity of metabolite names in biochemical databases used for genome-scale metabolic modelling

Pham, N., van Heck, R. G. A., van Dam, J. C. J., Schaap, P. J., Saccenti, E. & Suarez-Diez, M., 6 Feb 2019, In : Metabolites. 9, 2, 28.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

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

Subramanian, K., Mitusińska, K., Raedts, J., Almourfi, F., Joosten, H. J., Hendriks, S., Sedelnikova, S. E., Kengen, S. W. M., Hagen, W. R., Góra, A., Martins Dos Santos, V. A. P., Baker, P. J., van der Oost, J. & Schaap, P. J., 31 May 2019, In : Biomolecules. 9, 6, 212.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

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

Kampers, L. F. C., van Heck, R. G. A., Donati, S., Saccenti, E., Volkers, R. J. M., Schaap, P. J., Suarez-Diez, M., Nikel, P. I. & Martins Dos Santos, V. A. P., 22 Oct 2019, In : Microbial Cell Factories. 18, 1, 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Open Access
1 Citation (Scopus)
Open Access
2 Citations (Scopus)

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Kamminga, T., Slagman, S. J., Martins dos Santos, V. A. P., Bijlsma, J. J. E. & Schaap, P. J., Aug 2019, In : Trends in Biotechnology. 37, 8, p. 805-816

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Carreres, B. M., Mitsue León-Saiki, G., Schaap, P. J., Remmers, I. M., van der Veen, D., Martins dos Santos, V. A. P., Wijffels, R. H., Martens, D. E. & Suarez-Diez, M., 1 Jun 2019, In : Algal Research. 40, 101477.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

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

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., Martins dos Santos, V. A. P., Schaap, P. J. & Suarez-Diez, M., 4 Nov 2019, In : Scientific Data. 6, 1, 1 p., 254.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)
2018

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Versluis, D., Nijsse, B., Naim, M. A., Koehorst, J. J., Wiese, J., Imhoff, J. F., Schaap, P. J., van Passel, M. W. J., Smidt, H. & Sipkema, D., 8 Jan 2018, In : Genome Biology and Evolution. 10, 1, p. 125-142

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)
Open Access
14 Citations (Scopus)

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

Laothanachareon, T., Tamayo Ramos, J. A., Nijsse, B. & Schaap, P. J., 24 Sep 2018, In : Frontiers in Microbiology. 9, SEP, 14 p., 02269.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

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

Hugenholtz, F., Davids, M., Schwarz, J., Müller, M., Tomé, D., Schaap, P., Hooiveld, G. J. E. J., Smidt, H. & Kleerebezem, M., 1 Apr 2018, In : PLoS ONE. 13, 4, e0194066.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

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

van der Ark, K. C. H., Aalvink, S., Suarez-Diez, M., Schaap, P. J., de Vos, W. M. & Belzer, C., 1 May 2018, In : Microbial Biotechnology. 11, 3, p. 476-485

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Rienksma, R. A., Schaap, P. J., Martins Dos Santos, V. A. P. & Suarez-Diez, M., 3 Aug 2018, In : Frontiers in Cellular and Infection Microbiology. 8, 264.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

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

Subramanian, K., Góra, A., Spruijt, R., Mitusińska, K., Suarez-Diez, M., Martins Dos Santos, V. & Schaap, P. J., 1 Jan 2018, In : PLoS ONE. 13, 6, e0198990.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

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

de Jaeger, L., Carreres, B. M., Springer, J., Schaap, P. J., Eggink, G., Martins dos Santos, V. A. P., Wijffels, R. H. & Martens, D. E., 1 Apr 2018, In : PLoS ONE. 13, 4, e0194834.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

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

Ramiro-Garcia, J., Hermes, G. D. A., Giatsis, C., Sipkema, D., Zoetendal, E. G., Schaap, P. J. & Smidt, H., 23 Nov 2018, In : F1000Research. 5, 1791.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
28 Citations (Scopus)

Regulation of three virulence strategies of Mycobacterium tuberculosis: A success story

Zondervan, N. A., Van Dam, J. C. J., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez-Diez, M., 1 Feb 2018, In : International Journal of Molecular Sciences. 19, 2, 347.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

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

Koehorst, J. J., van Dam, J. C. J., Saccenti, E., Martins Dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 15 Apr 2018, In : Bioinformatics. 34, 8, p. 1401-1403

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

Studying microbial functionality within the gut ecosystem by systems biology

Hornung, B., Martins dos Santos, V. A. P., Smidt, H. & Schaap, P. J., 6 Mar 2018, In : Genes and Nutrition. 13, 1, 5.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)
2017

Aspergillus niger secretes citrate to increase iron bioavailability

Odoni, D. I., van Gaal, M. P., Schonewille, T., Tamayo-Ramos, J. A., Martins dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 2017, In : Frontiers in Microbiology. 8, AUG, 1424.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

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

Odoni, D. I., Tamayo-Ramos, J. A., Sloothaak, J., van Heck, R., Martins dos Santos, V. A. P., de Graaff, L. H., Suarez-Diez, M. & Schaap, P. J., 30 Mar 2017, In : PeerJ. 5, e3133.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Complete genome sequence of Akkermansia glycaniphila strain PytT, a mucin-degrading specialist of the reticulated python gut

Ouwerkerk, J. P., Koehorst, J. J., Schaap, P. J., Ritari, J., Paulin, L., Belzer, C. & de Vos, W. M., 5 Jan 2017, In : Genome Announcements. 5, 1, e01098-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Concurrent haloalkanoate degradation and chlorate reduction by Pseudomonas chloritidismutans AW-1T

Peng, P., Zheng, Y., Koehorst, J. J., Schaap, P. J., Stams, F., Smidt, H. & Atashgahi, S., 2017, In : Applied and Environmental Microbiology. 83, 12, 11 p., e00325-17.

