Molecular Cell Biology

Research Output

2015

Genomic, proteomic and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans

Kruse, T., van der Pas, B. A., Atteia, A., Krab, K., Hagen, W. R., Goodwin, L., Chain, P., Boeren, S., Maphosa, F., Schraa, G., Vos, W. M., van der Oost, J., Smidt, H. & Stams, A. J. M., Mar 2015, In : Journal of Bacteriology. 197, 5, p. 893-904 12 p.

Research output: Contribution to JournalArticle

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations.

Abdallah, A. M., Hill-Cawthorne, G. A., Otto, T. D., Coll, F., Guerra-Assuncão, J. A., Gao, G., Naeem, R., Ansari, H., Malas, T. B., Adroub, S. A., Verboom, T., Ummels, R., Zhang, H., Panigrahi, A. K., McNerney, R., Brosch, R., Clark, T. G., Behr, M. A., Bitter, W. & Pain, A., 2015, In : Scientific Reports. 5, 15443.

Research output: Contribution to JournalArticle

Open Access

G Protein–Coupled Receptor Signaling Networks from a Systems Perspective.

Roth, S., Kholodenko, B. N., Smit, M. J. & Bruggeman, F. J., 2015, In : Molecular Pharmacology. 88, 3, p. 604-616

Research output: Contribution to JournalArticle

Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae.

Kuipers, K., Gallay, C., Martínek, V., Rohde, M., Martínková, M., van der Beek, S. L., Jong, W. S. P., Venselaar, H., Zomer, A., Bootsma, H., Veening, J. W. & de Jonge, M. I., 2015, In : Molecular Microbiology. 21 Dec

Research output: Contribution to JournalArticle

Open Access

Impact of the blue mussel Mytilus edulis on the microbial food web in the western Wadden Sea, The Netherlands.

Jacobs, P., Riegman, R. & van der Meer, J., 2015, In : Marine Ecology Progress Series. 527, p. 119-131

Research output: Contribution to JournalArticle

Indirect effects of invasive species affecting the population structure of an ecosystem engineer.

Waser, A. M. W., Splinter, W. & van der Meer, J., 2015, In : Ecosphere. 6, p. 7

Research output: Contribution to JournalArticle

Open Access

Interplay between constraints, objectives, and optimality for genome-scale stoichiometric models.

Maarleveld, T. R., Wortel, M. T., Olivier, B. G., Teusink, B. & Bruggeman, F. J., 2015, In : PLoS Computational Biology. 7, 11, 4.

Research output: Contribution to JournalArticle

Open Access

Introduction computer-assisted analysis in hydrocarbon and lipid microbiology.

Roling, W. F. M., 2015, Hydrocarbon and Lipid Microbiology Protocols. McGenity, T. J., Timmis, K. N. & Nogales, B. (eds.). Humana Press, (Springer Protocols Handbooks).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Iron cycling potentials of arsenic-contaminated groundwater in Bangladesh as revealed by enrichment cultivation.

Hassan, Z., Sultana, M., Westerhoff, H. V., Khan, S. I. & Roling, W. F. M., 2015, In : Geomicrobiology Journal.

Research output: Contribution to JournalArticle

Open Access

Length- and weight-dependent clearance rates of juvenile mussels (Mytilus edulis) on various planktonic prey items.

Jacobs, P., Troost, K., Riegman, R. & van der Meer, J., 2015, In : Helgoland Marine Research. 69, p. 101-112 1.

Research output: Contribution to JournalArticle

Open Access

Locally sourced probiotics, the next opportunity for developing countries?

Sybesma, W., Kort, R. & Lee, Y. K., 2015, In : Trends in Biotechnology. 33, p. 197-200 4.

Research output: Contribution to JournalArticle

Longitudinal assessment of DNA methylation changes during HPVE6E7-induced immortalization of primary keratinocytes

Schütze, D. M., Kooter, J. M., Wilting, S. M., Meijer, C. J. L. M., Quint, W. G. V., Snijders, P. J. F. & Steenbergen, R. D. M., 2015, In : Epigenetics. 10, 1, p. 73-81

Research output: Contribution to JournalArticle

Open Access
File

Maths on microbes: adding microbial ecophysiology to metagenomics.

Roling, W. F. M., 2015, In : Microbial Biotechnology. 8, 1, p. 21-22

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Membrane-Protein Diffusion in E. coli: A Random Walk in a Heterogeneous Landscape

Varadarajan, A., Oswald, F., Bollen, Y. J. M. & Peterman, E. J. G., 2015, In : Biophysical Journal. 108, 2, p. 323A-323A

Research output: Contribution to JournalMeeting Abstract

Metabolism at Evolutionary Optimal States.

