Molecular Cell Biology

Research Output

Compartmentation protects trypanosomes from the dangerous design of glycolysis.

Bakker, B. M., Mensonides, F. I. C., Teusink, B., van Hoek, P., Michels, P. A. M. & Westerhoff, H. V., 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, p. 2087-2092 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Compathy or physical empathy: Implications for the caregiver relationship.

Morse, J. M., Mitcham, C. & vd Steen, W. J., 1998, In : Journal of Medical Humanities. 19, p. 73-87 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access
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Competition for light between phytoplankton species: experimental tests of mechanistic theory.

Huisman, J., Jonker, R. R., Zonneveld, C. & Weissing, F. J., 1999, In : Ecology. 80, 1, p. 211-222

Research output: Contribution to JournalArticleAcademicpeer-review

Complementation of Escherichia coli uncD mutant strains by a chimeric F1-beta subunit constructed from E. coli and spinach chloroplast F1-beta

Burkovski, A., Lill, H. & Engelbrecht, S., 29 Jul 1994, In : Biochimica et Biophysica Acta. 1186, 3, p. 243-6 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Complete genome sequence of Anoxybacillus flavithermus TNO-09.006, a thermophilic sporeformer associated with a dairy-processing environment.

Caspers, M. P., Boekhorst, J., Abee, T., Siezen, R. J. & Kort, R., 2013, In : Genome Announcements. 1, e00010-13.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment

Zhao, Y., Caspers, M. P., Abee, T., Siezen, R. J. & Kort, R., 2012, In : Journal of Bacteriology. 194, 15, p. 4118

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Complete genome sequence of Lactobacillus plantarum WCFS1

Kleerebezem, M., Boekhorst, J., Kranenburg, R., Molenaar, D., Kuipers, O. P., Leer, R., Tarchini, R., Peters, SA., Sandbrink, HM., Fiers, MWEJ., Stiekema, W. J., Klein-Lankhorst, R. M., Bron, P. A., Hoffer, S. M., Groot, MNN., Kerkhoven, R., de Vries, M., Ursing, B., Vos, W. M. & Siezen, R. J., 18 Feb 2003, In : Proceedings of the National Academy of Sciences of the United States of America. 100, 4, p. 1990-1995

Research output: Contribution to JournalArticleAcademicpeer-review

Complete genome sequence of Lactococcus lactis subsp. Lactis KF147, a plant-associated lactic acid bacterium.

Siezen, R. J., Bayjanov, J., Renckens, B., Wels, M., van Hijum, S. A. F. T., Molenaar, D. & van Hylckama Vlieg, J. E. T., 2010, In : Journal of Bacteriology. 192, p. 2649-2650

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Complete Genome Sequence of Mycobacterium fortuitum subsp. fortuitum Type Strain DSM46621

Ho, Y. S., Adroub, S. A., Aleisa, F., Mahmood, H., Othoum, G., Rashid, F., Zaher, M., Ali, S., Bitter, W., Pain, A. & Abdallah, A. M., 2012, In : Journal of Bacteriology. 194, 22, p. 6337-6338

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Complete genome sequence of Mycobacterium phlei type strain RIVM601174

Abdallah, A. M., Rashid, M., Adroub, S. A., Arnoux, M., Ali, S., van Soolingen, D., Bitter, W. & Pain, A., 2012, In : Journal of Bacteriology. 194, 12, p. 3284-3285

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Complete genome sequence of Mycobacterium vaccae type strain ATCC 25954

Ho, Y. S., Adroub, S. A., Abadi, M., Al Alwan, B., Gao, G., Alkhateeb, R., Ragab, A., Ali, S., van Soolingen, D., Bitter, W., Pain, A. & Abdallah, A. M., 2012, In : Journal of Bacteriology. 194, 22, p. 6339-6340

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Complete genome sequence of Mycobacterium xenopi type strain RIVM700367

Abdallah, A. M., Rashid, M., Adroub, S. A., Elabdalaoui, H., Ali, S., van Soolingen, D., Bitter, W. & Pain, A., 2012, In : Journal of Bacteriology. 194, 12, p. 3282-3283

Research output: Contribution to JournalArticleAcademicpeer-review

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Complete inhibition and partial re-activation of single F1-ATPase molecules by tentoxin: new properties of the re-activated enzyme.

Pavlova, P., Shimabukuro, K., Hisabori, T., Groth, G., Lill, H. & Bald, D., 2004, In : Journal of Biological Chemistry. 279, p. 9685-9688 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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Complete tracking of proton flow in thylakoids-the unit conductance of CF0 is greater than 10 fS

Schoenknecht, G., Junge, W., Lill, H. & Engelbrecht, S., 28 Jul 1986, In : FEBS Letters. 203, 2, p. 289-294 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity

Abudukelimu, A., Barberis, M., Redegeld, F., Sahin, N., Sharma, R. P. & Westerhoff, H. V., 14 Feb 2020, In : Frontiers in Immunology. 10, p. 1-20 20 p., 3091.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

Weedon, J. T., Kowalchuck, G. A., Aerts, M. A. P. A., Freriks, S., Roling, W. F. M. & van Bodegom, P. M., 2017, In : Frontiers in Microbiology. 8, MAR, 317.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Open Access
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Composition of the type VII secretion system membrane complex.

