Research Output

2012

Streamlining of a Pseudomonas putida Genome using a Combinatorial Deletion Method Based on Mini-transposon Insertion and the Flp-FRT Recombination System

Leprince, A., Timmis, K. N. & Martins Dos Santos, V. A. P., 2012, Synthetic Gene Networks. Weber, W. & Fussenegger, M. (eds.). Heidelberg, p. Part III-chapter 15 402 p. (Methods in Molecular Biology; no. 813).

Research output: Chapter in Book/Report/Conference proceedingChapter

10 Citations (Scopus)

The Arabidopsis thaliana SERK1 kinase domain spontaneously refolds to an active state in vitro

aan den Toorn, M., Huijbers, M. M. E., de Vries, S. C. & van Mierlo, C. P. M., 2012, In : PLoS ONE. 7, 12, e50907.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts

Hesselman, M. C., Koehorst, J. J., Slijkhuis, T., Hugenholtz, F., Odoni, D. I. & van Passel, M. W. J., 2012, In : Journal of Biological Engineering. 6, 6 p., 14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
4 Citations (Scopus)

The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

Poblete-Castro, I., Escapa, I., Jager, C., Puchalka, J., Lam, M. C., Schomburg, D., Prieto, M. & Martins Dos Santos, V. A. P., 2012, In : Microbial Cell Factories. 11, 34.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
62 Citations (Scopus)

Using semantic web technology to accelerate plant breeding

Chibon, P. Y., Carreres, B. M., de Weerd, H. H., Visser, R. G. F. & Finkers, H. J., 2012.

Research output: Contribution to conferenceConference paper

2011

A comprehensive metatranscriptomics analysis pipeline

Leimena, M. M., Schaap, P. J., Zoetendal, E. G., Smid, E. J. & Kleerebezem, M., 2011.

Research output: Contribution to conferenceAbstract

A limited LCA of bio-adipic acid: Manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks

van Duuren, J. B. J. H., Brehmer, B., Mars, A. E., Eggink, G., Martins Dos Santos, V. A. P. & Sanders, J. P. M., 2011, In : Biotechnology and Bioengineering. 108, 6, p. 1298-1306

Research output: Contribution to journalArticleAcademicpeer-review

33 Citations (Scopus)

An iterative workflow for mining the human intestinal metaproteome

Rooijers, K., Kolmeder, C., Juste, C., Doré, J., de Been, M., Boeren, S., Galan, P., de Vos, W. M., Schaap, P. J. & Beauvallet, C., 2011, In : BMC Genomics. 12, 11 p., 6.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
72 Citations (Scopus)

A quantitative account of genomic island acquisitions in prokaryotes

Roos, T. E. & van Passel, M. W. J., 2011, In : BMC Genomics. 12, 34 p., 427.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Kubichek, C. P. & Tamayo Ramos, J. A., 2011, In : Genome Biology. 12, 4, 15 p., R40.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
277 Citations (Scopus)

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

Andersen, M. R., Salazar, M. P. & Schaap, P. J., 2011, In : Genome Research. 21, 6, p. 885-897

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
214 Citations (Scopus)

Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger

Mela, F., Fritsche, K., de Boer, W., van Veen, J. A., de Graaff, L. H., van den Berg, M. & Leveau, J. H. J., 2011, In : ISME Journal. 5, 9, p. 1494-1504

Research output: Contribution to journalArticleAcademicpeer-review

56 Citations (Scopus)

Engineered host cells and methods for the production of cis, cis-muconic acid

van Duuren, J. B. J. H., Martins Dos Santos, V. A. P., van Marsen, A. & Eggink, G., 24 Aug 2011, Patent No. EP2562249

Research output: PatentOther research output

Open Access

Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction

Fang, K., Zhao, H., Changyue Sun, Lam, M. C., Chang, S., Zhang, K., Panda, G., Godinho, M., Martins Dos Santos, V. A. P. & Wang, J., 2011, In : BMC Systems Biology. 5, 16 p., 83.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
25 Citations (Scopus)

Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield

van Duuren, J. B. J. H., Wijte, D., Leprince, A., Karge, B., Puchalka, J., Wery, J., Martins Dos Santos, V. A. P., Eggink, G. & Mars, A. E., 2011, In : Journal of Biotechnology. 156, 3, p. 163-172

Research output: Contribution to journalArticleAcademicpeer-review

26 Citations (Scopus)

Genome sequence of Chthoniobacter flavus Ellin428, an aerobic heterotrophic soil bacterium

Kant, R., van Passel, M. W. J., de Vos, W. M. & Smidt, H., 2011, In : Journal of Bacteriology. 193, 11, p. 2902-2903

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
27 Citations (Scopus)

