Research Output

2016

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 journalArticleAcademicpeer-review

Open Access
14 Citations (Scopus)

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

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 journalArticleAcademicpeer-review

Open Access
4 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 journalArticleAcademicpeer-review

Open Access
10 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 journalArticleAcademicpeer-review

Open Access
11 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 journalArticleAcademicpeer-review

Open Access
12 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 journalArticleAcademicpeer-review

Open Access
8 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 journalArticleAcademicpeer-review

9 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 journalArticleAcademicpeer-review

51 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 journalArticleAcademicpeer-review

Open Access
16 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 journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

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 journalArticleAcademicpeer-review

6 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 journalArticleAcademicpeer-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 journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)
Open Access
9 Citations (Scopus)
Open Access
2 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 journalArticleAcademicpeer-review

Open Access
3 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 journalArticleAcademicpeer-review

Open Access
7 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 journalArticleAcademicpeer-review

Open Access
96 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 journalArticleAcademicpeer-review

Open Access
19 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 journalArticleAcademicpeer-review

Open Access
10 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 journalArticleAcademicpeer-review

9 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 journalArticleAcademicpeer-review

Open Access
7 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 journalArticleAcademicpeer-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 journalArticleAcademicpeer-review

30 Citations (Scopus)

Application of the Human Intestinal Tract Chip to the non-human primate gut microbiota

Bello Gonzalez, T. D. G., van Passel, M. W. J., Tims, S., Fuentes, S., de Vos, W. M., Smidt, H. & Belzer, C., 2015, In : Beneficial Microbes. 6, 3, p. 271-276

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)

Aspergillus niger membrane-associated proteome analysis for the identification of glucose transporters

Sloothaak, J., Odoni, D. I., de Graaff, L. H., Martins dos Santos, V. A. P., Schaap, P. J. & Tamayo Ramos, J. A., 2015, In : Biotechnology for Biofuels. 8, 15 p., 150.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
16 Citations (Scopus)

Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View

Saccenti, E., Nieuwenhuijse, D., Koehorst, J. J., Martins dos Santos, V. A. P. & Schaap, P. J., 2015, In : PLoS ONE. 10, 9, e0137908.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Comparative and Functional Metagenomics of Akkermansia muciniphila

Belzer, C., van Passel, M. W. J., Smidt, H. & de Vos, W. M., 2015, Encyclopedia of Metagenomics: Environmental Metagenomics. Springer, p. 99-102

Research output: Chapter in Book/Report/Conference proceedingEntry for encyclopedia/dictionaryAcademic

Comparative genomics of Streptococcus pyogenes M1 isolates differing in virulence and propensity to cause systemic infection in mice

Fiebig, A., Loof, T. G., Babbar, A., Itzeg, A., Koehorst, J. J., Schaap, P. J. & Nitsche-Schmitz, D. P., 2015, In : International Journal of Medical Microbiology. 305, 6, p. 532-543

Research output: Contribution to journalArticleAcademicpeer-review

14 Citations (Scopus)

Comprehensive insights into transcriptional adaptation of intracellular mycobacteria by microbe-enriched dual RNA sequencing

Rienksma, R. A., Suarez Diez, M., Mollenkopf, H. J., Dolganov, G. M., Dorhoi, A., Schoolnik, G. K., Martins Dos Santos, V. A. P., Kaufmann, S., Schaap, P. J. & Gengenbacher, M., 2015, In : BMC Genomics. 16, 31 p., 34.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
38 Citations (Scopus)

Covariances Simultaneous Component Analysis: a new method within a framework for modeling covariances

Smilde, A. K., Timmerman, M. E., Saccenti, E., Jansen, J. J. & Hoefsloot, H. C. J., 2015, In : Journal of Chemometrics. 29, 5, p. 277-288

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)
19 Citations (Scopus)

Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S

Goris, T., Hornung, B. V. H. K., Kruse, T., Reinhold, A., Westermann, M., Schaap, P. J., Smidt, H. & Diekert, G., 2015, In : Standards in Genomic Sciences. 10, 8 p., 15.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Draft genome sequence of Talaromyces (Penicillium) islandicus WF-38-12, a neglected mold with significant biotechnological potential - Genome announcement