Houben, E. N. G., Bestebroer, J., Ummels, R., Wilson, L., Piersma, S. R., Jimenez, C. R., Ottenhoff, T. H. M., Luirink, S. & Bitter, W., 2012, In : Molecular Microbiology. 86, 2, p. 472-484

Research output: Contribution to JournalArticleAcademicpeer-review

Comprehensive analysis of the 14-3-3 interactome in barley leaves using a complementary proteomics and two-hybrid approach.

Schoonheim, P. J., Veiga, H., da Costa Pereira, D., Friso, G., van Wijk, K. J. & de Boer, A. H., 2007, In : Plant Physiology. 143, p. 670-683

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Comprehensive characterization of the attenuated double auxotroph mycobacterium tuberculosisΔleudΔpanCD as an alternative to h37Rv

Mouton, J. M., Heunis, T., Dippenaar, A., Gallant, J. L., Kleynhans, L. & Sampson, S. L., 1 Jan 2019, In : Frontiers in Microbiology. 10, AUG, 1922.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Comprehensive GC–MS analysis of fatty acids and sterols using sequential one-pot silylation: quantification and isotopologue analysis

Kloos, D., Gay, E., Lingeman, H., Bracher, F., Müller, C., Mayboroda, O. A., Deelder, A. M., Niessen, W. M. A. & Giera, M., 2014, In : RCM. Rapid Communications in Mass Spectrometry. 28, p. 1507-1504

Research output: Contribution to JournalArticleAcademicpeer-review

Computational Biology: annotated glossary of terms (appendix 1).

Konopka, A. K., Bucher, P., Crabbe, M. J. C., Crochemore, M., Heringa, J., Lisacek, F., Makalowska, I., Makalowska, W., Pesole, G., Saccone, C., Sagot, M-F., Sarai, A., Stadler, P. & Taylor, W. R., 2004, Compact handbook of computational biology. Konopka, A. K. & Crabbe, M. J. C. (eds.). New York (NY - USA): Marcel Dekker, p. 451-501

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

Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies

Hettling, H., Alders, D. J., Heringa, J., Binsl, T. W., Groeneveld, A. B. J. & van Beek, J. H. G. M., 2013, In : BMC Systems Biology. 7, p. 82 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy.

Binsl, T. W., Alders, D. J. C., Heringa, J., Groeneveld, A. B. J. & van Beek, J. H. G. M., 2010, In : Bioinformatics. 26, 5, p. 653-660

Research output: Contribution to JournalArticleAcademicpeer-review

Computing life: add Logos to Biology and Bios to Physics

Kolodkin, A. N., Simeonidis, E. & Westerhoff, H. V., 2013, In : Progress in Biophysics and Molecular Biology. 111, p. 69-74

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Concepts of function in biology [Review of: C. Allen, M. Bekoff (1999) Nature's purposes: Analyses of function and design in biology.]

vd Steen, W. J., 1999, In : Journal of Evolutionary Biology. 12, p. 198-199

Research output: Contribution to JournalBook/Film/Article reviewAcademicpeer-review

Concurrent hexachlorobenzene and chloroethene transformation by endogenous dechlorinating microorganisms in the Ebro River sediment

Tas, N., Heilig, H. G. H. J., van Eekert, M., Schraa, G., Vos, W. M. & Smidt, H., 2010, In : FEMS Microbiology Ecology. 74, p. 682-692 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Conformational states of melittin in membranes.

Pandit, A., Visschers, R. W. & Kraayenhof, R., 1999, In : Biophysical Journal. 76, p. A66 1 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Conformation and orientation of a protein folding intermediate trapped by adsorption.

Engel, M. F. M., Visser, A. J. W. G. & Van Mierlo, C. P. M., 2004, In : Proceedings of the National Academy of Sciences of the United States of America. 101, p. 11316-11321

Research output: Contribution to JournalArticleAcademicpeer-review

Consensus-based standards and criteria for evaluating the content validity of patient-reported outcome measures: a COSMIN Delphi study

Terwee, C. B., Prinsen, C. A., Chiarotto, A., Westerman, M. J., de Vet, H. C. W., Patrick, D., Alonso, J., Bouter, L. M. & Mokkink, L. B., Oct 2016, In : Quality of Life Research. 25, p. 1-1

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access
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Consequences of depletion of stratospheric ozone for terrestrial Antarctic ecosystem: the response of Deschampsia antarctica to enhanced UV-B radiation in a controlled environment.

