Research Output

2014

Yeast engineered for the production of 1-alcohols from sugars under anoxic conditions

de Bont, J. A. M., Raab, A., Schilling, M., Martins Dos Santos, V. A. P., Arjona Antolín, R. & Gutiérrez Gómez, P., 31 Dec 2014, Patent No. WO2014207105, Priority date 26 Mar 2013

Research output: PatentOther research output

Open Access
2013

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

Leimena, M. M., Ramiro-Garcia, J., Davids, M., van den Bogert, B., Smidt, H., Smid, E. J., te Boekhorst, J., Zoetendal, E. G., Schaap, P. J. & Kleerebezem, M., 2013, In : BMC Genomics. 14, 14 p., 530.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
70 Citations (Scopus)

Archaeal (Per)Chlorate Reduction at High Temperature: An Interplay of Biotic and Abiotic Reactions

Liebensteiner, M., Pinkse, M. W. H., Schaap, P. J., Stams, A. J. M. & Lomans, B. P., 2013, In : Science. 340, 85, p. 85-87

Research output: Contribution to journalArticleAcademicpeer-review

36 Citations (Scopus)

Cloning and expression of candidate allergens from Culicoides obsoletus for diagnosis of insect bite hypersensitivity in horses

van der Meide, N. M. A., Roders, N., Sloet van Oldruitenborgh-Oosterbaan, M. M., Schaap, P. J., van Oers, M. M., Leibold, W., Savelkoul, H. F. J. & Tijhaar, E., 2013, In : Veterinary Immunology and Immunopathology. 153, 3-4, p. 227-239

Research output: Contribution to journalArticleAcademicpeer-review

23 Citations (Scopus)

Computational protein design with electrostatic focusing: experimental characterization of a conditionally folded helical domain with a reduced amino acid alphabet

Suarez Diez, M., Pujol, M., Matzapetakis, M., Jaramillo, A. & Iranzo, O., 2013, In : Biotechnology Journal. 8, 7, p. 855-864

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

Design and analysis of a tunable synchronized oscillator

Ryback, B. M., Odoni, D. I., van Heck, R. G. A., van Nuland, Y. M., Hesselman, M. C., Martins Dos Santos, V. A. P., van Passel, M. W. J. & Hugenholtz, F., 2013, In : Journal of Biological Engineering. 7, 10 p., 26.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Differential translation tunes uneven production of operon-encoded proteins

Quax, T. E. F., Wolf, Y. I., Koehorst, J. J., Wurtzel, O., van der Oost, R., Ran, W., Blombach, F., Makarova, K. S., Brouns, S. J. J., Forster, A. C., Wagner, E. G. H., Sorek, R., Koonin, E. V. & van der Oost, J., 2013, In : Cell Reports. 4, 5, p. 938-944

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
37 Citations (Scopus)

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

Wodke, J. A., Puchalka, J., Lluch-Senar, M., Marcos, J., Yus, E., Godinho, M., Gutierrez-Gallego, R., Martins Dos Santos, V. A. P., Serrano, L., Klipp, E. & Maier, T., 2013, In : Molecular Systems Biology. 9, 19 p., 653.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
31 Citations (Scopus)

Enhanced production of Aspergillus niger laccase-like multicopper oxidases through mRNA optimization of the glucoamylase expression system

Tamayo Ramos, J. A., Barends, S., Lange, D., de Jel, A., Verhaert, R. M. & de Graaff, L. H., 2013, In : Biotechnology and Bioengineering. 110, 2, p. 543-551

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites

Bielecki, P., Komor, U., Bielecka, A., Müsken, M., Puchalka, J., Pletz, M. W., Ballmann, M., Martins Dos Santos, V. A. P., Weiss, S. & Häussler, S., 2013, In : Environmental Microbiology. 15, 2, p. 570-587

Research output: Contribution to journalArticleAcademicpeer-review

29 Citations (Scopus)

Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity

Hernandez, E., Bargiela, R., Suarez Diez, M., Friedrichs, A., Pérez-Cobas, A. E., Gosalbes, M. J., Knecht, H., Martinez-Martinez, M., Seifert, J., von Bergen, M. & Martins Dos Santos, V. A. P., 2013, In : Gut Microbes. 4, 4, p. 306-315

Research output: Contribution to journalArticleAcademicpeer-review

53 Citations (Scopus)

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601(T.)

