Research Output

2015

On the use of the observation-wise k-fold operation in PCA cross-validation

Saccenti, E. & Camacho, J., 2015, In : Journal of Chemometrics. 29, 8, p. 467-478

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes

Liebensteiner, M. G., Pinkse, M. W. H., Nijsse, B., Verhaert, P. D. E. M., Tsesmetzis, N., Stams, A. J. M. & Lomans, B. P., 2015, In : Environmental Microbiology Reports. 7, 6, p. 936-945

Research output: Contribution to journalArticleAcademicpeer-review

12 Citations (Scopus)

Probabilistic networks of blood metabolites in healthy subjects as indicators of latent cardiovascular risk

Saccenti, E., Suarez Diez, M., Luchinat, C., Santucci, C. & Tenori, L., 2015, In : Journal of Proteome Research. 14, 2, p. 1101-1111

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)

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

Oosterkamp, M. J., Boeren, S., Atashgahi, S., Plugge, C. M., Schaap, P. J. & Stams, A. J. M., 2015, In : FEMS Microbiology Letters. 362, 11, 7 p., fnv080.

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Proteomics of Syntrophomonas zehnderi and Methanobacterium formicicum growing on long-chain fatty acids

Salvador, A. F., Strepis, N., Bize, A., Stams, A. J. M., Schaap, P. J., Alves, M. M., Bouchez, T. & Sousa, D. Z., 2015.

Research output: Contribution to conferenceAbstractAcademic

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

van Dam, J. C. J., Koehorst, J. J., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez Diez, M., 2015, In : Journal of Biomedical Semantics. 6, 12 p., 39.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Strategies for individual phenotyping of linoleic and arachidonic Acid metabolism using an oral glucose tolerance test

Saccenti, E., van Duynhoven, J. P. M., Jacobs, D. M., Smilde, A. K. & Hoefsloot, H. C., 2015, In : PLoS ONE. 10, 3, 16 p., e0119856.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Synthetische biologie komende jaren in het vizier

Sikkema, A. & Martins dos Santos, V. A. P., 2015, In : Resource: weekblad voor Wageningen UR. 9, 20, p. 12-13

Research output: Contribution to journalArticlePopular

Open Access

Systematic analysis of how phytochrome B dimerization determines its specificity

Klose, C., Venezia, F., Hussong, A., Kircher, S., Schäfer, E. & Fleck, C., 6 Jul 2015, In : Nature Plants. 1, 8 p., 15090.

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

Wageningen can become Synth City

Sikkema, A., Martins dos Santos, V. A. P. & Bosch, D., 2015

Research output: Non-textual formWeb publication/sitePopular

Open Access
2014

A continuum approximation to an off-lattice individual-cell based model of cell migration and adhesion

Middleton, A. M., Fleck, C. & Grima, R., 2014, In : Journal of Theoretical Biology. 359, p. 220-232

Research output: Contribution to journalArticleAcademicpeer-review

36 Citations (Scopus)

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

Worm, P., Koehorst, J. J., Visser, M., Sedano Nunez, V. T., Schaap, P. J., Plugge, C. M., Sousa, D. Z. & Stams, A. J. M., 2014, In : Biochimica et Biophysica Acta. B, Bioenergetics. 1837, 12, p. 2004-2016

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
42 Citations (Scopus)

A lipid zipper triggers bacterial invasion

Eierhoff, T., Bastian, B., Thuenauer, R., Madl, J., Audfray, A., Aigal, S., Juillot, S., Rydell, G. E., Müller, S., de Bentzmann, S., Imberty, A., Fleck, C. & Römer, W., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 35, p. 12895-12900

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
53 Citations (Scopus)

A Metabolomic Perspective on Coeliac Disease

Calabrò, A., Gralka, E., Luchinat, C., Saccenti, E. & Tenori, L., 2014, In : Autoimmune Diseases. 2014, 13 p., 756138.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)

A novel class of fungal lipoxygenases

Heshof, R., Jylhä, S., Haarmann, T., Jørgensen, A. L. W., Dalsgaard, T. K. & de Graaff, L. H., 2014, In : Applied Microbiology and Biotechnology. 98, 3, p. 1261-1270