Rozema, J., Broekman, R. A., Lud, D., Huiskes, A. H. J., Moerdijk, T., Bakker, N., Meijkamp, B. B. & van Beem, A. P., 2001, In : Plant Ecology. 154, 1-2, p. 101-115

Research output: Contribution to JournalArticleAcademicpeer-review

Consequences of depletion of the signal recognition particle in Escherichia coli

Wickstrom, D., Wagner, S., Baars, L., Ytterberg, A. J., Klepsch, M., van Wijk, K. J., Luirink, J. & de Gier, J. W., 2011, In : Journal of Biological Chemistry. 286, 286, p. 4598-609 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Consequences of population models on the dynamics of food chains.

Kooi, B. W., Boer, M. P. & Kooijman, S. A. L. M., 1998, In : Mathematical Biosciences. 153, p. 99-124 25 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Consequences of symbiosis for food web dynamics.

Kooi, B. W., Kuijper, L. D. J. & Kooijman, S. A. L. M., 2004, In : Journal of Physical Chemistry A. 3, p. 227-271

Research output: Contribution to JournalArticleAcademicpeer-review

Conserved Pro-Glu (PE) and Pro-Pro-Glu (PPE) Protein Domains Target LipY Lipases of Pathogenic Mycobacteria to the Cell Surface via the ESX-5 Pathway

Daleke, M. H., Cascioferro, A., de Punder, K., Ummels, R., Abdallah, A. M., Wel, N., Peters, P. J., Luirink, S., Manganelli, R. & Bitter, W., 2011, In : Journal of Biological Chemistry. 286, 21, p. 19024-19034

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Considerations for test design to accommodate energy-budget models in ecotoxicology: a case study for acetone in the pond snail lymnaea stagnalis.

Barsi, A., Jager, T., Collinet, M., Lagadic, L. & Ducrot, V., 2014, In : Environmental Toxicology and Chemistry. 33, p. 1466-1475

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Constraint-based models of microbial physiology: Surprisingly versatile

Teusink, B., Planqué, B., Molenaar, D. & Bruggeman, F., 1 Jan 2018, 10th International Conference on Simulation and Modelling in the Food and Bio-Industry 2018, FOODSIM 2018. Eurosis, p. 5-10 6 p.

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Constraint-based stochiometric modelling from single organisms to microbial communities.

Gottstein, W. G., Olivier, B. G., Bruggeman, F. J. & Teusink, B., 2016, In : Journal of the Royal Society Interface. 13, 124, 20160627.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Construction and characterization of an effector strain of streptococcus mutans for replacement therapy of dental caries.

Hillman, J. D., Brooks, T. A., Michalek, S. M., Harmon, C. C., van der Weijden, C. C. & Snoep, J. L., 2000, In : Infection and Immunity. 68, p. 543-549 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.

Assuncao, A. G. L., Pieper, B., Vromans, J., Lindhout, P., Aarts, M. G. M. & Schat, H., 2006, In : New Phytologist. 170, p. 2-32

Research output: Contribution to JournalArticleAcademicpeer-review

Consumption and release of dissolved organic carbon by marine bacteria in a pulsed-substrate environment: from experiments to modelling.

Eichinger, M., Kooijman, S. A. L. M., Sempere, R. & Poggiale, J. C., 2009, In : Aquatic Microbial Ecology. 56, p. 41-54

Research output: Contribution to JournalArticleAcademicpeer-review

Contact-based sequence alignment.

Kleinjung, J., Romein, J. W., Lin, K. & Heringa, J., 2004, In : Nucleic Acids Research. 32, 8, p. 2464-2473 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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Continuation of connecting orbits in 3d-ODEs. (ii) cycle-to-cycle connections.

Doedel, E. J., Kooi, B. W., van Voorn, G. A. K. & Kuznetzov, Y. A., 2009, In : International Journal of Bifurcation and Chaos. 19, p. 159-169

Research output: Contribution to JournalArticleAcademicpeer-review

Continuation of connecting orbits in 3d-ODEs' (i) point-to-cycle connections.

Doedel, E. J., Kooi, B. W., van Voorn, G. A. K. & Kuznetzov, Y. A., 2008, In : International Journal of Bifurcation and Chaos. 18, p. 1889-1903

Research output: Contribution to JournalArticleAcademicpeer-review

CONTINUOUS MEASUREMENT OF THE CYTOPLASMIC PH IN LACTOCOCCUS-LACTIS WITH A FLUORESCENT PH INDICATOR

MOLENAAR, D., Abee, T. & Konings, W. N., 14 Nov 1991, In : Biochimica et Biophysica Acta. 1115, 1, p. 75-83

Research output: Contribution to JournalArticleAcademicpeer-review

Contribution of different generations of the brown shrimp Crangon crangon (L.) in the dutch wadden sea to commercial fisheries: a dynamic energy budgets approach

Campos, J. C., v.d. Veer, H., Freitas, V. & Kooijman, S. A. L. M., Aug 2009, In : Journal of sea research. 62, 2-3, p. 106-113 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei.

Bakker, B. M., Walsh, M. C., ter Kuile, B., Mensonides, F. I. C., Michels, P. A. M., Opperdoes, F. R. & Westerhoff, H. V., 1999, In : Proceedings of the National Academy of Sciences of the United States of America. 96, p. 10098-10103 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review