Rabbers, I., van Heerden, J. H., Nordholt, N., Bachmann, H., Teusink, B. & Bruggeman, F. J., 2015, In : Metabolites. 5, 2, p. 311-343

Research output: Contribution to JournalArticle

Open Access

Metabolite profiling of CHO cells: Molecular reflections of bioprocessing effectiveness

Sellick, C. A., Croxford, A. S., Maqsood, A. R., Stephens, G. M., Westerhoff, H. V., Goodacre, R. & Dickson, A. J., 2015, In : Biotechnology Journal. 10, 9, p. 1434-1445

Research output: Contribution to JournalArticle

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis.

Willemsen, A. M., Hedrickx, D. M., Hoefsloot, H. C., Hendriks, M. M. W. B., Wahl, S. A., Teusink, B., Smilde, A. K. & van Kampen, A. H. C., 2015, In : Molecular BioSystems. 11, 11, p. 137-145 1.

Research output: Contribution to JournalArticle

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

Azarbad, H., Niklinska, M., Laskowski, R., van Straalen, N. M., van Gestel, C. A. M., Zhou, J., He, Z., Wen, C. & Roling, W. F. M., 2015, In : FEMS Microbiology Ecology. 91, 1, p. 1-11

Research output: Contribution to JournalArticle

Modelling the dynamics of traits involved in fighting-predators–prey system

Kooi, B. W., 2015, In : Journal of Mathematical Biology. 71, 6, p. 1575-1605

Research output: Contribution to JournalArticle

Open Access
File

Molecular analysis of the vaginal microbiome: an alternative for the diagnosis of bacterial vaginosis?

Dols, J. A. M., Molenaar, D., Helm, J., Caspers, M. P. M., de Kat-Angelino, A., Speksnijder, A. G. C. L., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de vries, H. J. C. & Kort, R., 2015, In : BMC Infectious Diseases.

Research output: Contribution to JournalArticle

Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes.

Wruck, W., Kashofer, K., Rehman, S., Daskalaki, A., Berg, D., Gralka, E., Jozefczuk, J., Drews, K., Pandey, V., Regenbrecht, C., Wierling, C., Turano, P., Korf, U., Zatloukal, K., Lehrach, H., Westerhoff, H. V. & Adjaye, J., 2015, In : Scientific Data. 2, 150068.

Research output: Contribution to JournalArticle

Open Access

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

Rybakova, E. N., Bruggeman, F. J., Tomaszewska, A., Mone, M. J., Carlberg, C. & Westerhoff, H. V., 2015, In : PLoS Computational Biology. 11, 4

Research output: Contribution to JournalArticle

Open Access

Networks, modules and breeding schedules: Applications of Combinatorial Optimization to Computational Biology

El-Kebir, M., 2015

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

Open Access
File

Of linkers and autochaperones: an unambiguous nomenclature to identify common and uncommon themes for autotransporter secretion.

Drobnak, I., Braselmann, E., Chaney, J. L., Leyton, D. L., Bernstein, H. D., Lithgow, T., Luirink, S., Nataro, J. P. & Clark, P. L., 2015, In : Molecular Microbiology. 95, 1, p. 1-16 1.

Research output: Contribution to JournalArticle

On the physiology and molecular genetics of salt tolerance in Salicornia

Katschnig, D., 2015, Zutphen: CPI - Koninklijke Wöhrmann. 195 p.

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

Open Access
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Parameterising a generic model for the dynamic energy budget of Antarctic krill, Euphausia superba.

Jager, T. & Ravagnan, E., 2015, In : Marine Ecology Progress Series. 519, 1, p. 115-128

Research output: Contribution to JournalArticle

Processing of cell-surface signalling anti-sigma factors prior to signal recognition is aconserved autoproteolytic mechanism that produces two functional domains.

Bastiaansen, K. C. J. T., Otero-Asman, J. R., Luirink, J., Bitter, W. & Llamas, M. A., 2015, In : Environmental Microbiology. 17, 9, p. 3263-3277

Research output: Contribution to JournalArticle

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Santos, F., Giera, M. A., Fusetti, F., Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P. & Teusink, B., 2015, In : Molecular Microbiology. 97, p. 77-92 1.

Research output: Contribution to JournalArticle

Proteolytic regulation of Cell-Surface Signalling in Pseudomonas bacteria

Bastiaansen, K. C. J. T., 2015

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

Open Access
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Reactive transport modeling of subsurface arsenic removal systems in rural Bangladesh.

Rahmann, M. M., Bakker, M., Patty, C. H. L., Hassan, Z., Roling, W. F. M., Ahmed, K. M. & van Breukelen, B. M., 2015, In : Science of the Total Environment. 15, p. 277-293 537.

Research output: Contribution to JournalArticle

Revealing the role of predator interference in a predator–prey system with disease in prey population

Chakraborty, S., Kooi, B. W., Biswas, A. & Chattopadhyay, P., 2015, In : Ecological Complexity. 21, p. 100-110

Research output: Contribution to JournalArticle

Open Access
File

Salmonella outer membrane vesicles displaying high densities of pneumococcal antigen at the surface offer protection against colonization.

