19972020

Research output per year

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Article
2020

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

Batianis, C., Kozaeva, E., Damalas, S., Martin Pascual, M., Volke, D., Nikel, P. I. & Martins dos Santos, V. A. P., Mar 2020, In : Microbial Biotechnology. 13, 2, p. 368-385

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Genetic Safeguards for Safety-by-design: So Close Yet So Far

Asín García, E., Kallergi, A., Landeweerd, L. & Martins dos Santos, V. A. P., 10 May 2020, In : Trends in Biotechnology. 1016.

Research output: Contribution to journalArticleAcademicpeer-review

Integrated Univariate, Multivariate, and Correlation-Based Network Analyses Reveal Metabolite-Specific Effects on Bacterial Growth and Biofilm Formation in Necrotizing Soft Tissue Infections

Afzal, M., Saccenti, E., Madsen, M. B., Hansen, M. B., Hyldegaard, O., Skrede, S., Martins Dos Santos, V. A. P., Norrby-Teglund, A. & Svensson, M., 7 Feb 2020, In : Journal of Proteome Research. 19, 2, p. 688-698

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2019

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Odoni, D. I., Vazquez-Vilar, M., van Gaal, M. P., Schonewille, T., Martins Dos Santos, V. A. P., Tamayo-Ramos, J. A., Suarez-Diez, M. & Schaap, P. J., 1 Apr 2019, In : FEMS Microbiology Letters. 366, 7, fnz071.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Cofactors revisited – Predicting the impact of flavoprotein-related diseases on a genome scale

Wegrzyn, A. B., Stolle, S., Rienksma, R. A., Martins dos Santos, V. A. P., Bakker, B. M. & Suarez-Diez, M., 1 Feb 2019, In : Biochimica et Biophysica Acta - Molecular Basis of Disease. 1865, 2, p. 360-370

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase

Subramanian, K., Mitusińska, K., Raedts, J., Almourfi, F., Joosten, H. J., Hendriks, S., Sedelnikova, S. E., Kengen, S. W. M., Hagen, W. R., Góra, A., Martins Dos Santos, V. A. P., Baker, P. J., van der Oost, J. & Schaap, P. J., 31 May 2019, In : Biomolecules. 9, 6, 212.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)
Open Access

In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions

Kampers, L. F. C., van Heck, R. G. A., Donati, S., Saccenti, E., Volkers, R. J. M., Schaap, P. J., Suarez-Diez, M., Nikel, P. I. & Martins Dos Santos, V. A. P., 22 Oct 2019, In : Microbial Cell Factories. 18, 1, 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Macrophage-Specific NF-κB Activation Dynamics Can Segregate Inflammatory Bowel Disease Patients

Papoutsopoulou, S., Burkitt, M. D., Bergey, F., England, H., Hough, R., Schmidt, L., Spiller, D. G., White, M. H. R., Paszek, P., Jackson, D. A., Martins Dos Santos, V. A. P., Sellge, G., Pritchard, D. M., Campbell, B. J., Müller, W. & Probert, C. S., 11 Sep 2019, In : Frontiers in Immunology. 10, 11 p., 2168.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Metabolomics in systems medicine: an overview of methods and applications

Karakitsou, E., Foguet, C., de Atauri, P., Kultima, K., Khoonsari, P. E., Martins dos Santos, V. A. P., Saccenti, E., Rosato, A. & Cascante, M., 1 Jun 2019, In : Current Opinion in Systems Biology. 15, p. 91-99 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)
Open Access
2 Citations (Scopus)

Patient’s characteristics and outcomes in necrotising soft-tissue infections: results from a Scandinavian, multicentre, prospective cohort study

Madsen, M. B., Skrede, S., Perner, A., Arnell, P., Nekludov, M., Bruun, T., Karlsson, Y., Hansen, M. B., Polzik, P., Hedetoft, M., Rosén, A., Saccenti, E., Bergey, F., Martins Dos Santos, V. A. P., Norrby-teglund, A. & Hyldegaard, O., Sep 2019, In : Intensive Care Medicine. 45, 9, p. 1241-1251

Research output: Contribution to journalArticleAcademicpeer-review

3 Citations (Scopus)

Risk-Based Bioengineering Strategies for Reliable Bacterial Vaccine Production

Kamminga, T., Slagman, S. J., Martins dos Santos, V. A. P., Bijlsma, J. J. E. & Schaap, P. J., Aug 2019, In : Trends in Biotechnology. 37, 8, p. 805-816

