Molecular Cell Biology

Research Output

2016

Public goods and metabolic strategies

Bachmann, H., Bruggeman, F. J., Molenaar, D., Santos, F. & Teusink, B., Jun 2016, In : Current Opinion in Microbiology. 31, p. 109-115

Research output: Contribution to JournalArticle

Open Access
Open Access
Open Access

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.

Cvijovic, M., Hofer, 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., Mauer-Oberthur, A., Regierer, B., Skene, B., Stalidzans, E., Stelling, J., Teusink, B., Workman, C. T. & Hohmann, S., 2016, In : NPJ systems biology and applications. 2, 16011.

Research output: Contribution to JournalArticle

Open Access

Synthesis, characterization and biological acitvity of fluorescently labeled bedaquiline analogues.

Rombouts, J. A., Veenboer, R. M. P., Villellas, C., Lu, P., Ehlers, A. W., Andries, K., Koul, A., Lill, H., Ruijter, E., Orru, R. V. A., Lammertsma, K., Bald, D. & Slootweg, J. C., 2016, In : RSC Advances. 6, p. 108708-108716

Research output: Contribution to JournalArticle

Open Access

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

He, F., Murabito, E. & Westerhoff, H. V., 2016, In : Journal of the Royal Society Interface. 117, pii:20151046.

Research output: Contribution to JournalArticle

Open Access

Systems Biology in the broad sense

Boogerd, F. C., 2016, Philosophy of Systems Biology: Perspectives form Scientists and Philosophers. Springer, p. 49-58 10 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

Targeting glycolysis in the malaria parasite Plasmodium falciparum.

van Niekerk, D. D., Penkler, G. P., du Toit, F. & Snoep, J. L., 2016, In : The FEBS Journal. 283, 4, p. 634-646

Research output: Contribution to JournalArticle

Open Access

The Ag85B protein of the BCG vaccine facilitates macrophage uptake but is dispensable for protection against aerosol Mycobacterium tuberculosis infection.

Prendergast, K. A., Counoupas, C., Leotta, L., Eto, C., Bitter, W., Winter, N. & Triccas, J. A., 2016, In : Vaccine. 34, 23, p. 2608-2615

Research output: Contribution to JournalArticle

The development of computational biology in South Africa: Successes achieved and lessons learnt.

Mulder, N. J., Christoffels, A., de Oliveira, T., Gamieldien, J., Hazelhurst, S., Joubert, F., Kumuthini, J., Pillay, C. S., Snoep, J. L., Tastan Bishop, O. & Tiffin, N., 2016, In : PLoS Computational Biology. 12, 2, e1004395.

Research output: Contribution to JournalArticle

Open Access

The ESX-5 system of pathogenic mycobacteria is involved in capsule integrity and virulence through its substrate PPE10

Ates, L. S., van der Woude, A. D., Bestebroer, J., van Stempvoort, G., Musters, R. J., Garcia Vallejo, J. J., Picavet, D. I., van de Weerd, R., Maletta, M., Kuijl, C. P., van der Wel, N. N. & Bitter, W., 2016, In : Plos Pathogens. 12, 6, e1005696.

Research output: Contribution to JournalArticle

Open Access

Top 10 metrics for life science software good practices.

Artaza, H., Chue Hong, N., Corpas, M., Corpuz, A., Hooft, R., Jimenez, R. C., Leskosek, B., Olivier, B. G., Stourac, J., Svobodova Varekova, R., van Parys, T. & Vaughan, D., 2016, In : F1000Research. 5, ELIXIR-2000.

Research output: Contribution to JournalArticle

Open Access

Type VII secretion: a highly versatile secretion system.

Ates, L. S., Houben, E. N. G. & Bitter, W., 2016, In : Microbiology spectrum. 1

Research output: Contribution to JournalArticle

Where is the bias?

Roth, S., 2016, 161 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
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2015

A comparative study of antimony accumulation in plants growing in two mining areas in Iran, Moghanlo, and Patyar

Hajiani, N. J., Ghaderian, S. M., Karimi, N. & Schat, H., 2015, In : Environmental Science and Pollution Research International. 22, 21, p. 16452-16553

Research output: Contribution to JournalArticle

A dynamic energy budget for the whole life-cycle of holometabolous insects.

Llandres, A. L., Marques, G. M., Maino, J. L., Kooijman, S. A. L. M., Kearney, M. R. & Casas, J., 2015, In : Ecological Monographs.

Research output: Contribution to JournalArticle

Amino acid analysis using chromatography–mass spectrometry: An inter platform comparison study

Krumpochova, P., Bruyneel, B., Molenaar, D., Koukou, A., Wuhrer, M., Niessen, W. M. A. & Giera, M. A., 2015, In : Journal of Pharmaceutical and Biomedical Analysis. 114, p. 398-407

Research output: Contribution to JournalArticle

Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores.

de Boer, P., Caspers, M., Sanders, J. W., Kemperman, R., Wijman, J., Lommerse, G., Roeselers, G., Montijn, R., Abee, T. & Kort, R., 2015, In : Microbiome. 27, p. 30 3.