Kuipers, K., Daleke, M. H., Jong, W. S. P., ten Hagen-Jongman ten, C. M., van Opzeeland, F., Simonneti, E., Luirink, S. & de Jonge, M. I., 2015, In : Vaccine. 33, 17, p. 2022-2029

Research output: Contribution to JournalArticle

SCRY: Enabling quantitative reasoning in SPARQL queries

Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S. & Heringa, J., 2015, In : CEUR Workshop Proceedings. 1546, p. 214-215 2 p.

Research output: Contribution to JournalArticle

SEEK: a systems biology data and model management platform.

Wolstencroft, K. J., Owen, S., Krebs, O., Nguyen, Q., Stanford, N. J., Golebiewski, M., Weidemann, A., Bittkowski, M., An, L., Shockley, D., Snoep, J. L., Mueller, W. & Goble, C., 2015, In : BMC Systems Biology. 9, 33

Research output: Contribution to JournalArticle

Open Access

Self-cleavage of the Pseudomonas aerugginosa cell-surface signaling anti-sigma factor FoxR occurs through an N-O acyl rearrangement.

Bastiaansen, K. C. J. T., van Ulsen, P., Wijtmans, M., Bitter, W. & Llamas, M. A., 2015, In : Journal of Biological Chemistry. 290, 19, p. 12237-12246

Research output: Contribution to JournalArticle

Sensitivity of animals to chemical compounds links to metabolic rate.

Baas, J. & Kooijman, S. A. L. M., 2015, In : Ecotoxicology. 24, p. 657-663

Research output: Contribution to JournalArticle

Silence on the relevant literature and errors in implementation.

Bastiaens, P., Birtwistle, M. R., Blüthgen, N., Bruggeman, F. J., Cho, K. H., Cosentino, C., de la Fuente, A., Hoek, J. B., Kiyatkin, A., Klamt, S., Kolch, W., Legewie, S., Mendes, P., Naka, T., Santra, T., Sontag, E., Westerhoff, H. V. & Kholodenko, B. N., 2015, In : Nature Biotechnology. 33, 4, p. 336-339

Research output: Contribution to JournalArticle

Stability and resilience of oral microcosms toward acidification and Candida outgrowth by arginine supplementation

Koopman, J. E., Roling, W. F. M., Buijs, M. J., Sissons, C., ten Cate, J. M., Keijser, B. J. F., Crielaard, W. & Zaura, E., 2015, In : Microbial Ecology. 69, 2, p. 422-433 2.

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 2015, In : Journal of Integrative Bioinformatics. 12, p. 271 2.

Research output: Contribution to JournalArticle

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

Hanemaaijer, M. J., Roling, W. F. M., Olivier, B. G., Khandelwal, R. A., Teusink, B. & Bruggeman, F. J., 2015, In : Frontiers in Microbiology. 6, 213.

Research output: Contribution to JournalArticle

Open Access

Systems Pharmacology: An opinion on how to turn the impossible into grand challenges.

Westerhoff, H. V., Nakayama, S., Mondeel, T. D. & Barberis, M., 2015, In : Drug Discovery Today: Technologies. 15, p. 23-31

Research output: Contribution to JournalArticle

The cytochrome bd-type quinol oxidase is important for survival of Mycobacterium smegmatis under peroxide and antibiotic-induced stress.

Lu, P., Heineke, M. H., Koul, A., Andries, K., Cook, G. M., Lill, H., van Spanning, R. J. M. & Bald, D., 2015, In : Scientific Reports. 5, 10333.

Research output: Contribution to JournalArticle

Open Access

The evolution of metabolic strategies

Wortel, M. T., 2015

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

Open Access
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The Importance of Body Size: Scaling of Physiological Traits in Insects

Maino, J. L., 2015

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

Open Access
File

The Significance of Microbe-Mineral-Biomarker Interactions in the Detection of Life on Mars and Beyond.

Roling, W. F. M., Aerts, J. W., Patty, C. H. L., ten Kate, I. L., Ehrenfreund, P. & Direito, S. O., 2015, In : Astrobiology. 15, p. 492-507 6.

Research output: Contribution to JournalArticle

The Soluble Periplasmic Domains of Escherichia coli Cell Division Proteins FtsQ/FtsB/FtsL Form a Trimeric Complex with Submicromolar Affinity.

Glas, M., van den Berg van Saparoea, H. B., Mclaughlin, S. H., Roseboom, W., Liu, F., Koningstein, G. M., Fish, A., den Blaauwen, T., Heck, A. J., de Jong, L. D., Bitter, W., de Esch, I. J. P. & Luirink, S., 2015, In : Journal of Biological Chemistry. 290, 35, p. 21498-21509

Research output: Contribution to JournalArticle

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

Olivier, B. G. & Bergmann, F. T., 2015, In : Journal of Integrative Bioinformatics. 12, p. 269 2.

Research output: Contribution to JournalArticle