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The diurnal transcriptional landscape of the microalga Tetradesmus obliquus

Carreres, B. M., Mitsue León-Saiki, G., Schaap, P. J., Remmers, I. M., van der Veen, D., Martins dos Santos, V. A. P., Wijffels, R. H., Martens, D. E. & Suarez-Diez, M., 1 Jun 2019, In : Algal Research. 40, 101477.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

van Dam, J. C. J., Koehorst, J. J., Vik, J. O., Martins dos Santos, V. A. P., Schaap, P. J. & Suarez-Diez, M., 4 Nov 2019, In : Scientific Data. 6, 1, 1 p., 254.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2018
Open Access
1 Citation (Scopus)

DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems

Smith, R. W., van Rosmalen, R. P., Martins dos Santos, V. A. P. & Fleck, C., 19 Jun 2018, In : BMC Systems Biology. 12, 72.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)

From correlation to causation: analysis of metabolomics data using systems biology approaches

Rosato, A., Tenori, L., Cascante, M., De Atauri Carulla, P. R., Martins dos Santos, V. A. P. & Saccenti, E., 1 Apr 2018, In : Metabolomics. 14, 4, 37.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
28 Citations (Scopus)

Genome sequence of two members of the chloroaromatic-degrading MT community: Pseudomonas reinekei MT1 and Achromobacter xylosoxidans MT3

Gutierrez-Urrutia, I., Miossec, M. J., Valenzuela, S. L., Meneses, C., Martins dos Santos, V. A. P., Castro-Nallar, E. & Poblete-Castro, I., 10 Jun 2018, In : Journal of Biotechnology. 275, p. 13-16

Research output: Contribution to journalArticleAcademicpeer-review

Modeling the Metabolic State of Mycobacterium tuberculosis Upon Infection

Rienksma, R. A., Schaap, P. J., Martins Dos Santos, V. A. P. & Suarez-Diez, M., 3 Aug 2018, In : Frontiers in Cellular and Infection Microbiology. 8, 264.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Modulating D-amino acid oxidase (DAAO) substrate specificity through facilitated solvent access

Subramanian, K., Góra, A., Spruijt, R., Mitusińska, K., Suarez-Diez, M., Martins Dos Santos, V. & Schaap, P. J., 1 Jan 2018, In : PLoS ONE. 13, 6, e0198990.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
10 Citations (Scopus)

Necrotizing soft tissue infections - a multicentre, prospective observational study (INFECT): Protocol and statistical analysis plan

Madsen, M. B., Skrede, S., Bruun, T., Arnell, P., Rosén, A., Nekludov, M., Karlsson, Y., Bergey, F., Saccenti, E., Martins dos Santos, V. A. P., Perner, A., Norrby-Teglund, A. & Hyldegaard, O., Feb 2018, In : Acta Anaesthesiologica Scandinavica. 62, 2, p. 272-279

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Neochloris oleoabundans is worth its salt: Transcriptomic analysis under salt and nitrogen stress

de Jaeger, L., Carreres, B. M., Springer, J., Schaap, P. J., Eggink, G., Martins dos Santos, V. A. P., Wijffels, R. H. & Martens, D. E., 1 Apr 2018, In : PLoS ONE. 13, 4, e0194834.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Recommended strategies for spectral processing and post-processing of 1D 1H-NMR data of biofluids with a particular focus on urine

Emwas, A. H., Saccenti, E., Gao, X., McKay, R. T., Martins dos Santos, V. A. P., Roy, R. & Wishart, D. S., 1 Mar 2018, In : Metabolomics. 14, 3, 31.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
14 Citations (Scopus)

Regulation of three virulence strategies of Mycobacterium tuberculosis: A success story

Zondervan, N. A., Van Dam, J. C. J., Schaap, P. J., Martins dos Santos, V. A. P. & Suarez-Diez, M., 1 Feb 2018, In : International Journal of Molecular Sciences. 19, 2, 347.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
6 Citations (Scopus)

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles

Koehorst, J. J., van Dam, J. C. J., Saccenti, E., Martins Dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 15 Apr 2018, In : Bioinformatics. 34, 8, p. 1401-1403

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
8 Citations (Scopus)

Studying microbial functionality within the gut ecosystem by systems biology

Hornung, B., Martins dos Santos, V. A. P., Smidt, H. & Schaap, P. J., 6 Mar 2018, In : Genes and Nutrition. 13, 1, 5.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
9 Citations (Scopus)