Research output: Contribution to journalArticleAcademicpeer-review

17 Citations (Scopus)

Anoxic biological production of fuels and of bulk chemicals from second generation feedstocks

de Bont, J. A. M., Raab, A., Schilling, M., Tamame González, M. M., De los Ángeles Santos García, M., Martins dos Santos, V. A. P., Arjona Antolín, R. & Gutiérrez Gómez, P., 31 Dec 2014, Patent No. WO2014207099, Priority date 26 Jun 2013

Research output: PatentOther research output

Open Access

Birth, death, and diversification of mobile promoters in prokaryotes

van Passel, M. W. J., Nijveen, H. & Wahl, L. M., 2014, In : Genetics. 197, 1, p. 291-299

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Degenerate target sites mediate rapid primed CRISPR adaptation

Fineran, P. C., Gerritzen, M. J. H., Suarez Diez, M., Künne, T. A., Boekhorst, J., van Hijum, S. A. F. T., Staals, R. H. J. & Brouns, S. J. J., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 16, p. E1629-E1638

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
142 Citations (Scopus)

Delineating the effect of host environmental signals on a fully virulent strain of Bacillus anthracis using an integrated transcriptomics and proteomics approach

Panda, G., Basak, T., Tanwer, P., Sengupta, S., Martins dos Santos, V. A. P. & Bhatnagar, R., 2014, In : Journal of Proteomics. 105, p. 242-265

Research output: Contribution to journalArticleAcademicpeer-review

4 Citations (Scopus)

Effects of selective digestive decontamination (SDD) on the gut resistome

Buelow, E., Bello Gonzalez, T. D. G., Versluis, D., Oostdijk, E. A. N., Ogilvie, L. A., van Mourik, M. S. M., Oosterink, L., van Passel, M. W. J., Smidt, H., D’Andrea, M. M., de Been, M., Jones, B. V., Willems, R. J. L., Bonten, M. J. M. & Schaik, W., 2014, In : Journal of Antimicrobial Chemotherapy. 69, 8, p. 2215-2223

Research output: Contribution to journalArticleAcademicpeer-review

50 Citations (Scopus)

Effects of ß-Lactam Antibiotics and Fluoroquinolones on Human Gut Microbiota in Relation to Clostridium difficile Associated Diarrhea

Knecht, H., Neulinger, S. C., Heinsen, F. A., Knecht, C., Schilhabel, A., Schmitz, R. A., Zimmermann, A., Martins dos Santos, V. A. P., Ferrer, R., Rosenstiel, P. C., Schreiber, S., Friedrichs, A. K. & Ott, S. J., 2014, In : PLoS ONE. 9, 2, e89417.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
36 Citations (Scopus)

Enhanced glycosyl hydrolase production in Aspergillus nidulans using transcription factor engineering approaches

Tamayo-Ramos, J. A. & Orejas, M., 4 Jul 2014, In : Biotechnology for Biofuels. 7, 1, 103.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
12 Citations (Scopus)

Expression of the Aspergillus terreus itaconic acid biosynthesis cluster in Aspergillus niger

van der Straat, L., Vernooij, M., Lammers, M., van den Berg, W. A. M., Schonewille, T., Cordewener, J., van der Meer, I., Koops, A. J. & de Graaff, L. H., 2014, In : Microbial Cell Factories. 13, 9 p., 11.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
53 Citations (Scopus)

Flavin dependent monooxygenases

Huijbers, M. M. E., Montersino, S., Westphal, A. H., Tischler, D. & van Berkel, W. J. H., 2014, In : Archives of Biochemistry and Biophysics. 544, p. 2-17

Research output: Contribution to journalArticleAcademicpeer-review

191 Citations (Scopus)

From the Environment to the Host: Re-Wiring of the Transcriptome of Pseudomonas aeruginosa from 22°C to 37°C

Barbier, M., Damron, F. H., Bielecki, P., Suarez Diez, M., Puchalka, J., Albertí, S., Martins Dos Santos, V. A. P. & Goldberg, J. B., 2014, In : PLoS ONE. 9, 2, e89941.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
17 Citations (Scopus)

Fungals strains with improved citric acid and itaconic acid production

van der Straat, L., Schonewille, T., Tamayo Ramos, J. A. & de Graaff, L. H., 18 Sep 2014, Patent No. WO2014142647, Priority date 14 Mar 2013

