Molecular Cell Physiology

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2015

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access

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 JournalArticleAcademicpeer-review

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 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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model.

Rybakova, E. N., Tomaszewska, A., van Mourik, A., Blom, J., Westerhoff, H. V., Carlberg, C. & Bruggeman, F. J., 2015, In : Nucleic Acids Research. 43, p. 153-161 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Using a genome-scale metabolic model of Enterococcus faecalis V583 to assess amino acid uptake and its impact on central metabolism

Veith, N., Solheim, M., van Grinsven, K. W. A., Olivier, B. G., Levering, J., Grosseholz, R., Hugenholtz, J., Holo, H., Nes, I., Teusink, B. & Kummer, U., Mar 2015, In : Applied and Environmental Microbiology. 81, 5, p. 1622-1633 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

2014

A data integration and visualization resource for the metabolic network of synechocystis sp. PCC6803.

Maarleveld, T. R., Boele, J., Bruggeman, F. J. & Teusink, B., 2014, In : Plant Physiology. 164, p. 1111-1121

Research output: Contribution to JournalArticleAcademicpeer-review

A kinetic model of catabolic adaptation and protein reprofiling in Saccharomyces cerevisiae druing temperature shift.

Mensonides, F. I. C., Brul, S., Hellingwerf, K. J., Bakker, B. M. & Teixeira de Mattos, M. J., 2014, In : The FEBS Journal. 281, 3, p. 825-841

Research output: Contribution to JournalArticleAcademicpeer-review

Allosteric regulation of phosphofructokinase controls the emergence of glycolytic oscillations in isolated yeast cells.

Gustavsson, A-K., van Niekerk, D. D., Adiels, C. B., Kooi, B. W., Goksor, M. & Snoep, J. L., 2014, In : The FEBS Journal. 281, 12, p. 2784-2793 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

An in vivo control map for the eukaryotic mRNA translation machinery

Firczuk, H., Kannambath, S., Pahle, J., Claydon, A., Beynon, R., Duncan, J., Westerhoff, H. V., Mendes, P. & McCarthy, J. E. G., 2014, In : Molecular Systems Biology. 6

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Biota and biomolecules in extreme environments on Earth: implications for life detection on Mars.

Aerts, J. W., Roling, W. F. M., Elsaesser, A. & Ehrenfreund, P., 2014, In : Life. 4, p. 535-565

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Chromatography-mass spectrometry based analysis of biologically active endogenous carboxylic acids

Kloos, D., Lingeman, H., Mayboroda, O. A., Deelder, A. M., Niessen, W. M. A. & Giera, M., 2014, In : TrAC. Trends in Analytical Chemistry. 61, p. 17-28

Research output: Contribution to JournalArticleAcademicpeer-review

Clusters of reaction rates and concentrations in protein networks such as phosphotransferase system

Hardin, H. M., Zagaris, A., Willms, A. R. & Westerhoff, H. V., 2014, In : The FEBS Journal. 281, p. 531-548

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Comparison of (bio-)transformation methods for the generation of metabolite-like compound libraries of p38α MAP kinase inhibitors using high-resolution screening.

Falck, D., Pirkolachachi, F. R., Giera, M., Honing, M., Kool, J. & Niessen, W. M. A., 2014, In : Journal of Pharmaceutical and Biomedical Analysis. 88, p. 235-244

Research output: Contribution to JournalArticleAcademicpeer-review

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

Development of a locally sustainable functional food based on mutandabota, a traditional food in southern Africa.

Mpofu, A., Linnemann, A. R., Sybesma, W., Kort, R., Nout, M. J. & Smid, E. J., 2014, (Accepted/In press) In : Journal of Dairy Science.