SyNDI: Synchronous network data integration framework

Lindfors, E., van Dam, J. C. J., Lam, C. M. C., Zondervan, N. A., Martins dos Santos, V. A. P. & Suarez-Diez, M., 6 Nov 2018, In : BMC Bioinformatics. 19, 1, 403.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2017

Aspergillus niger secretes citrate to increase iron bioavailability

Odoni, D. I., van Gaal, M. P., Schonewille, T., Tamayo-Ramos, J. A., Martins dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 2017, In : Frontiers in Microbiology. 8, AUG, 1424.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
5 Citations (Scopus)

Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation

Odoni, D. I., Tamayo-Ramos, J. A., Sloothaak, J., van Heck, R., Martins dos Santos, V. A. P., de Graaff, L. H., Suarez-Diez, M. & Schaap, P. J., 30 Mar 2017, In : PeerJ. 5, e3133.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)

Draft genome sequence of the oleaginous green alga Tetradesmus obliquus UTEX 393

Carreres, B. M., de Jaeger, L., Springer, J., Barbosa, M. J., Breuer, G., van den End, E. J., Kleinegris, D. M. M., Schäffers, I., Wolbert, E. J. H., Zhang, H., Lamers, P. P., Martins dos Santos, V. A. P., Wijffels, R. H., Eggink, G., Schaap, P. J. & Martens, D. E., 2017, In : Genome Announcements. 5, 3, e01449-16.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
13 Citations (Scopus)
27 Citations (Scopus)

Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

Gerritsen, J., Hornung, B., Renckens, B., van Hijum, S. A. F. T., Martins dos Santos, V. A. P., Rijkers, G. T., Schaap, P. J., de Vos, W. M. & Smidt, H., 2017, In : PeerJ. 2017, 9, 3698.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
15 Citations (Scopus)

Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni

Schulze, S., Urzica, E., Reijnders, M. J. M. F., van de Geest, H., Warris, S., Bakker, L. V., Fufezan, C., Martins dos Santos, V. A. P., Schaap, P. J., Peters, S. A. & Hippler, M., 2017, In : New Phytologist. 215, 4, p. 1361-1369

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
7 Citations (Scopus)

Metabolic modeling of energy balances in Mycoplasma hyopneumoniae shows that pyruvate addition increases growth rate

Kamminga, T., Slagman, S. J., Bijlsma, J. J. E., Martins dos Santos, V. A. P., Suarez-Diez, M. & Schaap, P. J., 2017, In : Biotechnology and Bioengineering. 114, 10, p. 2339-2347

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

van der Ark, K. C. H., van Heck, R. G. A., Martins Dos Santos, V. A. P., Belzer, C. & de Vos, W. M., 14 Jul 2017, In : Microbiome. 5, 1, p. 78

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
19 Citations (Scopus)

Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them

Benis, N., Kar, S. K., Martins dos Santos, V. A. P., Smits, M. A., Schokker, D. & Suarez-Diez, M., 2017, In : Frontiers in Physiology. 8, 11 p., 388.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)

Persistence of functional protein domains in mycoplasma species and their role in host specificity and synthetic minimal life

Kamminga, T., Koehorst, J. J., Vermeij, P., Slagman, S. J., dos Santos, V. A. P. M., Bijlsma, J. J. E. & Schaap, P. J., 2017, In : Frontiers in Cellular and Infection Microbiology. 7, 31.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3 Citations (Scopus)
Open Access
3 Citations (Scopus)
Open Access
7 Citations (Scopus)

Use of Microarray Datasets to generate Caco-2-dedicated Networks and to identify Reporter Genes of Specific Pathway Activity

Venkatasubramanian, P. B., Toydemir, G., de Wit, N., Saccenti, E., Martins dos Santos, V. A. P., van Baarlen, P., Wells, J. M., Suarez-Diez, M. & Mes, J. J., Jan 2017, In : Scientific Reports. 7, 1, 6778.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2 Citations (Scopus)
2016

Characterizing the optimal flux space of genome-scale metabolic reconstructions through modified latin-hypercube sampling

Chaudhary, N., Tøndel, K., Bhatnagar, R., Martins dos Santos, V. A. P. & Puchalka, J., 2016, In : Molecular BioSystems. 12, 3, p. 994-1005

Research output: Contribution to journalArticleAcademicpeer-review

1 Citation (Scopus)

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)

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)

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)

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

56 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
17 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)

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)
Open Access