Research output: PatentOther research output

Open Access

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

Visser, M., Parshina, S. N., Alves, J. I., Sousa, D. Z., Pereira, I. A. C., Muyzer, G., Kuever, J., Lebedinsky, A. V., Koehorst, J. J., Worm, P., Plugge, C. M., Schaap, P. J., Goodwin, L. A., Lapidus, A., Kyrpides, N. C., Detter, J. C., Woyke, T., Chain, P., Davenport, K. W., Spring, S. & 3 others, Rohde, M., Klenk, H. P. & Stams, A. J. M., 2014, In : Standards in Genomic Sciences. 9, 3, p. 655-675

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

Kuever, J., Visser, M., Loeffler, C., Boll, M., Worm, P., Sousa, D. Z., Plugge, C. M., Schaap, P. J., Muyzer, G., Pereira, I. A., Parshina, S. N., Goodwin, L. A., Kyrpides, N. C., Detter, J., Woyke, T., Chain, P., Davenport, K. W., Rohde, M., Spring, S., Klenk, H. P. & 1 others, Stams, A. J. M., 2014, In : Standards in Genomic Sciences. 9, 3, p. 821-839

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

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

Reijnders, M. J. M. F., van Heck, R. G. A., Lam, C. M. C., Scaife, M. A., Martins dos Santos, V. A. P., Smith, A. G. & Schaap, P. J., 2014, In : Trends in Biotechnology. 32, 12, p. 617-626

Research output: Contribution to journalArticleAcademicpeer-review

32 Citations (Scopus)

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

Ferrer, M., Martins dos Santos, V. A. P., Ott, S. J. & Moya, A., 2014, In : Gut Microbes. 5, 1, p. 64-70

Research output: Contribution to journalArticleAcademicpeer-review

37 Citations (Scopus)

Heterologous expression of Gaeumannomyces graminis lipoxygenase in Aspergillus nidulans

Heshof, R., van Schayck, J. P., Tamayo Ramos, J. A. & de Graaff, L. H., 2014, In : AMB Express. 4, 6 p., 65.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Identification and production of recombinant Culicoides obsoletus allergens for diagnosis and immunotherapy of insect bite hypersensitive horses

van der Meide, N. M. A., Schurink, A., Sloet van Oldruitenborgh-Oosterbaan, M. M., Schaap, P. J., Savelkoul, H. F. J. & Tijhaar, E. J., 2014.

Research output: Contribution to conferenceAbstract

Improved production of medium-chain-length Polyhydroxyalkanotes in glucose-based fed-batch cultivations of metabolically engineered Pseudomonas putida strains

Poblete-Castro, I., Rodriguez, A. L., Lam, M. C. & Kessler, W., 2014, In : Journal of Microbiology and Biotechnology. 24, 1, p. 59-69

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Integration of growth and patterning during vascular tissue formation in Arabidopsis

De Rybel, B., Adibi, M., Breda, A. S., Wendrich, J. R., Smit, M. E., Novák, O., Yamaguchi, N., Yoshida, S., van Isterdael, G., Palovaara, J., Nijsse, B., Boekschoten, M. V., Hooiveld, G. J. E. J., Beeckman, T., Wagner, D., Ljung, K., Fleck, C. & Weijers, D., 2014, In : Science. 345, 6197, 9 p., 1255215.

Research output: Contribution to journalArticleAcademicpeer-review

137 Citations (Scopus)

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

van Dam, J. C. J., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez Diez, M., 2014, In : BMC Systems Biology. 8, 21 p., 111.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Mathematical Models Light Up Plant Signaling

Chew, Y. H., Smith, R. W., Jones, H. J., Seaton, D. D., Grima, R. & Halliday, K. J., 2014, In : The Plant Cell. 26, 1, p. 5-20

Research output: Contribution to journalArticleAcademicpeer-review

24 Citations (Scopus)

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

Méndez-Garcia, C., Mesa, V., Sprenger, R. R., Richter, M., Suarez Diez, M., Solano, J., Bargiela, R., Golyshina, O. V., Manteca, A., Ramos, J. L., Gallego, J. R., Llorente, I., Martins Dos Santos, V. A. P., Jensen, O. N., Paláez, A. I., Sánchez, J. & Ferrer, M., 2014, In : ISME Journal. 8, p. 1259-1274