Research output: Contribution to JournalArticleAcademicpeer-review

Development of the recombinase-based in vivo expression technology in Streptococcus thermophilus and validation using the lactose operon promoter

Junjua, M., Galia, W., Gaci, N., Uriot, O., Genay, M., Bachmann, H., Kleerebezem, M., Dary, A. & Roussel, Y., 2014, In : Journal of Applied Microbiology. 116, 3, p. 620-631 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Effects of cadmium and mercury on theupper part of skeletal muscle glycolysis in mice.

Ramirez-Bajo, M. J., de Atauri, P., Ortega, F., Westerhoff, H. V., Gelpi, J. L., Centelles, J. J. & Cascante, M., 2014, In : PLoS ONE. 9, 1, e80018.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids.

Szoor, B., Haanstra, J. R., Gualdron-Lopez, M. & Michels, P. A. M., 2014, In : Current Opinion in Microbiology. 22, p. 79-87 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Gene Drives and CRISPR could revolutionize exocsystem management.

Esvelt, K., Church, G. M. & Lunshof, J. E., 17 Jul 2014, In : Scientific American. 4 p.

Research output: Contribution to JournalArticlePopular

Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendatiosn from an African workshop.

Reid, G., Nduti, N., Sybesma, W., Kort, R., Kollmann, T. R., Adam, R., Boga, H., Brown, E. M., Einerhand, A., El-Nezami, H., Gloor, G. B., Kavere, I. I., Lindahl, J., Manges, A., Mamo, W., Martin, R., McMillan, A., Obiero, J., Ochieng, P. A., Onyango, A. & 8 others, Rulisa, S., Salminen, E., Salminen, S., Sije, A., Swann, J. R., van Treuren, W., Wawery, D. & Kemp, S. J., 2014, In : Microbiome. 2, 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Harvard Personal Genome Project: Lessons from Participatory Public Research

Ball, M. P., Bobe, J. R., Chou, M. F., Clegg, T., Estep, P. W., Lunshof, J. E., Vandewege, W., Wait Zaranek, A. & Church, G. M., 2014, In : Genome Medicine. 6, p. 10

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells.

Gustavsson, A-K., van Niekerk, D. D., Adiels, C. B., Goksor, M. & Snoep, J. L., 2014, In : FEBS Letters. 588, p. 3-7

Research output: Contribution to JournalArticleAcademicpeer-review

Innovation dynamics in cassava production systems in Uganda

Wendiro, D., Watu Wamae, W., Kingiri, A., Dhabangi, M. & Wacoo, P. A., 25 Sep 2014, In : Journal of Agricultural Biotechnology and Sustainable Development. 6, 5, p. 50 to 59 10 p., 2EA519747628.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

In or out? On the tightness of glycosomal compartmentalizatin of metabolites and enzymes in Trypanosoma brucei.

Haanstra, J. R., Bakker, B. M. & Michels, P. A. M., 2014, In : Molecular and Biochemical Parasitology. 198, p. 18-28

Research output: Contribution to JournalArticleAcademicpeer-review

Interactions between accumulated copper, bacterial community structure and histamine levels in crayfish meat during storage.

Soedarini, B., van Gestel, C. A. M., van Straalen, N. M., Widianarko, B. & Roling, W. F. M., 2014, In : Journal of the Science of Food and Agriculture. 94, p. 2023-2029

Research output: Contribution to JournalArticleAcademicpeer-review

Macromolecular networks and intelligence in microorganisms.

Westerhoff, H. V., Brooks, A., Simeonidis, E., Garcia-Contreras, R., He, F., Boogerd, F. C., Jackson, V. J., Goncharuk, V. & Kolodkin, A. N., 2014, In : Frontiers in Microbiology. 5, p. 1-17 379.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Methods for Detection of Aflatoxins in Agricultural Food Crops

Wacoo, P. A., Wendiro, D., Vuzi, P. C. & Hawumba, J. F., 13 Nov 2014, In : Journal of Applied Chemistry. 2014, 2014, p. 1-15 15 p., 10.1155/2014/706291.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: Insigths into metabolic regulation.