Schafhauser, T., Wibberg, D., Rueckert, C., Winkler, A., Flor, L., van Pée, K. H., Fewer, D. P., Sivonen, K., Jahn, L., Ludwig-Müller, J., Caradec, T., Jacques, P., Huijbers, M. M. E., van Berkel, W. J. H., Weber, T., Wohlleben, W. & Kalinowsky, J., 2015, In : Journal of Biotechnology. 211, p. 101-102

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

Effects of Argonaute on Gene Expression in Thermus thermophilus

Swarts, D. C., Koehorst, J. J., Westra, E. R., Schaap, P. J. & van der Oost, J., 2015, In : PLoS ONE. 10, 4, 13 p., e0124880.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
20 Citations (Scopus)

Effects of bowel cleansing on the intestinal microbiota

Jalanka, J., Salonen, A., Salojärvi, J., Ritari, J., Immonen, O., Marciani, L., Gowland, P., Hoad, C., Garsed, K., Lam, M. C., Palva, A., Spiller, R. C. & de Vos, W. M., 2015, In : Gut. 64, 10, p. 1562-1568

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
78 Citations (Scopus)
9 Citations (Scopus)

Erratum to: Green genes: Bioinformatics and systems-biology innovations drive algal biotechnology [Trends in Biotechnology 32 (2014) 617-626].

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., 2015, In : Trends in Biotechnology. 33, 5, p. 315

Research output: Contribution to journalArticleAcademic

Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains

Varga, J. J., Barbier, M., Mulet, X., Bielecki, P., Bartell, J. A., Owings, J. P., Martinez-Ramos, I., Hittle, L. E., Davis, M. R., Damron, F. H., Liechti, G. W., Puchałka, J., Martins dos Santos, V., Ernst, R. K., Papin, J. A., Albertí, S., Oliver, A. & Goldberg, J. B., 2015, In : BMC Genomics. 16, 1, 27 p., 883.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

High yields of active Thermus thermophilus proline dehydrogenase are obtained using maltose-binding protein as a solubility tag.

Huijbers, M. M. E. & van Berkel, W. J. H., 2015, In : Biotechnology Journal. 10, 3, p. 395-403

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments

Cacciatore, S., Saccenti, E. & Piccioli, M., 2015, In : OMICS - A Journal of Integrative Biology. 19, 3, p. 147-156

Research output: Contribution to journalArticleAcademicpeer-review

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

Atashgahi, S., Aydin, R., Rocha Dimitrov, M., Sipkema, D., Hamonts, K., Lahti, L., Maphosa, F., Kruse, T., Saccenti, E., Springael, D., Dejonghe, W. & Smidt, H., 26 Nov 2015, In : Scientific Reports. 5, 17284.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
31 Citations (Scopus)

Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea

Ingle, R. A., Stoker, C., Stone, W., Adams, N., Smith, R. W., Grant, M., Carré, I., Roden, L. C. & Denby, K. J., 2015, In : The Plant Journal. 84, 5, p. 937-948

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
33 Citations (Scopus)

Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature

Seaton, D. D., Smith, R. W., Young Hun Song, MacGregor, D. R., Stewart, K., Steel, G., Foreman, J., Penfield, S., Imaizumi, T., Miller, A. J. & Halliday, K. J., 2015, In : Molecular Systems Biology. 11, 1, 776.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
50 Citations (Scopus)

Lipoxygenase : a game-changing enzyme

Heshof, R., 2015, Wageningen: Wageningen University. 160 p.

Research output: Thesisinternal PhD, WU

Open Access

Method for the single step introduction of a plurality of genes in microbial cells

van der Straat, L. & de Graaff, L. H., 25 Feb 2015, Patent No. EP2840139

Research output: PatentOther research output

Open Access
Open Access
12 Citations (Scopus)

Multivariate Modeling of the collaboration between Luigi Illica and Giuseppe Giacosa for the librettos of three operas by Giacomo Puccini

Saccenti, E. & Tenori, L., 2015, In : Digital Scholarship in the Humanities. 30, 3, p. 405-422

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Network analysis of temporal functionalities of the gut induced by perturbations in new-born piglets

Benis, N., Schokker, D., Suarez Diez, M., Martins dos Santos, V. A. P., Smidt, H. & Smits, M. A., 2015, In : BMC Genomics. 16, 556.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)