Genome sequence of "Pedosphaera parvula" Ellin514, an aerobic Verrucomicrobial isolate from pasture soil

Kant, R., van Passel, M. W. J., de Vos, W. M. & Smidt, H., 2011, In : Journal of Bacteriology. 193, 11, p. 2900-2901

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems

van Passel, M. W. J., de Vos, W. M. & Smidt, H., 2011, In : Journal of Bacteriology. 193, 9, p. 2367-2368

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
26 Citations (Scopus)
Open Access
9 Citations (Scopus)

Genomic approaches for identification of the biopolymer degrading enzyme network of Aspergillus niger

van der Kaaij, R. M., Ram, A. F., Schaap, P. J. & Punt, P. J., 2011, Industrial Applications. Hofrichter, M. (ed.). Berlin Heidelberg, p. 407-424 (The Mycota; no. 10).

Research output: Chapter in Book/Report/Conference proceedingChapter

Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid

Koutinas, M., Kiparissides, A., Lam, M. C., Silva-Rocha, R., de Lorenzo, V., Godinho, M., Martins Dos Santos, V. A. P., Pistikopoulos, E. N. & Mantalaris, A., 2011, In : Biochemical Engineering Journal. 55, 2, p. 108-118

Research output: Contribution to journalArticleAcademicpeer-review

8 Citations (Scopus)

In-Vivo Expression Profiling of Pseudomonas aeruginosa Infections Reveals Niche-Specific and Strain-Independent Transcriptional Programs

Bielecki, P., Puchalka, J., Wos-Oxley, M. L. & Martins Dos Santos, V. A. P., 2011, In : PLoS ONE. 6, 11 p., e24235.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
33 Citations (Scopus)

Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach

Koutinas, M., Kiparissides, A., Silva-Rocha, R., Lam, M. C., Martins Dos Santos, V. A. P., de Lorenzo, V., Pistikopoulos, E. N. & Mantalaris, A., 2011, In : Metabolic Engineering. 13, 4, p. 401-413

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger

Omony, J., de Graaff, L. H., van Straten, G. & van Boxtel, A. J. B., 2011, In : BMC Systems Biology. 5, Suppl. 1, 14 p., S14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Optimization of Pseudomonas putida KT2440 as host for the production of cis, cis-muconate from benzoate

van Duuren, J. B. J. H., 2011, {S.l.]: S.n.. 132 p.

Research output: Thesisinternal PhD, WU

Open Access

Parameter estimation in genetic networks using a constrained stochastic space search method

Omony, J., de Graaff, L. H., van Straten, G. & van Boxtel, A. J. B., 2011, 30th Benelux Meeting on Systems and Control, Lommel, Belgium, 15 - 17 March, 2011. p. 129-129

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Open Access

Predicting microbial growth kinetics with the use of genetic circuit models

Koutinas, M., Kiparissides, A., de Lorenzo, V., Martins Dos Santos, V. A. P., Pistikopoulos, E. N. & Mantalaris, A., 2011, 21st European Symposium on Computer Aided Process Engineering. Pistikopoulos, E. N., Georgiadis, M. C. & Kokossis, A. C. (eds.). Elsevier, p. 1321-1325 (Computer Aided Chemical Engineering; vol. 29).

Research output: Chapter in Book/Report/Conference proceedingConference paper

Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose

Ferreira de Oliveira, J. M. P., van Passel, M. W. J., Schaap, P. J. & de Graaff, L. H., 2011, In : PLoS ONE. 6, 6, e20865.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
40 Citations (Scopus)

Proteomics of industrial fungi: trends and insights for biotechnology

Oliveira, J. M. & de Graaff, L. H., 2011, In : Applied Microbiology and Biotechnology. 89, 2, p. 225-237

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
34 Citations (Scopus)

Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis

Oberhardt, M., Puchalka, J., Martins Dos Santos, V. A. P. & Papin, J. A., 2011, In : PLoS Computational Biology. 7, 3, 18 p., e1001116.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
74 Citations (Scopus)
56 Citations (Scopus)

Systems biology of Host-Food-Microbe interactions in the mammalian gut

Martins Dos Santos, V. A. P., Müller, M. R., de Vos, W. M., Wells, J., te Pas, M. F. W., Hooiveld, G. J., van Baarlen, P., Smits, M. A. & Keijer, J., 2011, Systems Biology and Livestock Science. te Pas, M. (ed.). John Wiley and Sons, p. 109-135 332 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

The Aspergillus niger multicopper oxidase family: analysis and overexpression of laccase-like encoding genes

Tamayo Ramos, J. A., Barends, S., Verhaert, R. M. & de Graaff, L. H., 2011, In : Microbial Cell Factories. 10, p. 78-78

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
28 Citations (Scopus)

