Molecular Cell Physiology

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2012

Whole genomes, small children, big questions.

Lunshof, J. E., 2012, In : Personalized Medicine. 9, p. 667-669

Research output: Contribution to JournalArticleAcademicpeer-review

2011

A domino effect in drug action: from metabolic assault towards parasite differentiation.

Haanstra, J. R., Kerkhoven, E. J., van Tuijl, J. H., Blits, M., Wurst, M., van Nuland, R., Albert, M. A., Michels, P. A. M., Bouwman, J., Clayton, C., Westerhoff, H. V. & Bakker, B. M., 2011, In : Molecular Microbiology. 79, 1, p. 94-108

Research output: Contribution to JournalArticle

A mixed-species microarray for identification of food spoilage bacilli

Caspers, M. P. M., Schuren, F. H. J., van Zuijlen, A. C. M., Brul, S., Montijn, R. C., Abee, T. & Kort, R., Apr 2011, In : Food microbiology. 28, 2, p. 245-51 7 p.

Research output: Contribution to JournalArticle

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4+/NH3

Boogerd, F. C., Ma, H., Bruggeman, F. J., van Heeswijk, W. C., Garcia-Contreras, R., Molenaar, D., Krab, K. & Westerhoff, H. V., 3 Jan 2011, In : FEBS Letters. 585, 1, p. 23-28

Research output: Contribution to JournalArticle

Analysis of single quantum-dot mobility inside 1D nanochannel devices

Hoang, T. H., Segers-Nolten, I. M. J., Tas, N. R., van Honschoten, J. W., Subramaniam, V. & Elwenspoek, M. C., 8 Jul 2011, In : Nanotechnology. 22, 27, p. 275201

Research output: Contribution to JournalArticle

A probabilistic approach to identify putative drug targets in biochemical networks.

Murabito, E., Smalbone, K., Swinton, J., Westerhoff, H. V. & Steuer, R., 2011, In : Journal of the Royal Society Interface. 8, p. 880-895

Research output: Contribution to JournalArticle

Open Access

Astrobiology and habitability studies in preparation for future Mars missions: trends from investigating minerals, organics and biota

Ehrenfreund, P., Roling, W. F. M., Thiel, C. S., Quin, R., Septhon, M. A., Stoker, C., Kotler, M., Oliveira Lebre Direito, M. S., Martins, Z., Orzechowska, G., Kidd, R. D., van Sluis, C. A. & Foing, H., 2011, In : International Journal of Astrobiology. 10, 10, p. 239-253 14 p., 3.

Research output: Contribution to JournalArticle

A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station.

Oliveira Lebre Direito, M. S., Ehrenfreund, P., Marees, A., Staats, M. & Roling, W. F. M., 2011, In : International Journal of Astrobiology. 10, 10, p. 191-207 16 p., 3.

Research output: Contribution to JournalArticle

Challenges and advances in systems biology analysis of Bacillus spore physiology; molecular differences between an extreme heat resistant spore forming Bacillus subtilis food isolate and a laboratory strain

Brul, S., van Beilen, J., Caspers, M. P. M., O'Brien, A., de Koster, C., Oomes, S., Smelt, J., Kort, R. & Ter Beek, A., Apr 2011, In : Food microbiology. 28, 2, p. 221-7 7 p.

Research output: Contribution to JournalArticle

De eerste microbe

Boogerd, F. C., 2011, In : Bionieuws. p. 14-14 1 p.

Research output: Contribution to JournalArticle

Dupuytren's: a systems biology disease.

Rehman, S., Goodacre, R., Day, P. J., Bayat, A. & Westerhoff, H. V., 2011, In : Arthritis Research & Therapy. 13, 328, p. 1-12

Research output: Contribution to JournalArticle

Open Access

Editorial: Genetic and genomic research - Changing patterns of accountability.

Lunshof, J. & Chadwick, R., 2011, In : Accountability in Research. 18, p. 121-131

Research output: Contribution to JournalArticle

Explaining the enigmatic Km for oxygen in cytochrome c oxidase.

Krab, K., Kempe, H. & Wikstrom, M., 2011, In : Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1807, p. 348-358

Research output: Contribution to JournalArticle

Open Access

Explorin metabolic pathway reconstruction and genome-wide expression profiling in lactobacillus reuteri to define functional probiotic features.

