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2019

Acetogenins: Chemoenzymatic synthesis and molecular probing of respiratory NADH-dehydrogenases

van Lint, M., 12 Sep 2019, 326 p.

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

Circular spectropolarimetric sensing of life

Patty, C. H. L., 2019, 174 p.

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

Open Access
File

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

Damiani, C., Maspero, D., Di Filippo, M., Colombo, R., Pescini, D., Graudenzi, A., Westerhoff, H. V., Alberghina, L., Vanoni, M. & Mauri, G., 28 Feb 2019, In : PLoS Computational Biology. 15, 2, p. 1-25 25 p., e1006733.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Population Model
RNA
Metabolism
cancer
Cancer

Neural plasticity and adult neurogenesis: the deep biology perspective

Colangelo, A., Cirillo, G., Alberghina, L., Papa, M. & Westerhoff, H., 1 Feb 2019, In : Neural Regeneration Research. 14, 2, p. 201-205 5 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Neuronal Plasticity
Neurogenesis
Energy Metabolism
Growth Differentiation Factors
Mitochondrial Dynamics
Ammonium
Ammonium Compounds
Escherichia coli
Escherichia Coli
Ranking

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

Maeda, K., Westerhoff, H. V., Kurata, H. & Boogerd, F. C., 12 Apr 2019, In : NPJ systems biology and applications. 5, p. 1-11 11 p., 14.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ammonium
Ammonium Compounds
Escherichia coli
Escherichia Coli
Ranking
2018

Integrative Systems Toxicology for Human Health

Sharma, R. P., 2018, 402 p.

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

Open Access
File

Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats

Marozava, S., Vargas-López, R., Tian, Y., Merl-Pham, J., Braster, M., Meckenstock, R. U., Smidt, H., Röling, W. F. M. & Westerhoff, H. V., Jul 2018, In : Environmental Microbiology. 20, 7, p. 2652-2669 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Desulfitobacterium hafniense
Desulfitobacterium
Fumarates
chemostat
lactates

Microbial networks for bioremediation of chlorinated ethenes

Vargas Lopez, R., 2018, 214 p.

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

Open Access
File

NET works after all? Engineering robustness through diversity

Mondeel, T. D. G. A., Astrologo, S., Zhang, Y. & Westerhoff, H. V., 2018, In : IFAC-PapersOnLine. 51, 19, p. 128-137 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Thermodynamics
Kinetics
Engineers
Planets
Transcription

Predictable irreversible switching between acute and chronic inflammation

Abudukelimu, A., Barberis, M., Redegeld, F. A., Sahin, N. & Westerhoff, H. V., 7 Aug 2018, In : Frontiers in Immunology. 9, AUGUST, p. 1-16 16 p., 1596.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Inflammation
Antigens
Fibroblasts
Phenotype
Antigen-Antibody Complex

Rational cell culture optimization enhances experimental reproducibility in cancer cells

Wright Muelas, M., Ortega, F., Breitling, R., Bendtsen, C. & Westerhoff, H. V., 14 Feb 2018, In : Scientific Reports. 8, 1, p. 1-16 16 p., 3029.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Glutaminase
Cell Culture Techniques
Glutamine
Neoplasms
Metabolomics

STRENDA DB: enabling the validation and sharing of enzyme kinetics data

Swainston, N., Baici, A., Bakker, B. M., Cornish-Bowden, A., Fitzpatrick, P. F., Halling, P., Leyh, T. S., O'Donovan, C., Raushel, F. M., Reschel, U., Rohwer, J. M., Schnell, S., Schomburg, D., Tipton, K. F., Tsai, M. D., Westerhoff, H. V., Wittig, U., Wohlgemuth, R. & Kettner, C., 1 Jun 2018, In : FEBS Journal. 285, 12, p. 2193-2204 12 p.

Research output: Contribution to JournalComment / Letter to the editorAcademic

2017

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Damiani, C., Colombo, R., Gaglio, D., Mastroianni, F., Pescini, D., Westerhoff, H. V., Mauri, G., Vanoni, M. & Alberghina, L., 1 Sep 2017, In : PLoS Computational Biology. 13, 9, e1005758.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cell growth
Glutamine
Glucose
glutamine
lactates

Identification of Three Early Phases of Cell-Fate Determination during Osteogenic and Adipogenic Differentiation by Transcription Factor Dynamics

van de Peppel, J., Strini, T., Tilburg, J., Westerhoff, H., van Wijnen, A. J. & van Leeuwen, J. P., 11 Apr 2017, In : Stem cell reports. 8, 4, p. 947-960 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bone
Transcription Factors
Mesenchymal Stromal Cells
Osteoporosis
Bone and Bones

Learning to read and write in evolution: From static pseudoenzymes and pseudosignalers to dynamic gear shifters

Abudukelimu, A., Mondeel, T. D. G. A., Barberis, M. & Westerhoff, H. V., 15 Jun 2017, In : Biochemical Society Transactions. 45, 3, p. 635-652 18 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Gears
Adenosine Triphosphate
Learning
Proton-Motive Force
Systems Biology

Preconditioning and Dynamic Stimuli

Sahin, N., 2017, 199 p.

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

Open Access
File

Signaling at the tumorigenesis-inflammation interface: developing systems immunology to resolve a paradox

Abulikemu, A., 2017, 197 p.

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

Open Access
File

Targeting pathogen metabolism without collateral damage to the host.

