Research Output

2017

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)

Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimentabolous insect, the damselfly Ischnura elegans

Simon, S., Sagasser, S., Saccenti, E., Brugler, M. R., Schranz, M. E., Hadrys, H., Amato, G. & DeSalle, R., 19 Oct 2017, In : Scientific Reports. 7, 1, 14 p., 13547.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 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)

Considering Horn’s Parallel Analysis from a Random Matrix Theory Point of View

Saccenti, E. & Timmerman, M. E., 2017, In : Psychometrika. 82, 1, p. 186-209

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans

Snoek, B. L., Sterken, M. G., Bevers, R. P. J., Volkers, R. J. M., van 't Hof, A., Brenchley, R., Riksen, J. A. G., Cossins, A. & Kammenga, J. E., 2017, In : BMC Genomics. 18, 15 p., 500.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)
19 Citations (Scopus)

Designing synthetic networks in silico: A generalised evolutionary algorithm approach

Smith, R. W., van Sluijs, B. & Fleck, C., 2 Dec 2017, In : BMC Systems Biology. 11, 1, 118.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine

Kar, S. K., Jansman, A. J. M., Benis, N., Ramiro-Garcia, J., Schokker, D., Kruijt, L., Stolte, E. H., Taverne-Thiele, J. J., Smits, M. A. & Wells, J. M., 1 Nov 2017, In : PLoS ONE. 12, 11, e0188282.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Diurnal dynamics of gaseous and dissolved metabolites and microbiota composition in the bovine rumen

van Lingen, H. J., Edwards, J. E., Vaidya, J. D., van Gastelen, S., Saccenti, E., van den Bogert, B., Bannink, A., Smidt, H., Plugge, C. M. & Dijkstra, J., 2017, In : Frontiers in Microbiology. 8, MAR, 425.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)

Draft genome sequence of Actinomyces succiniciruminis strain Am4T, isolated from cow rumen fluid

Palakawong Na Ayudthaya, S., Hornung, B., Ravikumar Varadarajan, A., Plugge, W. & Plugge, C. M., 20 Jul 2017, In : Genome Announcements. 5, 29, e01587-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (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
13 Citations (Scopus)

Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months

Hugenholtz, F., Ritari, J., Nylund, L., Davids, M., Satokari, R. & De Vos, W. M., 2017, In : International Journal of Microbiology. 2017, 9547063.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)
25 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
15 Citations (Scopus)

Geochemical and microbial community determinants of reductive dechlorination at a site biostimulated with glycerol

Atashgahi, S., Lu, Y., Zheng, Y., Saccenti, E., Suarez-Diez, M., Ramiro-Garcia, J., Eisenmann, H., Elsner, M., J.M. Stams, A., Springael, D., Dejonghe, W. & Smidt, H., 2017, In : Environmental Microbiology. 19, 3, p. 968-981

Research output: Contribution to journalArticleAcademicpeer-review

28 Citations (Scopus)

Group-wise Principal Component Analysis for Exploratory Data Analysis

Camacho, J., Rodriquez-Gomez, R. A. & Saccenti, E., 2017, In : Journal of Computational and Graphical Statistics. 26, 3, p. 501-512

Research output: Contribution to journalArticleAcademicpeer-review

7 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)

Interactions and functionalities of the gut revealed by computational approaches

Benis, N., 2017, Wageningen: Wageningen University. 247 p.

Research output: Thesisinternal PhD, WU

Open Access

Interactions Between phyB and PIF Proteins Alter Thermal Reversion Reactions in vitro

Smith, R. W., Helwig, B., Westphal, A. H., Pel, E., Borst, J. W. & Fleck, C., 1 Nov 2017, In : Photochemistry and Photobiology. 93, 6, p. 1525-1531

Research output: Contribution to journalArticleAcademicpeer-review

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)

Metabolic modeling to understand and redesign microbial systems

van Heck, R. G. A., 2017, Wageningen: Wageningen University. 239 p.

Research output: Thesisinternal PhD, WU

Modeling spatial pattern formation in plant development

Adibi, M., 2017, Wageningen: Wageningen University. 209 p.

Research output: Thesisinternal PhD, WU

Open Access

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)

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

van der Ark, K. C. H., van Heck, R. G. A., Martins Dos Santos, V. A. P., Belzer, C. & de Vos, W. M., 14 Jul 2017, In : Microbiome. 5, 1, p. 78

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them

Benis, N., Kar, S. K., Martins dos Santos, V. A. P., Smits, M. A., Schokker, D. & Suarez-Diez, M., 2017, In : Frontiers in Physiology. 8, 11 p., 388.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Organic acid production in Aspergillus niger and other filamentous fungi

Odoni, D. I., 2017, Wageningen: Wageningen University. 207 p.