Saulnier, D. M. A., Santos, F., Roos, S., Mistretta, T-A., Spinler, J. K., Molenaar, D., Teusink, B. & Versalovic, J., 2011, In : PLoS ONE. 6, p. e18783

Research output: Contribution to JournalArticle

Open Access
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Field astrobiology research instruments and methods in moon-mars analogue site.

Foing, B. H., Stoker, C., Zavaleta, J., Ehrenfreund, P., Sarrazin, P., Blake, D., Page, J., Pletser, V., Hendrikse, J., Oliveira Lebre Direito, M. S., Kotler, M., Martins, Z., Orzechowska, G., Thiel, C. S., Clarke, J., Gross, J., Wendt, L., Borst, A., Peters, S., Wilhelm, M-B. & 2 others, Davies, G. R. & EuroGeoMars 2009 Team, ILEWG., 2011, In : International Journal of Astrobiology. 10, 10, p. 141-160 2 p., 3.

Research output: Contribution to JournalArticle

Flux balance analysis for ethylene formation in genetically engineered Saccharaomyces cerevisiae.

Larsson, C., Snoep, J. L., Norbeck, J. & Albers, E., 2011, In : IET Systems Biology. 5, p. 245-251

Research output: Contribution to JournalArticle

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis

Rud, I., Naterstad, K., Bongers, R. S., Molenaar, D., Kleerebezem, M. & Axelsson, L., 2011, In : Microbial Biotechnology. 4, p. 345-356

Research output: Contribution to JournalArticle

Open Access

Functional Dissection of the PE Domain Responsible for Translocation of PE_PGRS33 across the Mycobacterial Cell Wall

Cascioferro, A., Daleke, M. H., Ventura, M., Dona, V., Delogu, G., Palu, G., Bitter, W. & Manganelli, R., 2011, In : PLoS ONE. 6, 11, e27713.

Research output: Contribution to JournalArticle

Open Access
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Functional Identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis.

Santos, F., Spinler, J. K., Saulnier, D. M. A., Molenaar, D., Teusink, B., de Vos, D. L., Versalovic, J. & Hugenholtz, J., 2011, In : Microbial Cell Factories. 10, p. 55

Research output: Contribution to JournalArticle

Open Access
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Gel-free proteomic identification of the Bacillus subtilis insoluble spore coat protein fraction.

Abhyankar, W., Beek, A. T., Dekker, H., Kort, R., Brul, S. & de Koster, C. G., 2011, In : Journal of Proteomics. 11, p. 4541-4550

Research output: Contribution to JournalArticle

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

Siezen, R. J., Bayjanov, J. R., Felis, G. E., van der Sijde, M. R., Starrenburg, M., Molenaar, D., Wels, M., Hijum, S. A. & van Hylckama Vlieg, J. E. T., 2011, In : Microbial Biotechnology. 4, p. 383-402

Research output: Contribution to JournalArticle

Open Access

Health technology assessment in the era of personalized health care.

Becla, L., Lunshof, J. E., Gurwitz, D., Schulte in de Baumen, T., Westerhoff, H. V., Lange, B. & Brand, A., 2011, In : International Journal of Technology Assessessment in Health Care. 27, p. 118-126

Research output: Contribution to JournalArticle

Het spel tussen profiteurs en sukkels.

Teusink, B., 2011, In : Unknown journal. 09, 28-05-2011

Research output: Contribution to JournalArticle

High local substrate availability stabilizes a cooperative trait.

Bachmann, H., Molenaar, D., Kleerebezem, M. & van Hylckama Vlieg, J. E. T., 2011, In : ISME Journal. 5, p. 929-932

Research output: Contribution to JournalArticle

Open Access

How molecular competition influences fluxes in gene expression networks.

de Vos, D. L., Bruggeman, F. J., Westerhoff, H. V. & Bakker, B. M., 2011, In : PLoS ONE. 6, 12, e28494.

Research output: Contribution to JournalArticle

Open Access
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HPLC-MS/MS methods for the quantitative analysis of 5-oxoproline (pyroglutamate) in rat plasma and hepatic cell line culture medium.