Oosterkamp, M. J., Veuskens, T., Talarico Saia, F., Weelink, S. A. B., Goodwin, L. A., Daligault, H. E., Bruce, D. C., Detter, J. C., Tapia, R., Han, C. S., Land, M., Hauser, L., Langenhoff, A. A. M., Gerritse, J., van Berkel, W. J. H., Pieper, D. H., Junca, H., Smidt, H., Schraa, G., Davids, M. & 3 others, Schaap, P. J., Plugge, C. M. & Stams, A. J. M., 2013, In : PLoS ONE. 8, 6, e66971.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
18 Citations (Scopus)

Genome analysis of Desulfotomaculum kuznetsovii strain 17T reveals a physiological similarity with Pelotomaculum thermopropionicum SIT

Visser, M., Worm, P., Muyzer, G., Pereira, I. A. C., Schaap, P. J., Plugge, C. M., Kuever, J., Parshina, S. N., Nazina, T. N., Ivanova, A. E., Bernier-Latmani, R., Goodwin, L. A., Kyrpides, N., Woyke, T., Chain, P., Davenport, K. W., Spring, S., Klenk, H. P. & Stams, A. J. M., 2013, In : Standards in Genomic Sciences. 8, 1, p. 69-87

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation

Flahaut, N. A. L., Wiersma, A., van der Bunt, B., Martens, D. E., Schaap, P. J., Sijtsma, L., Martins Dos Santos, V. A. P. & de Vos, W. M., 2013, In : Applied Microbiology and Biotechnology. 97, 19, p. 8729-8739

Research output: Contribution to journalArticleAcademicpeer-review

54 Citations (Scopus)

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

Pérez-Cobas, A. E., Gosalbes, M. J., Friedrichs, A., Knecht, H. & Martins Dos Santos, V. A. P., 2013, In : Gut. 62, 11, p. 1591-1601

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
259 Citations (Scopus)

Hydroperoxide production from linoleic acid by heterologous Gaeumannomyces graminis tritici lipoxygenase: Optimization and scale-up

Villaverde, J. J., van der Vlist, V., Santos, S. A. O., Haarmann, T., Langfelder, K., Pirttimaa, M., Nyyssola, A., Jylhä, S., Tamminen, T., Kruus, K., de Graaff, L. H., Pascoal Neto, C., Simoes, M. M. Q., Domingues, M. R. M., Silvestre, A. J. D., Eidner, J. & Buchert, J., 2013, In : Chemical Engineering Journal. 217, p. 82-90

Research output: Contribution to journalArticleAcademicpeer-review

20 Citations (Scopus)

Immunoglobulins drive terminal maturation of splenic dendritic cells

Zietara, N., Lyszkiewicz, M., Puchalka, J., Gutierrez, M. G., Lienenklaus, S., Hobeika, E., Reth, M., Martins Dos Santos, V. A. P., Krueger, A. & Weiss, S., 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 6, p. 2282-2287

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

Poblete-Castro, I., Binger, D., Rodrigues, A., Becker, J., Martins Dos Santos, V. A. P. & Wittmann, C., 2013, In : Metabolic Engineering. 15, p. 113-123

Research output: Contribution to journalArticleAcademicpeer-review

80 Citations (Scopus)

ISBE – set out for a Systems Biology Infrastructure for Europe

Hollmann, S., Martins dos Santos, V. A. P. & Regierer, B., 2013, In : EMBnet.journal. 19, 1, p. 3-4

Research output: Contribution to journalArticleProfessional

Open Access

Metabolic response of Alicycliphilus denitrificans strain BC towards electron acceptor variation

Oosterkamp, M. J., Boeren, S., Plugge, C. M., Schaap, P. J. & Stams, A. J. M., 2013, In : Proteomics. 13, 18-19, p. 2886-2894

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)

ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

Vos, M., Beek, T. A. H., van Driel, M. A., Huynen, M. A., Eyre-Walker, A. & van Passel, M. W. J., 2013, In : PLoS ONE. 8, 5, e62447.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Overexpression of a modified 6-phosphofructo-1-kinase results in an increased itaconic acid productivity in Aspergillus niger

van der Straat, L., Tamayo Ramos, J. A., Schonewille, T. & de Graaff, L. H., 2013, In : AMB Express. 3, 57.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
14 Citations (Scopus)
Open Access

Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms

Claassens, N. J. H. P., Volpers, M., Martins Dos Santos, V. A. P., van der Oost, J. & de Vos, W. M., 2013, In : Trends in Biotechnology. 31, 11, p. 633-642

Research output: Contribution to journalArticleAcademicpeer-review

17 Citations (Scopus)

Proteomics of Filamentous Fungi

van Passel, M. W. J., Schaap, P. J. & de Graaff, L. H., 2013, Proteomics in Foods. New York, p. 563-578 (Food Microbiology and Food Safety; no. 2).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Protoanemonin: a natural quorum sensing inhibitor that selectively activates iron starvation response

Fazzini, R. A., Skindersoe, M., Bielecki, M., Puchalka, J., Givskov, M. & Martins Dos Santos, V. A. P., 2013, In : Environmental Microbiology. 15, 1, p. 111-120

Research output: Contribution to journalArticleAcademicpeer-review

25 Citations (Scopus)

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

van Duuren, J. B. J. H., Puchalka, J., Mars, A. E., Bücker, R., Eggink, G., Wittmann, C. & Martins Dos Santos, V. A. P., 2013, In : BMC Biotechnology. 13, 93.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
21 Citations (Scopus)

Signatures of nonlinearity in single cell noise-induced oscillations

Thomas, P., Straube, A. V., Timmer, J., Fleck, C. & Grima, R., 2013, In : Journal of Theoretical Biology. 335, p. 222-234

Research output: Contribution to journalArticleAcademicpeer-review

26 Citations (Scopus)

Structure and Activity of the RNA-Targeting Type III-B CRISPR-Cas Complex of Thermus thermophilus

Staals, R. H. J., Agari, Y., Maki-Yonekura, S., Zhu, Y., Taylor, D. W., van Duijn, E., Barendregt, A., Vlot, M., Koehorst, J. J., Sakamoto, K., Masuda, A., Dohmae, N., Schaap, P. J., Doudna, J. A., Heck, A., Yonekura, K., van der Oost, J. & Shinkai, A., 2013, In : Molecular Cell. 52, 1, p. 135-145

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
127 Citations (Scopus)
2012

A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis

Hesselman, M. C., Odoni, D. I., Ryback, B. M., de Groot, S., van Heck, R. G. A., Keijsers, J., Kolkman, P., Nieuwenhuijse, D., Nuland, Y. M., Sebus, E., Spee, R., de Vries, H., Wapenaar, M. T., Ingham, C. J., Schroen, K., Martins Dos Santos, V. A. P., Spaans, S. K., Hugenholtz, F. & van Passel, M. W. J., 2012, In : PLoS ONE. 7, 5, e36982.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

Biocatalytic potential of laccase-like multicopper oxidases from Aspergillus niger

Tamayo Ramos, J. A., van Berkel, W. J. H. & de Graaff, L. H., 2012, In : Microbial Cell Factories. 11, 11 p., 165.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

Spring, S., Visser, M., Lu, M., Copeland, A., Lapidus, A., Lucas, S., Cheng, J. F., Han, C., Tapia, R., Goodwin, L. A., Pitluck, S., Ivanova, N., Land, M., Hauser, L., Larimer, F., Rohde, M., Göker, M., Detter, J. C., Kyrpides, N., Woyke, T. & 9 others, Schaap, P. J., Plugge, C. M., Muyzer, G., Kuever, J., Pereira, I. A. C., Parshina, S. N., Bernier-Latmani, R., Stams, A. J. M. & Klenk, H. P., 2012, In : Standards in Genomic Sciences. 7, p. 304-319

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)

CRISPR Interference Directs Strand Specific Spacer Acquisition

Swarts, D. C., Mosterd, C., van Passel, M. W. J. & Brouns, S. J. J., 2012, In : PLoS ONE. 7, 4, e35888.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
222 Citations (Scopus)

D-Xylose Concentration-Dependent Hydrolase Expression Profiles and the Function of CreA and XlnR in Aspergillus niger

Mach-Aigner, A. R., Omony, J., Jovanovic, B., van Boxtel, A. J. B. & de Graaff, L. H., 2012, In : Applied and Environmental Microbiology. 78, 9, p. 3145-3155