The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms

Silva-Rocha, R., Tamames, J., Martins Dos Santos, V. A. P. & de Lorenzo, V., 2011, In : Environmental Microbiology. 13, 9, p. 2389-2402

Research output: Contribution to journalArticleAcademicpeer-review

27 Citations (Scopus)

The ten grand challenges of synthetic life

Porcar, M., Danchin, A., de Lorenzo, V., Martins Dos Santos, V. A. P., Krasnogor, V., Rasmussen, S. & Moya, A., 2011, In : Systems and synthetic biology. 5, 1-2, p. 1-9

Research output: Contribution to journalArticleAcademicpeer-review

32 Citations (Scopus)

Tracing common origins of Genomic Islands in prokaryotes based on genome signature analyses

van Passel, M. W. J., 2011, In : Mobile Genetic Elements. 1, 3, p. 247-249

Research output: Contribution to journalArticleAcademicpeer-review

Tracy-Widom statistic for the largest eigenvalue of autoscaled real matrices

Saccenti, E., Smilde, A. K., Westerhuis, J. A. & Hendriks, M. M. W. B., 1 Dec 2011, In : Journal of Chemometrics. 25, 12, p. 644-652

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)
2010

Combining Genetic Circuit and Microbial Growth Kinetic Models: A Challenge for Biological Modelling

Koutinas, M., Kiparissides, A., Lam, M. C., Silva-Rocha, R., de Lorenzo, V., Martins Dos Santos, V. A. P., Pistikopoulos, E. N. & Mantalaris, A., 2010, Computer Aided Process Engineering. Elsevier, Vol. 28. p. 301-306

Research output: Chapter in Book/Report/Conference proceedingConference paper

1 Citation (Scopus)

Consortia modulation of the stress response: proteomic analysis of single strain versus mixed culture

Fazzini, R. A. & Martins Dos Santos, V. A. P., 2010, In : Environmental Microbiology. 12, 9, p. 2436-2449

Research output: Contribution to journalArticleAcademicpeer-review

21 Citations (Scopus)

Exploring Networks at the genome scale

Lam, M. C., Puchalka, J., Diez, M. S. & Martins Dos Santos, V. A. P., 2010, In : European Biotechnology Science and Industry News. 9, 1-2, p. 40-42

Research output: Contribution to journalArticleAcademicpeer-review

Novel tools for extraction and validation of disease-related mutations applied to fabry disease

Kuipers, R. K. P., Bergh, T., Joosten, H. J., Lekanne dit Deprez, R. H., Mannens, M. M. A. M. & Schaap, P. J., 2010, In : Human Mutation. 31, 9, p. 1026-1032

Research output: Contribution to journalArticleAcademicpeer-review

20 Citations (Scopus)

Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface

Martins Dos Santos, V. A. P., Müller, M. R. & de Vos, W. M., 2010, In : Current Opinion in Biotechnology. 21, 4, p. 539-550

Research output: Contribution to journalArticleAcademicpeer-review

44 Citations (Scopus)

The alpha/beta-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein Engineering

Kourist, R., Jochens, H., Bartsch, S., Kuipers, R. K. P., Padhi, S. K., Gall, M., Bottcher, D., Joosten, H. J. & Bornscheuer, U. T., 2010, In : ChemBioChem. 11, 12, p. 1635-1643

Research output: Contribution to journalArticleAcademicpeer-review

100 Citations (Scopus)

The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid

Koutinas, M., Lam, M. C., Kiparissides, A., Silva-Rocha, R., Godinho, M., Livingston, A. G., Pistikopoulos, E. N., de Lorenzo, V., Martins Dos Santos, V. A. P. & Mantalaris, A., 2010, In : Environmental Microbiology. 12, 6, p. 1705-1718

Research output: Contribution to journalArticleAcademicpeer-review

27 Citations (Scopus)
2009

(Re-)construction, characterization and modeling of systems for synthetic biology

Diez, M. S., Lam, M. C., Leprince, A. & Martins Dos Santos, V. A. P., 2009, In : Biotechnology Journal. 4, 10, p. 1382-1391

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Scopus)

Individual human phenotypes in metabolic space and time

Bernini, P., Bertini, I., Luchinat, C., Nepi, S., Saccenti, E., Schäfer, H., Schütz, B., Spraul, M. & Tenori, L., 19 Oct 2009, In : Journal of Proteome Research. 8, 9, p. 4264-4271 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
95 Citations (Scopus)

The metabonomic signature of celiac disease

Bertini, I., Calabró, A., De Carli, V., Luchinat, C., Nepi, S., Porfirio, B., Renzi, D., Saccenti, E. & Tenori, L., 1 Jan 2009, In : Journal of Proteome Research. 8, 1, p. 170-177 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
112 Citations (Scopus)