Systems and Synthetic Biology

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 journal › Abstract › Academic

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 journal › Article › Academic › peer-review

Open Access

8 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 journal › Article › Academic › peer-review

Open Access

27 Citations (Scopus)

Predicting the murine enterocyte metabolic response to diets that differ in lipid and carbohydrate composition

Sinha, N., Suarez-Diez, M., Van Schothorst, E. M., Keijer, J., Martins dos Santos, V. & Hooiveld, G. J. E. J., 18 Aug 2017, In: Scientific Reports. 7, 11 p., 8784.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

6 Citations (Scopus)

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

Koehorst, J. J., Saccenti, E., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez-Diez, M., 27 Jun 2017, In: F1000 Research. 5, 1987.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

13 Citations (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 journal › Article › Academic › peer-review

Open Access

8 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 journal › Article › Academic › peer-review

Open Access

147 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 journal › Article › Academic › peer-review

Open Access

18 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 journal › Article › Academic › peer-review

Open Access

Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production

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

Research output: Thesis › internal PhD, WU

Open Access

The uptake of carbon sources by Aspergillus niger

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

Research output: Thesis › internal PhD, WU

Open Access

Tuning for light and more: engineering phototrophy and membrane proteins in Escherichia coli

Claassens, N. J. H. P., 2017, Wageningen: Wageningen University. 328 p.

Research output: Thesis › internal PhD, WU

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 journal › Article › Academic › peer-review

Open Access

4 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 journal › Article › Academic › peer-review

Open Access

47 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 journal › Article › Academic › peer-review

33 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 journal › Article › Academic › peer-review

Open Access

64 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 journal › Article › Academic › peer-review

Open Access

3 Citations (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 journal › Article › Academic › peer-review

Open Access

75 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 journal › Article › Academic › peer-review

Open Access

19 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 journal › Article › Academic › peer-review

1 Citation (Scopus)

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 journal › Article › Academic › peer-review

Open Access

29 Citations (Scopus)

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216^T

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 journal › Article › Academic › peer-review

Open Access

8 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 journal › Article › Academic › peer-review

Open Access

19 Citations (Scopus)

Efficient Reconstruction of Predictive Consensus Metabolic Network Models

van Heck, R. G. A., Ganter, M., Martins dos Santos, V. A. P. & Stelling, J., 2016, In: PLoS Computational Biology. 12, 8, e1005085.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

13 Citations (Scopus)

Entropy-Based Network Representation of the Individual Metabolic Phenotype

Saccenti, E., Menichetti, G., Ghini, V., Remondini, D., Tenori, L. & Luchinat, C., 2016, In: Journal of Proteome Research. 15, 9, p. 3298-3307

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

18 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 journal › Article › Academic › peer-review

Open Access

10 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 journal › Article › Academic › peer-review

14 Citations (Scopus)

Harnessing the power of microbial autotrophy

Claassens, N. J., Machado de Sousa, D., Martins dos Santos, V., de Vos, W. M. & van der Oost, J., 2016, In: Nature Reviews Microbiology. 14, p. 692-706

Research output: Contribution to journal › Article › Academic › peer-review

93 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 journal › Article › Academic › peer-review

Open Access

32 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 journal › Article › Academic › peer-review

Open Access

24 Citations (Scopus)

Impact of Dietary Carbohydrate: Lipid ratio modelled in murine Small Intestinal Epithelial Cells

Sinha, N., Suarez Diez, M., van Schothorst, E. M., Keijer, J., Martins dos Santos, V. & Hooiveld, G. J. E. J., 12 Nov 2016.