Geenen, A., Guallar-Hoays, C., Michopoulos, F., Kenna, J. G., Kolaja, K. L., Westerhoff, H. V., Thomas, P. & Wilson, I., 2011, In : Journal of Pharmaceutical and Biomedical Analysis. 56, p. 655-663

Research output: Contribution to JournalArticle

HPLC-MS/MS methods for the quantitative analysis of ophthalmic acid in rodent plasma and hepatic cell line culture medium

Geenen, S., Michopoulos, F., Kenna, J. G., Kolaja, K. L., Westerhoff, H. V. & Wilson, I., 2011, In : Journal of Pharmaceutical and Biomedical Analysis. 54, p. 1128-1135

Research output: Contribution to JournalArticle

Identification of lactobacillus plantarum genes modulating, the cytokine response of human peripheral blood mononuclear cells.

van Hemert, S., Meijerink, M., Molenaar, D., Bron, P. A., de Vos, D. L., Kleerebezem, M., Wells, J. M. & Marco, M. L., 2011, In : BMC Microbiology. 10, p. 293

Research output: Contribution to JournalArticle

Open Access
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ITFoM - The IT Future of Medicine

Lehrach, H., Subrak, R., Boyle, P., Pasterk, M., Zatloukal, K., Muller, H., Hubbard, T., Brand, A., Girolami, M., Jameson, D., Bruggeman, F. J. & Westerhoff, H. V., 2011, In : Procedia Computer Science. 7, p. 26-29

Research output: Contribution to JournalArticle

Open Access

Metabolic regulation rather than de novo enzyme synthesis dominates the osmo-adaptation of yeast.

Bouwman, J., Kiewiet, J. A. L., Lindenbergh, A., Van Eunen, K., Siderius, M. H. & Bakker, B. M., 2011, In : Yeast. 28, p. 43-53 11 p.

Research output: Contribution to JournalArticle

Metabolite profiling of recombinant CHO cells: Designing tailored feeding regimes that enhance recombinant antibody production.

Sellick, C. A., Croxford, A. S., Maqsood, A. R., Stephens, G., Westerhoff, H. V., Goodacre, R. & Dickson, A. J., 2011, In : Biotechnology and Bioengineering. 108, 12, p. 3025-3031

Research output: Contribution to JournalArticle

Microarray-based identification of clinically relevant vaginal bacteria in relation to bacterial vaginosis

Dols, J. A. M., Smit, P. W., Kort, R., Reid, G., Schuren, F. H. J., Tempelman, H., Bontekoe, T. R., Korporaal, H. & Boon, M. E., Apr 2011, In : American Journal of Obstetrics and Gynecology. 204, 4, p. 305.e1-7

Research output: Contribution to JournalArticle

Mineralogical, chemical, organic and microbial properties of subsurface soil cores from Mars Desert Research Station (Utah, USA): Phyllosilicate and sulfate analogues to Mars mission landing sites

Stoker, C. R., Clarke, J., Oliveira Lebre Direito, M. S., Martin, K., Zavaleta, J., Blake, D. & Foing, B. H., 2011, In : International Journal of Astrobiology. 10, 10, p. 269-289 20 p., 3.

Research output: Contribution to JournalArticle

Minimum information about a simulation experiment (MIASE).

Waltemath, D., Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U. S., Britten, R., Chelliah, V., Cooling, M. T., Cooper, J., Crampin, E. J., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C., Miller, A. K., Moraru, K., Nickerson, D., Nielsen, P. & 8 others, Nikolski, M., Sahle, S., Sauro, H. M., Schmidt, H., Snoep, J. L., Tolle, D., Wolkenhauer, O. & le Novere, N., 2011, In : PLoS Computational Biology. 7, 4, e1001122.

Research output: Contribution to JournalArticle

Open Access
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Molecular diversity and distribution of aromatic hydrocarbon-degrading anaerobes across a landfill leachate plume.

Staats, M., Braster, M. & Roling, W. F. M., 2011, In : Environmental Microbiology. 13, p. 1216-1227

Research output: Contribution to JournalArticle

Multiparameter viability assay for stress profiling applied to the food pathogen listeria.