Research output: Thesisinternal PhD, WU

Open Access

P316 New approaches for IBD management based on text mining of digitalised medical reports and latent class modelling

Bergey, F., Saccenti, E., Jonkers, D., Van Den Heuvel, T., Jeuring, S., Pierik, M. & Martins Dos Santos, V., 1 Feb 2017, In : Journal of Crohn's and Colitis. 11, suppl_1, p. S237-S238

Research output: Contribution to journalAbstractAcademic

Open Access

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
2 Citations (Scopus)

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling

Suarez-Diez, M., Adam, J., Adamski, J., Chasapi, S. A., Luchinat, C., Peters, A., Prehn, C., Santucci, C., Spyridonidis, A., Spyroulias, G. A., Tenori, L., Wang-Sattler, R. & Saccenti, E., 2017, In : Journal of Proteome Research. 16, 7, p. 2547-2559

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)
Open Access
3 Citations (Scopus)
Open Access
1 Citation (Scopus)

Read all about it!? Public accountability, fragmented global climate governance and the media

Karlsson-Vinkhuyzen, S. I., Friberg, L. & Saccenti, E., 2017, In : Climate Policy. 17, 8, p. 982-997

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

Timmers, P. H. A., Welte, C. U., Koehorst, J. J., Plugge, C. M., Jetten, M. S. M. & Stams, A. J. M., 2017, In : Archaea : an international microbiological journal. 2017, 1654237.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
81 Citations (Scopus)

Stochastic gene expression in Arabidopsis thaliana

Araújo, I. S., Pietsch, J. M., Keizer, E. M., Greese, B., Balkunde, R., Fleck, C. & Hülskamp, M., 1 Dec 2017, In : Nature Communications. 8, 1, 2132.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Structure and function of Aspergillus niger laccase McoG

Ferraroni, M., Westphal, A. H., Borsani, M., Tamayo Ramos, J. A., Briganti, F., de Graaff, L. H. & van Berkel, W. J. H., 8 Feb 2017, In : Biocatalysis. 3, 1, p. 1-21

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

Kamminga, T., 2017, Wageningen: Wageningen University. 152 p.

Research output: Thesisinternal PhD, WU

The effect of Mycobacterium avium subspecies paratuberculosis infection on clinical mastitis occurrence in dairy cows

Rossi, G., Grohn, Y. T., Schukken, Y. H. & Smith, R. L., 2017, In : Journal of Dairy Science. 100, 9, p. 7446-7454

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

The uptake of carbon sources by Aspergillus niger

Sloothaak, J., 2017, Wageningen: Wageningen University. 179 p.

Research output: Thesisinternal PhD, WU

Open Access
Open Access

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity

Venkatasubramanian, P. B., Toydemir, G., de Wit, N., Saccenti, E., Martins dos Santos, V. A. P., van Baarlen, P., Wells, J. M., Suarez-Diez, M. & Mes, J. J., Jan 2017, In : Scientific Reports. 7, 1, 6778.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)
2016

Adaptation of Akkermansia muciniphila to the oxic-anoxic interface of the mucus layer

Ouwerkerk, J. P., van der Ark, K. C. H., Davids, M., Claassens, N. J., Finestra, T. R., de Vos, W. M. & Belzer, C., 2016, In : Applied and Environmental Microbiology. 82, 23, p. 6983-6993

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
28 Citations (Scopus)

Approaches to sample size determination for multivariate data: Applications to PCA and PLS-DA of omics data

Saccenti, E. & Timmerman, M. E., 2016, In : Journal of Proteome Research. 15, 8, p. 2379-2393 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

Bacterial antisense RNAs are mainly the product of transcriptional noise

Lloréns-Rico, V., Cano, J., Kamminga, T., Gil, R., Latorre, A., Chen, W-H., Bork, P., Glass, J. I., Serrano, L. & Lluch-Senar, M., 4 Mar 2016, In : Science Advances. 2, 3, e1501363.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
42 Citations (Scopus)

Building pathway graphs from BioPAX data in R

Benis, N., Schokker, D., Kramer, F., Smits, M. & Suarez-Diez, M., 2016, In : F1000 Research. 5, 13 p., 2414.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation

Künne, T., Kieper, S. N., Bannenberg, J. W., Vogel, A., Miellet, W. R., Klein, M., Depken, M., Suarez-Diez, M. & Brouns, S. J. J., 2016, In : Molecular Cell. 63, 5, p. 852-864

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
53 Citations (Scopus)

Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization

Adibi, M., Yoshida, S., Weijers, D. & Fleck, C., 1 Feb 2016, In : PLoS ONE. 11, 2, e0147830.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling

Chaudhary, N., Tøndel, K., Bhatnagar, R., Martins dos Santos, V. A. P. & Puchalka, J., 2016, In : Molecular BioSystems. 12, 3, p. 994-1005

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)