Research output: Contribution to conference › Poster

Industrial potential of lipoxygenases

Heshof, R., de Graaff, L. H., Villaverde, J. J., Silvestre, A. J. D., Haarmann, T., Dalsgaard, T. K. & Buchert, J., 2016, In: Critical Reviews in Biotechnology. 36, 4, p. 665-674

Research output: Contribution to journal › Article › Academic › peer-review

14 Citations (Scopus)

Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy

Volpers, M., Claassens, N. J., Noor, E., van der Oost, J., de Vos, W. M., Kengen, S. W. M. & Martins dos Santos, V., 2016, In: PLoS ONE. 11, 6, e0157851.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

7 Citations (Scopus)

Natural genetic variation differentially affects the proteome and transcriptome in Caenorhabditis elegans

Kamkina, P., Snoek, L. B., Grossmann, J., Volkers, R. J. M., Sterken, M. G., Daube, M., Roschitzki, B., Fortes, C., Schlapbach, R., Roth, A., von Mering, C., Hengartner, M. O., Schrimpf, S. P. & Kammenga, J. E., 2016, In: Molecular and Cellular Proteomics. 15, 5, p. 1670-1680

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

13 Citations (Scopus)

Screening and characterization of novel specific peptides targeting MDA-MB-231 claudin-low breast carcinoma by computer-aided phage display methodologies

Nobrega, F. L., Ferreira, D., Martins, I. M., Suarez-Diez, M., Azeredo, J., Kluskens, L. D. & Rodrigues, L. R., 2016, In: BMC Cancer. 16, 1, 881.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

4 Citations (Scopus)

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

Cvijovic, M., Höfer, T., Acimovic, J., Alberghina, L., Almaas, E., Besozzi, D., Blomberg, A., Bretschneider, T., Cascante, M., Collin, O., de Atauri, P., Depner, C., Dickinson, R., Dobrzynski, M., Fleck, C., Garcia-Ojalvo, J., Gonze, D., Hahn, J., Hess, H. M., Hollmann, S. & 13 others, Krantz, M., Kummer, U., Lundh, T., Martial, G., Martins dos Santos, V. A. P., Mauer-Oberthür, A., Regierer, B., Skene, B., Stalidzans, E., Stelling, J., Teusink, B., Workman, C. T. & Hohmann, S., 2016, In: npj Systems Biology and Applications. 2, 7 p., 16011.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

11 Citations (Scopus)

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

Belda, E., van Heck, R. G. A., José Lopez-Sanchez, M., Cruveiller, S., Barbe, V., Fraser, C., Klenk, H. P., Petersen, J., Morgat, A., Nikel, P. I., Vallenet, D., Rouy, Z., Sekowska, A., Martins dos Santos, V. A. P., de Lorenzo, V., Danchin, A. & Médigue, C., 2016, In: Environmental Microbiology. 18, 10, p. 3403-3424

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

172 Citations (Scopus)

The Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires

Ceapa, C. D., Davids, M., Ritari, J., Lambert, J., Wels, M., Douillard, F. P., Smokvina, T., de Vos, W. M., Knol, J. & Kleerebezem, M., 20 May 2016, In: Genome Biology and Evolution. 8, 6, p. 1889-1905

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

36 Citations (Scopus)

Unearthing the transition rates between photoreceptor conformers

Smith, R. W., Helwig, B., Westphal, A. H., Pel, E., Hörner, M., Beyer, H. M., Samodelov, S. L., Weber, W., Zurbriggen, M. D., Borst, J. & Fleck, C., 2016, In: BMC Systems Biology. 10, 1, 110.

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

12 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 journal › Article › Academic › peer-review

18 Citations (Scopus)

Weight loss predictability by plasma metabolic signatures in adults with obesity and morbid obesity of the DiOGenes study

Stroeve, J. H. M., Saccenti, E., Bouwman, J., Dane, A., Strassburg, K., Vervoort, J., Hankemeier, T., Astrup, A., Smilde, A. K., Van Ommen, B. & Saris, W. H. M., 2016, In: Obesity. 24, 2, p. 379-388

Research output: Contribution to journal › Article › Academic › peer-review

Open Access

14 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 journal › Article › Academic › peer-review

Allostasis and Resilience of the Human Individual Metabolic Phenotype

Ghini, V., Saccenti, E., Tenori, L., Assfalg, M. & Luchinat, C., 2015, In: Journal of Proteome Research. 14, 7, p. 2951-2962

Research output: Contribution to journal › Article › Academic › peer-review

37 Citations (Scopus)

Systems and Synthetic Biology

Research output

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