Nocker, A., Caspers, M., Esveld-Amanatidou, A., van der Vossen, J., Schuren, F., Montijn, R. & Kort, R., 2011, In : Applied and Environmental Microbiology. 77, p. 6433-6440

Research output: Contribution to JournalArticle

Open Access
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Personalized participatory medicine: sharing knowledge and uncertainty

Gurwitz, D. & Lunshof, J. E., 2011, In : Genome Medicine. 3, p. 69-69

Research output: Contribution to JournalArticle

Open Access

Predicting metabolic fluxes using gene expression differences as constraints.

van Berlo, R. J. P., de Ridder, D., Daran, J-MD., Daran-Lapujade, P., Teusink, B. & Reinders, M. J. T., 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, p. 206-216

Research output: Contribution to JournalArticle

Probiotics and prebiotics to combat enteric infections and HIV in the developing world: a consensus report

Monachese, M., Cunningham-Rundles, S., Diaz, M. A., Guerrant, R., Hummelen, R., Kemperman, R., Kerac, M., Kort, R., Merenstein, D., Panigrahi, P., Ramakrishna, B., Safdar, N., Shane, A., Trois, L. & Reid, G., May 2011, In : Gut Microbes. 2, 3, p. 198-207 10 p.

Research output: Contribution to JournalArticle

Progressive methylation of aging histones by Dot1 acts as a timer.

de Vos, D. L., Frederiks, F., Terweij, M., van Welsem, T., Verzijlbergen, K. F., Iachina, E., de Graaf, E. L., Altelaar, A. F. M., Oudgenoeg, G., Heck, A. J. R., Krijgsveld, J., Bakker, B. M. & van Leeuwen, F., 2011, In : EMBO Reports. 12, p. 956-962

Research output: Contribution to JournalArticle

Protein analysis tools and services at IBIVU.

Brandt, B. W. & Heringa, J., 2011, In : Journal of Integrative Bioinformatics. 8, p. 168

Research output: Contribution to JournalArticle

Open Access

Recommendations for terminology and databases for biochemical thermodynamics.

Alberty, R. A., Cornish-Bowden, A., Goldberg, R. N., Hammes, G. G., Tipton, K. & Westerhoff, H. V., 2011, In : Biophysical Chemistry. 155, p. 89-103

Research output: Contribution to JournalArticle

Systems Biology of lactic acid bacteria: a critical review.

Teusink, B., Bachmann, H. & Molenaar, D., 2011, In : Microbial Cell Factories. 10, A11, 17 p.

Research output: Contribution to JournalArticle

Open Access
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Volatile compound fingerprinting of mixed-culture fermentations.

de Bok, F. A. M., Janssen, P. W. M., Bayjanov, J. R., Sieuwerts, S., Lommen, A., van Hylckama Vlieg, J. E. T. & Molenaar, D., 2011, In : Applied and Environmental Microbiology. 77, p. 6233-6239

Research output: Contribution to JournalArticle

Open Access
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What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics-pharmacodynamics platform.

Swat, M., Kielbasa, S. M., Polak, S., Olivier, B. G., Bruggeman, F. J., Quinton Tulloch, M., Snoep, J. L., Verhoeven, A. J. & Westerhoff, H. V., 2011, In : Interfaces. 1, p. 16-23

Research output: Contribution to JournalArticle

2010

Accurate confidence aware clustering of array CGH tumor profiles.

van Houte, B. P. P. & Heringa, J., 2010, In : Bioinformatics. 26, p. 6-14

Research output: Contribution to JournalArticle

Acetate formation int he energy metabolism of parasitic helminths and protists.

Tielens, A. G. M., van Grinsven, K. W. A., Henze, K., van Hellemond, J. J. & Martin, W. ., 2010, In : International Journal for Parasitology. 40, p. 387-384

Research output: Contribution to JournalArticleAcademicpeer-review

Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach

Hettling, H., Heringa, J. & van Beek, J. H. G. M., 2010, In : BMC Bioinformatics. 11, Suppl. 10, p. O9

Research output: Contribution to JournalArticle

Open Access
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Biomodels database: an enhanced curated and annotated resource for published quantitative kinetic models

Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., Snoep, J. L., Hucka, M., le Novere, N. & Laibe, C., 2010, In : BMC Systems Biology. 4, p. 92 14 p.

Research output: Contribution to JournalArticle

Open Access
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