Murabito, E., Verma, M., Bekker, M., Bellomo, D., Westerhoff, H. V., Teusink, B. & Steuer, R., 2014, In : PLoS ONE. 9, 9, e106453.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Multiscale modelling approach combining a kinetic model of glutathione metabolism with PBPK models of paracetamol and the potential glutathione-depletion biomarkes ophthalmic acid and 5-oxoproline in humans and rats

Geenen, S., Yates, J. W. T., Kenna, J. G., Bois, F. Y., Wilson, I. D. & Westerhoff, H. V., 2014, In : Integrative Biology. 5, p. 877-888

Research output: Contribution to JournalArticleAcademicpeer-review

Optimization of stress response through the nuclear receptor-mediated cortisol signalling network.

Kolodkin, A., Sahin, N., Phillips, A., Hood, S. R., Bruggeman, F. J., Westerhoff, H. V. & Plant, N., 2014, In : Nature Communications. 4

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

PAPD5-mediated 3'adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

Boele, J., Persson, H., Shin, J. W., Ishizu, Y., Newie, I. S., Sokilde, R., Hawkins, S. M., Coarfa, C., Ikeda, K., Takayama, K-I., Hori-Inoue, K., Ando, Y., Maxwell Burroughs, A., Sasaki, C., Suzuki, C., Sakai, M., Aoki, S., Ogawa, A., Hasegawa, A., Lizio, M. & 9 others, Kaida, K., Teusink, B., Caminic, P., Suzuki, H., Inoue, S., Gunaratne, P. H., Rovira, C., Hayashizaki, Y. & de Hoon, M. J. L., 2014, (Accepted/In press) In : Proceedings of the National Academy of Sciences of the United States of America. 111, 31, p. 11467-11472

Research output: Contribution to JournalArticleAcademicpeer-review

Personalized therapy with probiotics from the host Triple A.

Kort, R., 2014, In : Trends in Biotechnology. 32, p. 291-293 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part I. Batch cultivation with excess of carbon sources.

Marozava, S., Roling, W. F. M., Seifert, J., Kuffner, R., van Bergen, M. & Meckenstock, R. U., 2014, In : Systematic and Applied Microbiology. 37, p. 287-295

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Physiology of Geobacter metallireducens under excess and limitation of electron donors. Part II. Mimicking environmental conditions during cultivation in retentostats.

Marozava, S., Roling, W. F. M., Seifert, J., Kuffner, R., van Bergen, M. & Meckenstock, R. U., 2014, In : Systematic and Applied Microbiology. 37, p. 277-285

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Raw Personal Data: Providing Access

Lunshof, J. E., Church, G. M. & Prainsack, B., 2014, In : Science. 343, p. 373-374

Research output: Contribution to JournalArticleAcademicpeer-review

Reciprocity and transparancy: Normative principles of data sharing.

Barash, C. I. & Lunshof, J. E., 2014, In : Applied and Translational Genomics. 3, p. 122-123 2 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria

Feldman-Salit, A., Hering, S., Messiha, H., Veith, N., Cojocaru, V., Sieg, A., Westerhoff, H. V., Kreikemeyer, B., Wade, R. & Fiedler, T., 2014, In : Journal of Biological Chemistry. 288, p. 21295-21306

Research output: Contribution to JournalArticleAcademicpeer-review

Response

Lunshof, J. E., Church, G. M. & Prainsack, B., 2014, In : Science. 343, p. 969

Research output: Contribution to JournalArticleAcademic

Shaping the oral microbiota through intimate kissing.

Kort, R., Caspers, M., van der Graaf, A., van Egmond, W., Keijser, B. & Roeselers, G., 2014, In : Microbiome. 2, p. 41

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Systematic evaluation of bias in microbial community profiles induced by whole genome amplification.

Direito, S., Zaura, E., Little, M., Ehrenfreund, P. & Roling, W. F. M., 2014, In : Environmental Microbiology. 16, p. 643-657

Research output: Contribution to JournalArticleAcademicpeer-review