Haanstra, J. R., Gerding, A., Dolga, A. M., Sorgdrager, F. J., Buist-Homan, M., du Toit, F., Faber, K. N., Holzhutter, H. G., Szoor, B., Matthews, K. R., Snoep, J. L., Westerhoff, H. V. & Bakker, B. M., 2017, In : Scientific Reports. 7, 40406.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The peculiar glycolytic pathway in hyperthermophylic archaea: Understanding its whims by experimentation in silico

Zhang, Y., Kouril, T., Snoep, J. L., Siebers, B., Barberis, M. & Westerhoff, H. V., 20 Apr 2017, In : International Journal of Molecular Sciences. 18, 4, 876.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Glyceraldehyde-3-Phosphate Dehydrogenases
Archaea
experimentation
dehydrogenases
Computer Simulation
2016

Clinical Perspective on the Vaginal Microbiome

Dols, J. A. M., 2016

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

Open Access
File
Microbiota

Microbial Ecology of Arsenic Contaminated Aquifers and Potential Bioremediation

Hassan, Z., 2016, 196 p.

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

Open Access
File

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity.

Dols, J. A. M., Molenaar, D., van der Helm, J. J., Caspers, M. P., de Kat Angelino-Bart, A., Schuren, F. H., Speksnijder, A. G., Westerhoff, H. V., Richardus, J. H., Boon, M. E., Reid, G., de Vries, H. J. & Kort, R., 2016, In : BMC Infectious Diseases. 16, 180.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

MUFINS: multi-formalism interaction network simulator

Wu, H., von Kamp, A., Leoncikas, V., Mori, W., Sahin, N., Gevorgyan, A., Linley, C., Grabowski, M., Mannan, A. A., Stoy, N., Stewart, G. R., Ward, L. T., Lewis, D. J. M., Sroka, J., Matsuno, H., Klamt, S., Westerhoff, H. V., McFadden, J., Plant, N. J. & Kierzek, A. M., 2016, In : NPJ systems biology and applications. 2, 16032.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access
2015

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 JournalArticleAcademicpeer-review

Tumors
Tumor
Fasting
Glucose
Breast Neoplasms

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 JournalArticleAcademicpeer-review

Open Access
Bangladesh
Groundwater
Arsenic
arsenic
Iron

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

CHO Cells
Citric Acid Cycle
Sorbitol
Metabolic Networks and Pathways
Recombinant Proteins

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
Ratchet
Bursting
Chromatin
Cycling
Transcription

Oncogenic properties and targeting of chemokine receptors CXCR4, CXCR7 and US28

Delic, A., 2015, 167 p.

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

Open Access
File
Chemokine Receptors

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

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

Pharmacology
Systems Biology
Genomics
Pharmaceutical Preparations
Pharmacokinetics

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
Theoretical Models
RNA Stability
Messenger RNA
Transcription Factors
Peroxisome Proliferator-Activated Receptors
2014

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
Protein Biosynthesis
Messenger RNA
translation (genetics)
Machinery
Eukaryotic Small Ribosome Subunits

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
Reaction rates
Cluster Analysis
Phosphotransferases
Signal transduction
Proteins

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
glycolysis
Glycolysis
Mercury
Cadmium
mercury

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
Intelligence
Brain
Biotechnology
Human Activities
Computer Simulation

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
Lactococcus lactis
Metabolic Networks and Pathways
Metabolism
Carbon
Starvation

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

Pyrrolidonecarboxylic Acid
Enzyme kinetics
Pharmacokinetics
Acetaminophen
Metabolism

Non-genetic cell-to-cell variability: theory and experiments

Schwabe, A., 2014

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

Open Access
File

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
Cytoplasmic and Nuclear Receptors
Hydrocortisone
optimization
Biological Adaptation
affinity

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

Lactate Dehydrogenases
Lactic Acid
Bacteria
Enzymes
Enzyme activity

The control analysis of signal transduction.

Westerhoff, H. V., Rehman, S., Boogerd, F. C., Yilmaz, N. & Verma, M., 2014, Systems biology of metabolic and signaling networks. Aon, M. (ed.). Berlin - Germany: Springer Verlag, p. 39-62

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

2013
Open Access
Gene expression regulation
Metabolic Engineering
Metabolic Network
Gene Expression Regulation
Metabolic Networks and Pathways

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., Thorleifsson, S. G., Agren, R., Bölling, C., Bordel, S., Chavali, A. K., Dobson, P., Dunn, W. B., Endler, L., Hala, D., Hucka, M. & 26 othersHull, D., Jameson, D., Jamshidi, N., Jonsson, J. J., Juty, N., Keating, S., Nokaew, I., Le Novère, N., Malys, N., Mazein, A., Papin, J. A., Price, N. D., Selkov, E., Sigurdsson, M. I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J. H. G. M., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H. V., Kell, D. B., Mendes, P. & Palsson, B. O., 2013, In : Nature Biotechnology. 31, 5, p. 419-425

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolism
Metabolites
Inborn Errors Metabolism
Metabolomics
Biomarkers

A kinetic model of glucose catabolism in Plasmodium falciparum

Penkler, G. P., 2013, 143 p.

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

Open Access
File

A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., Pir, P., Simeonidis, E., Spasic, I., Wishart, J., Weichart, D., Hayes, N. W., Jameson, D., Broomhead, D. S., Oliver, S. G., Gaskell, S. J. & 5 othersMcCarthy, J. E. G., Paton, N. W., Westerhoff, H. V., Kell, D. B. & Mendes, P., 2013, In : The FEBS Journal. 587, p. 2832-2841

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides--illustrated for the glycolytic enzymes of Saccharomyces cerevisiae

Mensonides, F. I. C., Bakker, B. M., Cremazy, F., Messiha, H. L., Mendes, P., Boogerd, F. C. & Westerhoff, H. V., 2013, In : FEBS Letters. 587, 17, p. 2860-2867 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biochemistry
Adenine Nucleotides
Yeast
Saccharomyces cerevisiae
Enzymes