Research Output per year
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. 467-478Research output: Contribution to journal › Article › Academic › peer-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. 936-945Research output: Contribution to journal › Article › Academic › peer-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. 1101-1111Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 conference › Abstract › Academic
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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 12-13Research output: Contribution to journal › Article › Popular
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 journal › Article › Academic › peer-review
35
Citations
(Scopus)
Wageningen can become Synth City
Sikkema, A., Martins dos Santos, V. A. P. & Bosch, D., 2015Research output: Non-textual form › Web publication/site › Popular
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. 220-232Research output: Contribution to journal › Article › Academic › peer-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. 2004-2016Research output: Contribution to journal › Article › Academic › peer-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. 12895-12900Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 1261-1270Research output: Contribution to journal › Article › Academic › peer-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 2013Research output: Patent › Other 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. 291-299Research output: Contribution to journal › Article › Academic › peer-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-E1638Research output: Contribution to journal › Article › Academic › peer-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. 242-265Research output: Contribution to journal › Article › Academic › peer-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. 2215-2223Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 2-17Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 2013Research output: Patent › Other 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, , 2014, In : Standards in Genomic Sciences. 9, 3, p. 655-675Research output: Contribution to journal › Article › Academic › peer-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, , 2014, In : Standards in Genomic Sciences. 9, 3, p. 821-839Research output: Contribution to journal › Article › Academic › peer-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. 617-626Research output: Contribution to journal › Article › Academic › peer-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. 64-70Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 conference › Abstract
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. 59-69Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 5-20Research output: Contribution to journal › Article › Academic › peer-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. 1259-1274Research output: Contribution to journal › Article › Academic › peer-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 journal › Article › Academic › peer-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 journal › Article › Academic › peer-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. 335-339Research output: Contribution to journal › Article › Academic › peer-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 2013Research output: Patent › Other 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 journal › Article › Academic › peer-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. 518-530Research output: Contribution to journal › Article › Academic › peer-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. 36-46Research output: Contribution to journal › Article › Academic › peer-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 MediaResearch output: Chapter in Book/Report/Conference proceeding › Chapter
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 journal › Article › Academic › peer-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. 610-622Research output: Contribution to journal › Article › Academic › peer-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. 8475-8481Research output: Contribution to journal › Article › Academic › peer-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. 995-998Research output: Contribution to journal › Editorial › Academic › peer-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 journal › Article › Academic › peer-review
Open Access
175
Citations
(Scopus)