Research output: Contribution to JournalArticle

Open Access

Animal models of tuberculosis: Zebrafish

van Leeuwen, L. M., van der Sar, A. M. & Bitter, W., 2015, (Accepted/In press) In : Cold Spring Harbor perspectives in medicine. 5, 3, a018580.

Research output: Contribution to JournalArticle

A novel consortium of Lactobacillus rhamnosus and Streptococcus thermophilus for increased access to functional fermented foods

Kort, R., Westerik, N., Mariela Serrano, L., Douillard, F. P., Gottstein, W. G., Mukisa, I. M., Tuijn, C. J., Basten, L., Hafkamp, B., Meijer, W. C., Teusink, B., de Vos, W. M., Reid, G. & Sybesma, W., 2015, In : Microbial Cell Factories. 14, 195

Research output: Contribution to JournalArticle

Open Access

A reason for intermittent fasting to suppress the awakening of dormant breast tumors.

Lankelma, J., Kooi, B. W., Krab, K., Dorsman, J. C., Joenje, H. & Westerhoff, H. V., 2015, In : BioSystems. 127, p. 1-6

Research output: Contribution to JournalArticle

A review on emerging diagnostic assay for viral detection: the case of avian influenza virus.

Roodbar Shojaei, T., Tabatabaei, M., Shawky, S., Salleh, M. A. M. & Bald, D., 2015, In : Molecular Biology Reports. 42, 1, p. 187-199

Research output: Contribution to JournalArticle

Autotransporter-based antigen display in bacterial ghosts.

Hjelm, A., Söderström, B., Vikström, D., Jong, W. S. P., Luirink, S. & de Gier, J. W., Jan 2015, In : Applied and Environmental Microbiology. 81, 2, p. 726-735 10 p.

Research output: Contribution to JournalArticle

Bactericidal mode of action of bedaquiline.

Hards, K., Robson, J. R., Berney, M., Shaw, L., Bald, D., Koul, A., Andries, K. & Cook, G. M., 2015, In : Journal of Antimicrobial Chemotherapy. 70, 7, p. 2028-2037

Research output: Contribution to JournalArticle

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

Bosdriesz, E., Magnúsdóttir, S., Bruggeman, F. J., Teusink, B. & Molenaar, D., 2015, In : The FEBS Journal. 282, p. 2394-2407 12.

Research output: Contribution to JournalArticle

Biofumigation using a wild Brassica oleracea accession with high glucosinolate content affects beneficial soil invertebrates

Zuluaga, D. L., van Ommen Kloeke, A. E. E., Verkerk, R., Roling, W. F. M., Ellers, J., Roelofs, D. & Aarts, M. G. M., 2015, In : Plant and Soil. 394, 1, p. 155-163

Research output: Contribution to JournalArticle

Open Access

Both the concentration and redox state of glutathione and ascorbate influence the sensitivity of arabidopsis to cadmium

Jozefczak, M., Bohler, S., Schat, H., Horemans, N., Guisez, Y., Remans, T., Vangronsveld, J. & Cuypers, A., 2015, In : Annals of Botany. 116, 4, p. 601-612

Research output: Contribution to JournalArticle

Open Access

Cadmium tolerance and accumulation in Excluder Thlaspi arvense and various accessions of hyperaccumulator Noccaea caerulescens

Seregin, I. V., Kozhevnikova, A. D., Zhukovskaya, V. & Schat, H., 2015, In : Russian Journal of Plant Physiology. 62, 6, p. 837-846

Research output: Contribution to JournalArticle

Capturing the life history of the marine copepod Calanus sinicus into a generic bioenergetics framework.`

Jager, T., Salaberria, I. & Hansen, B. H., 2015, In : Ecological Modelling. 299, p. 114-120

Research output: Contribution to JournalArticle

Cell age dependent concentration of Escherichia coli divisome proteins analyzed with ImageJ and ObjectJ.

Vischer, N. O., Verheul, J., Postma, M., van den Berg van Saparoea, H. B., Galli, E., Natale, P., Gerdes, K., Luirink, J., Vollmer, W., Vicente, M. & den Blaauwen, T., 2015, In : Frontiers in Microbiology. 11, p. 586 6.

Research output: Contribution to JournalArticle

Open Access

Challenges of achieving Good Environmental Status in the Northeast Atlantic

Alexander, K. A., Kershaw, P., Cooper, P., Gilbert, A. J., Hall-Spencer, J. M., Heymans, J. J., Kannen, A., Los, H. J., O'Higgins, T., O'Mahony, C., Tett, P., Troost, T. A. & van Beusekom, J., 2015, In : Ecology and Society. 20, 1, 49.

Research output: Contribution to JournalArticle

Open Access

Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures.