Research output: Contribution to journalArticleAcademicpeer-review

41 Citations (Scopus)

Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species

Saccenti, E., Tenori, L., Verbruggen, P., Timmerman, M. E., Bouwman, J., de Greef, J., Luchinat, C. & Smilde, A. K., 2014, In : PLoS ONE. 9, 9, e106077.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

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

Sloothaak, J., Schilders, M., Schaap, P. J. & de Graaff, L. H., 2014, In : AMB Express. 4, 9 p., 66.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

Pathway transfer in fungi: Transporters are the key to success

van der Straat, L. & de Graaff, L. H., 2014, In : Bioengineered. 5, 5, p. 335-339

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

Production of advanced fuels and of chemicals by yeasts on the basis of second generation feedstocks

de Bont, J. A. M., Raab, A., Schilling, M., Tamame González, M. M., De los Ángeles Santos García, M., Martins Dos Santos, V. A. P., Arjona Antolín, R. & Gutiérrez Gómez, P., 31 Dec 2014, Patent No. WO2014207087, Priority date 26 Jun 2013

Research output: PatentOther research output

Open Access

Quantification of variability in trichome patterns

Greese, B., Huelskamp, M. & Fleck, C., 2014, In : Frontiers in Plant Science. 5, 596.

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

RNA Targeting by the Type III-A CRISPR-Cas Csm Complex of Thermus thermophilus

Staals, R. H. J., Zhu, Y., Taylor, D. W., Kornfeld, J. E., Sharma, K., Barendregt, A., Koehorst, J. J., Vlot, M., Neupane, N., Varossieau, K., Sakamoto, K., Suzuki, T., Schaap, P. J., Urlaub, H., Heck, A. J. R., Nogales, E., Doudna, J. A., Shinkai, A. & van der Oost, J., 2014, In : Molecular Cell. 56, 4, p. 518-530

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
130 Citations (Scopus)

Shedding (far-red) light on phytochrome mechanisms and responses in land plants

Possart, A., Fleck, C. & Hiltbrunner, A., 2014, In : Plant Science. 217-218, p. 36-46

Research output: Contribution to journalArticleAcademicpeer-review

37 Citations (Scopus)

Synthetic Biology in Health and Disease

van Passel, M. W. J., Lam, C. M. C., Martins dos Santos, V. A. P. & Suarez Diez, M., 2014, Synbio and Human Health - A Challenge to the Current IP Framework?. Dordrecht: Springer Science + Business Media

Research output: Chapter in Book/Report/Conference proceedingChapter

System size expansion using Feynman rules and diagrams

Thomas, P., Fleck, C., Grima, R. & Popovic, N., 2014, In : Journal of Physics. A, Mathematical and Theoretical. 47, 45, 455007.

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

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

Rienksma, R. A., Suarez Diez, M., Spina, L., Schaap, P. J. & Martins dos Santos, V. A. P., 2014, In : Seminars in Immunology. 26, 6, p. 610-622

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)

The ratio of the lateral correlation length and particle radius determines the density profile of spherical molecules near a fluctuating membrane

Córdoba-Valdés, F., Castañeda-Priego, R., Timmer, J. & Fleck, C., 2014, In : Soft Matter. 10, p. 8475-8481

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)

Toolkit for Visualization of the Cellular Structure and Organelles in Aspergillus niger

ten Buren, E. B. J., Karrenbelt, M. A. P., Lingemann, M., Chordia, S., Deng, Y., Hu, J. J., Verest, J. M., Wu, V., Bello Gonzalez, T. D. G., van Heck, R. G. A., Odoni, D. I., Schonewille, T., van der Straat, L., de Graaff, L. H. & van Passel, M. W. J., 2014, In : ACS synthetic biology. 3, 12, p. 995-998

Research output: Contribution to journalEditorialAcademicpeer-review

3 Citations (Scopus)

Understanding the antimicrobial mechanism of TiO2-based nanocomposite films in a pathogenic bacterium

Kubacka, A., Suarez Diez, M., Rojo, D., Bargiela, R., Ciordia, S., Zapico, I., Albar, J. P., Barbas, C., Martins Dos Santos, V. A. P., Fernández-García, M. & Ferrer, M., 2014, In : Scientific Reports. 4, 4134.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
175 Citations (Scopus)