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Draft genome sequence of the oleaginous green alga Tetradesmus obliquus UTEX 393

Carreres, B. M., de Jaeger, L., Springer, J., Barbosa, M. J., Breuer, G., van den End, E. J., Kleinegris, D. M. M., Schäffers, I., Wolbert, E. J. H., Zhang, H., Lamers, P. P., Martins dos Santos, V. A. P., Wijffels, R. H., Eggink, G., Schaap, P. J. & Martens, D. E., 2017, In : Genome Announcements. 5, 3, e01449-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)
29 Citations (Scopus)

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

Gerritsen, J., Hornung, B., Renckens, B., van Hijum, S. A. F. T., Martins dos Santos, V. A. P., Rijkers, G. T., Schaap, P. J., de Vos, W. M. & Smidt, H., 2017, In : PeerJ. 2017, 9, 3698.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

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

Schulze, S., Urzica, E., Reijnders, M. J. M. F., van de Geest, H., Warris, S., Bakker, L. V., Fufezan, C., Martins dos Santos, V. A. P., Schaap, P. J., Peters, S. A. & Hippler, M., 2017, In : New Phytologist. 215, 4, p. 1361-1369

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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
7 Citations (Scopus)

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., Schaap, P. J. & Suarez-Diez, M., 5 Sep 2017, BioRxiv, 9 p.

Research output: Working paperAcademic

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

Kamminga, T., Slagman, S. J., Bijlsma, J. J. E., Martins dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 2017, In : Biotechnology and Bioengineering. 114, 10, p. 2339-2347

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 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

3 Citations (Scopus)

Persistence of functional protein domains in mycoplasma species and their role in host specificity and synthetic minimal life

Kamminga, T., Koehorst, J. J., Vermeij, P., Slagman, S. J., dos Santos, V. A. P. M., Bijlsma, J. J. E. & Schaap, P. J., 2017, In : Frontiers in Cellular and Infection Microbiology. 7, 31.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)
Open Access
7 Citations (Scopus)
2016

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

Koehorst, J. J., van Dam, J. C. J., van Heck, R. G. A., Saccenti, E., Martins dos Santos, V., Suarez-Diez, M. & Schaap, P. J., 2016, In : Scientific Reports. 6, 13 p., 38699.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
14 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
4 Citations (Scopus)

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

Strepis, N., Sánchez-Andrea, I., van Gelder, T., van Kruistum, H., Shapiro, N., Kyrpides, N., Göker, M., Klenk, H. P., Schaap, P., Stams, F. & Sousa, D. Z., 2016, In : International Journal of Systematic and Evolutionary Microbiology. 66, 10, p. 3957-3963

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

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

Davids, M., Hugenholtz, F., Martins dos Santos, V. A. P., Smidt, H., Kleerebezem, M. & Schaap, P. J., 2016, In : PLoS ONE. 11, 1, 18 p., e0146423.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

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

Mehboob, F., Oosterkamp, M. J., Koehorst, J. J., Farrakh, S., Veuskens, T., Plugge, C. M., Boeren, S., de Vos, W. M., Schraa, G., Stams, A. J. M. & Schaap, P. J., 2016, In : Environmental Microbiology. 18, 10, p. 3247-3257

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)

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

Sloothaak, J., Tamayo-Ramos, J. A., Odoni, D. I., Laothanachareon, T., Derntl, C., Mach-Aigner, A. R., Martins Dos Santos, V. A. P. & Schaap, P. J., 2016, In : Biotechnology for Biofuels. 9, 1, 148.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
17 Citations (Scopus)

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

Sloothaak, J., Odoni, D. I., Martins dos Santos, V. A. P., Schaap, P. J. & Tamayo Ramos, J. A., 16 Dec 2016, In : Plos Genetics. 12, 12, e1006468.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

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

Visser, M., Pieterse, M. M., Pinkse, M. W. H., Nijsse, B., Verhaert, P. D. E. M., de Vos, W. M., Schaap, P. J. & Stams, A. J. M., 2016, In : Environmental Microbiology. 18, 9, p. 2843-2855

Research output: Contribution to journalArticleAcademicpeer-review

9 Citations (Scopus)
2015

Algal Omics: The Functional Annotation Challenge

Reijnders, M. J. M. F., Carreres, B. M. & Schaap, P. J., 2015, In : Current Biotechnology. 4, 4, p. 457-463

Research output: Contribution to journalArticleAcademicpeer-review