Research Output

2019

Transcriptional landscapes of lipid producing microalgae

Carrères, B. M., 2019, Wageningen: Wageningen University. 249 p.

Research output: Thesisinternal PhD, WU

Open Access

Vaccination of carp against SVCV with an oral DNA vaccine or an insect cells-based subunit vaccine

Embregts, C. W. E., Rigaudeau, D., Tacchi, L., Pijlman, G. P., Kampers, L., Veselý, T., Pokorová, D., Boudinot, P., Wiegertjes, G. F. & Forlenza, M., Feb 2019, In : Fish and Shellfish Immunology. 85, p. 66-77

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)
2018

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Atashgahi, S., Hornung, B., van der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 1 Dec 2018, In : Scientific Reports. 8, 1, 4490.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
12 Citations (Scopus)

A computational approach to study the transcriptional response of enterocytes exposed to luminal factors

Venkatasubramanian, P. B., 2018, Wageningen: Wageningen University. 214 p.

Research output: Thesisinternal PhD, WU

Open Access
1 Citation (Scopus)

Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects

Vignoli, A., Tenori, L., Luchinat, C. & Saccenti, E., 5 Jan 2018, In : Journal of Proteome Research. 17, 1, p. 97-107

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

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
8 Citations (Scopus)

Comparison of dimensionality assessment methods in Principal Component Analysis based on permutation tests

Vitale, R. & Saccenti, E., 15 Oct 2018, In : Chemometrics and Intelligent Laboratory Systems. 181, p. 79-94

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake

Middleton, A. M., Dal Bosco, C., Chlap, P., Bensch, R., Harz, H., Ren, F., Bergmann, S., Wend, S., Weber, W., Hayashi, K. I., Zurbriggen, M. D., Uhl, R., Ronneberger, O., Palme, K., Fleck, C. & Dovzhenko, A., 13 Mar 2018, In : Cell Reports. 22, 11, p. 3044-3057

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)
Open Access
14 Citations (Scopus)

Diabetes and necrotizing soft tissue infections—A prospective observational cohort study: Statistical analysis plan

Rosén, A., Arnell, P., Madsen, M. B., Nedrebø, B. G., Norrby-Teglund, A., Hyldegaard, O., dos Santos, V. M., Bergey, F., Saccenti, E. & Skrede, S., 1 Sep 2018, In : Acta Anaesthesiologica Scandinavica. 62, 8, p. 1171-1177

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Smith, R. W., van Rosmalen, R. P., Martins dos Santos, V. A. P. & Fleck, C., 19 Jun 2018, In : BMC Systems Biology. 12, 72.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

DNA assembly standards: Setting the low-level programming code for plant biotechnology

Vazquez-Vilar, M., Orzaez, D. & Patron, N., Aug 2018, In : Plant Science. 273, p. 33-41

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

Domesticated equines differ in their faecal microbiota composition

Edwards, J. E., Schennink, A., Burden, F., Long, S., van Doorn, D. A., Pellikaan, W. F., Dijkstra, J., Saccenti, E., Everts, H. & Smidt, H., 16 Aug 2018. 1 p.

Research output: Contribution to conferenceAbstract

Open Access

Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

Daas, M. J. A., Nijsse, B., van de Weijer, A. H. P., Groenendaal, B. W. A. J., Janssen, F., van der Oost, J. & van Kranenburg, R., 27 Jun 2018, In : BMC Biotechnology. 18, 1, 42.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Expression of the alternative oxidase influences jun n-terminal kinase signaling and cell migration

Andjelković, A., Mordas, A., Bruinsma, L., Ketola, A., Cannino, G., Giordano, L., Dhandapani, P. K., Szibor, M., Dufour, E. & Jacobs, H. T., Dec 2018, In : Molecular and Cellular Biology. 38, 24, e00110-18. .

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 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

From correlation to causation: analysis of metabolomics data using systems biology approaches

Rosato, A., Tenori, L., Cascante, M., De Atauri Carulla, P. R., Martins dos Santos, V. A. P. & Saccenti, E., 1 Apr 2018, In : Metabolomics. 14, 4, 37.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
25 Citations (Scopus)

Genetic variation causes differential viral susceptibilities in the model organism Caenorhabditis elegans

van Sluijs, L., Sterken, M. G., Wang, Y. A., Ritmahan, W., Gultom, M., Pankok, F., Blokhina, T., Riksen, J. A. G., Volkers, J. M., Snoek, L. B., Pijlman, G. P. & Kammenga, J. E., 23 May 2018.

Research output: Contribution to conferencePoster

Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3

Gutierrez-Urrutia, I., Miossec, M. J., Valenzuela, S. L., Meneses, C., Martins dos Santos, V. A. P., Castro-Nallar, E. & Poblete-Castro, I., 10 Jun 2018, In : Journal of Biotechnology. 275, p. 13-16

Research output: Contribution to journalArticleAcademicpeer-review

Group-wise ANOVA simultaneous component analysis for designed omics experiments

Saccenti, E., Smilde, A. K. & Camacho, J., 1 Jun 2018, In : Metabolomics. 14, 6, 73.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Group-wise partial least square regression

Camacho, J. & Saccenti, E., Mar 2018, In : Journal of Chemometrics. 32, 3, e2964.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Improved functional annotations are key to realize the potential of algal biotechnology

Reijnders, M. J. M. F., 2018, Wageningen: Wageningen University. 194 p.