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
33 Citations (Scopus)

Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger

Omony, J., Mach-Aigner, A. R., de Graaff, L. H., van Straten, G. & van Boxtel, A. J. B., 2012, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9, 5, p. 1316-1325

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
Open Access

Industrial biotechnology of Pseudomonas putida and related species

Poblete-Castro, I., Becker, J., Dohnt, K., Martins Dos Santos, V. A. P. & Wittmann, C., 2012, In : Applied Microbiology and Biotechnology. 93, 6, p. 2279-2290

Research output: Contribution to journalArticleAcademicpeer-review

162 Citations (Scopus)

Influence of cell-to-cell variability on spatial pattern formation

Greese, B., Wester, K., Bensch, R., Ronneberger, O., Timmer, J., Huulskamp, M. & Fleck, C., 2012, In : IET Systems Biology. 6, 4, p. 143-153

Research output: Contribution to journalArticleAcademicpeer-review

6 Citations (Scopus)

Metabolic engineering of Rhizopus oryzae for the production of platform chemicals

Meussen, B. J., de Graaff, L. H., Sanders, J. P. M. & Weusthuis, R. A., 2012, In : Applied Microbiology and Biotechnology. 94, 4, p. 875-886

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
45 Citations (Scopus)

Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in coculture with Sedimentibacter sp.

Maphosa, F., van Passel, M. W. J., de Vos, W. M. & Smidt, H., 2012, In : Environmental Microbiology Reports. 4, 6, p. 604-616

Research output: Contribution to journalArticleAcademicpeer-review

40 Citations (Scopus)

Methods for identifying lipoxygenase producing microorganisms on agar plates

Nyyssola, A., Heshof, R., Haarmann, T., Eidner, J., Westerholm-Parvinen, A., Langfelder, K., Kruus, K., de Graaff, L. H. & Buchert, J., 2012, In : AMB Express. 2, 17.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

Modeling and analysis of flux distributions in the two branches of the phosphotransferase system in Pseudomonas putida

Kremling, A., Plufger-Grau, K., Silva-Rocha, R., Puchalka, J., Martins Dos Santos, V. A. P. & de Lorenzo, V., 2012, In : BMC Systems Biology. 6, 25 p., 149.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

pH-stat fed-batch process to enhance the production of cis, cis-muconate from benzoate by Pseudomonas putida KT2440-JD1

van Duuren, J. B. J. H., Wijte, D., Karge, B., Martins Dos Santos, V. A. P., Yang, Y., Mars, A. E. & Eggink, G., 2012, In : Biotechnology Progress. 28, 1, p. 85-92

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)

Production of cyanophycin in Rhizopus oryzae through the expression of a cyanophycin synthetase encoding gene

Meussen, B. J., Weusthuis, R. A., Sanders, J. P. M. & de Graaff, L. H., 2012, In : Applied Microbiology and Biotechnology. 93, 3, p. 1167-1174

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

Programmable bacterial catalysis – designing cells for biosynthesis of value-added compounds

Lam, M. C., Suarez Diez, M., Godinho, M. & Martins Dos Santos, V. A. P., 2012, In : FEBS Letters. 586, 15, p. 2184-2190

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Promoter propagation in prokaryotes

Matus-Garcia, M., Nijveen, H. & van Passel, M. W. J., 2012, In : Nucleic acids research. 40, 20, p. 10032-10040

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
11 Citations (Scopus)

Promoter reuse in prokaryotes

Nijveen, H., Matus-Garcia, M. & van Passel, M. W. J., 2012, In : Mobile Genetic Elements. 2, 6, p. 1-3

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida

Leprince, A., de Lorenzo, V., Völler, P., van Passel, M. W. J. & Martins Dos Santos, V. A. P., 2012, In : Environmental Microbiology. 14, 6, p. 1444-1453

Research output: Contribution to journalArticleAcademicpeer-review

33 Citations (Scopus)

Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands

Bohlin, J. & van Passel, M. W. J., 2012, In : BMC Genomics. 13, 35 p., 66.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

Leprince, A., van Passel, M. W. J. & Martins Dos Santos, V. A. P., 2012, In : Current Opinion in Biotechnology. 23, 5, p. 651-658

Research output: Contribution to journalArticleAcademicpeer-review

15 Citations (Scopus)