Kusters, E., Della Pina, S., Castel, R., Souer, E. J. & Koes, R. E., 2015, In : Development (Cambridge). 142, p. 2822-2831

Research output: Contribution to JournalArticle

Characterization of antibacterial drugs and drug combinations targeting oxidative phosphorylation in Mycobacteria

Lu, P., 2015, 177 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
File

Competition for Light and Nutrients in Layered Communities of Aquatic Plants

van Gerven, L. P. A., Klein, J. J. M., Gerla, D. J., Kooi, B. W., Kuiper, J. J. & Mooij, W. M., 2015, In : The American Naturalist. 186, p. 72-83

Research output: Contribution to JournalArticle

Open Access
File

Constitutive high-level SOS1 expression and absence of HKT1;1 expression in the salt-accumulating halophyte Salicornia dolichostachya

Katschnig, D., Bliek, M., Rozema, J. & Schat, H., 2015, In : Plant Science. 234, p. 144-154

Research output: Contribution to JournalArticle

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum.

Penkler, G. P., du Toit, F., Adams, W., Rautenbach, M., Palm, D. C., van Niekerk, D. D. & Snoep, J. L., 2015, In : The FEBS Journal. 282, p. 1481-1511 2.

Research output: Contribution to JournalArticle

Darwin s invisible hand

Bosdriesz, E., 2015

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
File

Direct quantitative detection of Doc2b-induced hemifusion in optically trapped membranes

Brouwer, I., Giniatullina, A., Laurens, N., van Weering, J. R. T., Bald, D., Wuite, G. J. L. & Groffen, A. J. A., 2015, In : Nature Communications. 6, p. 8387 8387.

Research output: Contribution to JournalArticle

Open Access

Diverse arsenic- and iron-cycling microbial communities in arsenic-contaminated aquifers used for drinking water in Bangladesh.

Hassan, Z., Sultana, M., van Breukelen, B. M., Kahn, S. I. & Roling, W. F. M., 2015, In : FEMS Microbiology Ecology. 91, 4.

Research output: Contribution to JournalArticle

Drug target identification through systems biology.

Haanstra, J. R. & Bakker, B. M., 2015, In : Drug Discovery Today: Technologies. 15, p. 17-22

Research output: Contribution to JournalArticle

Ecoepidemic models with prey group defense and feeding saturation

Gimmelli, G., Kooi, B. W. & Venturino, E., 2015, In : Ecological Complexity. 22, p. 50-58

Research output: Contribution to JournalArticle

Open Access
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Effects of chronic exposure to environmentally relevant concentrations of waterborne uranium an the digestive tract of zebrafish, Danio rerio.

Augustine, S., Pereira, S., Floriani, M., Camilleri, V., Kooijman, S. A. L. M., Gagnaire, B. & Adam-Guillermin, A., 2015, In : Journal of Environmental Radioactivity. 142, p. 45-53

Research output: Contribution to JournalArticle

Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria.

Ates, L. S., Ummels, R., Commandeur, S., van de Weerd, R., Sparrius, M., Weerdenburg, E., Alber, M., Kalscheuer, R., Piersma, S. R., Abdallah, A., Abd El Ghany, M., Abdel-Haleem, A. M., Pain, A., Jimenez, C. R., Bitter, W. & Houben, E. N. G., 2015, In : PLoS Genetics. 4, 11, 5.

Research output: Contribution to JournalArticle

Open Access

Evolutionary engineering to enhance starter culture performance in food fermentations.

Bachmann, H., Pronk, J. T., Kleerebezem, M. & Teusink, B., 2015, In : Current Opinion in Biotechnology. p. 1-7 32.

Research output: Contribution to JournalArticle

Fast flux module detection using matroid theory.

Reimers, A. C., Bruggeman, F. J., Olivier, B. G. & Stougie, L., 2015, In : Journal of Computational Biology. 22, p. 414-424 5.

Research output: Contribution to JournalArticle

Fluxes and fluctuations in biochemical models

Maarleveld, T. R., 2015

Research output: PhD ThesisPhD Thesis - Research external, graduation VU

Open Access
File
Open Access

Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders

Arloth, J., Bogdan, R., Weber, P., Frishman, G., Menke, A., Wagner, K. V., Balsevich, G., Schmidt, M. V., Karbalai, N., Czamara, D., Altmann, A., Trümbach, D., Wurst, W., Mehta, D., Uhr, M., Klengel, T., Erhardt, A., Carey, C. E., Drabant Conley, E., Boomsma, D. I. & 10 others, Penninx, B. W. J. H., de Geus, E. J. C., Hottenga, J. J., Middeldorp, C. M., Willemsen, G., Smit, J. H., Ruepp, A., Müller-Myhsok, B., Hariri, A. & Binder, E. B., 2015, In : Neuron. 86, p. 1189-1202 15 p.

Research output: Contribution to JournalArticle

Open Access

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

Weerdenburg, E. M., Abdallah, A., Rangkuti, F., Abd El Ghany, M., Otto, T. D., Adroub, S. A., Molenaar, D., Ummels, R., Ter Veen, K., van Stempvoort, G., van der Sar, A. M., Ali, S., Langridge, G. C., Thomson, N. R., Pain, A. & Bitter, W., 2015, In : Infection and Immunity. 83, p. 1778-1788 5.

Research output: Contribution to JournalArticle