Research output: Thesisinternal PhD, WU

Insight into nuclear body formation of phytochromes through stochastic modelling and experiment

Grima, R., Sonntag, S., Venezia, F., Kircher, S., Smith, R. W. & Fleck, C., 18 May 2018, In : Physical Biology. 15, 5, 056003.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

Interactive functional networks in microbiota

Hornung, B. V. H., 2018, Wageningen: Wageningen University. 176 p.

Research output: Thesisinternal PhD, WU

Open Access

Itaconic acid production in Aspergillus niger

van der Straat, L., 2018, Wageningen: Wageningen University. 144 p.

Research output: Thesisinternal PhD, WU

Open Access

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)

Milk Metabolomics Data Reveal the Energy Balance of Individual Dairy Cows in Early Lactation

Xu, W., Vervoort, J., Saccenti, E., van Hoeij, R., Kemp, B. & van Knegsel, A., 25 Oct 2018, In : Scientific Reports. 8, 15828.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 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
7 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
8 Citations (Scopus)

Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT): Protocol and statistical analysis plan

Madsen, M. B., Skrede, S., Bruun, T., Arnell, P., Rosén, A., Nekludov, M., Karlsson, Y., Bergey, F., Saccenti, E., Martins dos Santos, V. A. P., Perner, A., Norrby-Teglund, A. & Hyldegaard, O., Feb 2018, In : Acta Anaesthesiologica Scandinavica. 62, 2, p. 272-279

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 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
23 Citations (Scopus)

OP002 Assessment of disease activity patterns during the first 10 years after diagnosis in a population-based Crohn’s disease cohort shows a quiescent disease course for a substantial proportion of the population

Wintjens, D., Bergey, F., Saccenti, E., Jeuring, S., Romberg-Camps, M., Oostenbrug, L., Masclee, A., Jonkers, D., Martins Dos Santos, V. & Pierik, M., 16 Jan 2018, In : Journal of Crohn's and Colitis. 12, supplement 1, p. S001-S003

Research output: Contribution to journalAbstractAcademic

Open Access

Paracrine mechanisms in early differentiation of human pluripotent stem cells: Insights from a mathematical model

Gaspari, E., Franke, A., Robles-Diaz, D., Zweigerdt, R., Roeder, I., Zerjatke, T. & Kempf, H., Oct 2018, In : Stem Cell Research. 32, p. 1-7

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Population complexity trumps model complexity in understanding trait variation

Sterken, M. G., Snoek, L. B., Bevers, R. P. J., Volkers, J. M., Riksen, J. A. G. & Kammenga, J. E., 16 May 2018.

Research output: Contribution to conferencePosterAcademic

Predicting individual differences in viral susceptibility caused by natural genetic variation within species

van Sluijs, L., Sterken, M. G., Wang, Y. A., Ritmahan, W., Gultom, M., Pankok, F., Blokhina, T., Riksen, J. A. G., Volkers, J. M., Snoek, L. B., Pijlman, G. P. & Kammenga, J. E., 17 Jun 2018.

Research output: Contribution to conferencePoster

Prediction of Metabolic Status of Dairy Cows in Early Lactation Using On-farm Cow Data with Machine Learning Algorithms

Xu, W., Saccenti, E., Vervoort, J. J. M., Kemp, B. & van Knegsel, A. T. M., 5 Feb 2018, Abstract of the WIAS Science Day 2018. p. 22-22

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine

Emwas, A. H., Saccenti, E., Gao, X., McKay, R. T., Martins dos Santos, V. A. P., Roy, R. & Wishart, D. S., 1 Mar 2018, In : Metabolomics. 14, 3, 31.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 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
5 Citations (Scopus)

Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent

Gerritsen, J., Umanets, A., Staneva, I., Hornung, B., Ritari, J., Paulin, L., Rijkers, G. T., de Vos, W. M. & Smidt, H., 1 Nov 2018, In : International Journal of Systematic and Evolutionary Microbiology. 68, 11, p. 3479-3486

Research output: Contribution to journalArticleAcademicpeer-review

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
8 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)

SyNDI: Synchronous network data integration framework

Lindfors, E., van Dam, J. C. J., Lam, C. M. C., Zondervan, N. A., Martins dos Santos, V. A. P. & Suarez-Diez, M., 6 Nov 2018, In : BMC Bioinformatics. 19, 1, 403.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The effect of DNA extraction methods on observed microbial communities from fibrous and liquid rumen fractions of dairy cows

Vaidya, J. D., van den Bogert, B., Edwards, J. E., Boekhorst, J., van Gastelen, S., Saccenti, E., Plugge, C. M. & Smidt, H., 31 Jan 2018, In : Frontiers in Microbiology. 9

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

The Role of Endocrine and Dioxin-Like Activity of Extracts of Petroleum Substances in Developmental Toxicity as Detected in a Panel of CALUX Reporter Gene Assays

Kamelia, L., Louisse, J., de Haan, L., Maslowska-Gornicz, A., Ketelslegers, H. B., Brouwer, A., Rietjens, I. M. C. M. & Boogaard, P. J., 1 Aug 2018, In : Toxicological sciences. 164, 2, p. 576-591

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

Use of proteomics to detect sex-related differences in effects of toxicants: implications for using proteomics in toxicology

Rietjens, I. M. C. M., Vervoort, J., Maslowska-Górnicz, A., Van den Brink, N. & Beekmann, K., 14 Sep 2018, In : Critical Reviews in Toxicology. 48, 8, p. 666-681

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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
4 Citations (Scopus)