• De Boelelaan 1108, O|2 building

    1081 HZ Amsterdam

    Netherlands

Research Output 1977 2019

2019

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
strength (mechanics)
glucose
mutation
chemostat
fitness

A Fast and Economical Sample Preparation Protocol for Interaction Proteomics Analysis

Gonzalez-Lozano, M. A., Koopmans, F., Paliukhovich, I., Smit, A. B. & Li, K. W., May 2019, In : Proteomics. 19, 9, p. 1-3 3 p., 1900027.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Immunoprecipitation
Proteomics
Proteins
Staphylococcal Protein A
Throughput

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

Özcan, E., Selvi, S. S., Nikerel, E., Teusink, B., Toksoy Öner, E. & Çakır, T., 1 Jan 2019, In : Applied Microbiology and Biotechnology.

Research output: Contribution to JournalArticleAcademicpeer-review

Metabolic Networks and Pathways
Citric Acid
Genome
Bacteria
phosphoketolase

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors

de Heuvel, E., Singh, A. K., Edink, E., van der Meer, T., van der Woude, M., Sadek, P., Krell-Jørgensen, M. P., van den Bergh, T., Veerman, J., Caljon, G., Kalejaiye, T. D., Wijtmans, M., Maes, L., de Koning, H. P., Jan Sterk, G., Siderius, M., de Esch, I. J. P., Brown, D. G. & Leurs, R., 18 Jun 2019, In : Bioorganic and Medicinal Chemistry. p. 1-15 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Trypanosoma brucei brucei
Phosphoric Diester Hydrolases
Parasites
Cyclic Nucleotides
Cytotoxicity

Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

de Heuvel, E., Singh, A. K., Boronat, P., Kooistra, A. J., van der Meer, T., Sadek, P., Blaazer, A. R., Shaner, N. C., Bindels, D. S., Caljon, G., Maes, L., Sterk, G. J., Siderius, M., Oberholzer, M., de Esch, I. J. P., Brown, D. G. & Leurs, R., 15 Sep 2019, In : Bioorganic and Medicinal Chemistry. 27, 18, p. 4013-4029 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phosphodiesterase Inhibitors
Parasites
African Trypanosomiasis
Trypanosoma brucei brucei
Trypanosomiasis

A mode-of-action ontology model for safety evaluation of chemicals: Outcome of a series of workshops on repeated dose toxicity

Desprez, B., Birk, B., Blaauboer, B., Boobis, A., Carmichael, P., Cronin, M. T. D., Curie, R., Daston, G., Hubesch, B., Jennings, P., Klaric, M., Kroese, D., Mahony, C., Ouédraogo, G., Piersma, A., Richarz, A. N., Schwarz, M., van Benthem, J., van de Water, B. & Vinken, M., 1 Sep 2019, In : Toxicology in Vitro. 59, p. 44-50 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Chemical Safety
Ontology
Toxicity
Education
Cosmetics

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P. & Bachmann, H., 1 Dec 2019, In : Scientific Reports. 9, 1, 9867.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
ampicillin
antibiotics
viability
cells

Analysis of Arabidopsis thaliana HKT1 and Eutrema salsugineum/botschantzevii HKT1;2 Promoters in Response to Salt Stress in Athkt1:1 Mutant

Nawaz, I., Iqbal, M., Hakvoort, H. W. J., de Boer, A. H. & Schat, H., 1 Jun 2019, In : Molecular Biotechnology. 61, 6, p. 442-450 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Arabidopsis
Salts
Agricultural Crops
Cathode ray tubes
Level control

A Photoswitchable Agonist for the Histamine H 3 Receptor, a Prototypic Family A G-Protein-Coupled Receptor

Hauwert, N. J., Mocking, T. A. M., Da Costa Pereira, D., Lion, K., Huppelschoten, Y., Vischer, H. F., De Esch, I. J. P., Wijtmans, M. & Leurs, R., 26 Mar 2019, In : Angewandte Chemie - International Edition. 58, 14, p. 4531-4535 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Histamine Agonists
G-Protein-Coupled Receptors
Histamine
Proteins
Chemical activation

Application of three approaches for quantitative AOP development to renal toxicity

Zgheib, E., Gao, W., Limonciel, A., Aladjov, H., Yang, H., Tebby, C., Gayraud, G., Jennings, P., Sachana, M., Beltman, J. B. & Bois, F. Y., 1 Aug 2019, In : Computational Toxicology. 11, p. 1-13 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
Toxicity
Kidney
Chronic Renal Insufficiency
Calibration

Approximating one-matrix functionals without generalized Pauli constraints

Gritsenko, O. V. & Pernal, K., 15 Jul 2019, In : Physical Review A. 100, p. 1-6 6 p., 012509.

Research output: Contribution to JournalArticleAcademicpeer-review

functionals
matrices
approximation
occupation
energy

A protocol for one-step differentiation of human induced pluripotent stem cells into mature podocytes

Murphy, C., Feifel, E., Jennings, P., Gstraunthaler, G. & Wilmes, A., 1 Jan 2019, Cell-Based Assays Using iPSCs for Drug Development and Testing. Mandenius, C. F. & Ross, J. (eds.). Humana Press Inc., Vol. 1994. p. 93-99 7 p. (Methods in Molecular Biology; vol. 1994).

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

Induced Pluripotent Stem Cells
Podocytes
Glomerular Filtration Barrier
Cell Culture Techniques
Epithelial Cells

Automated partial atomic charge assignment for drug-like molecules: A fast knapsack approach

Engler, M. S., Caron, B., Veen, L., Geerke, D. P., Mark, A. E. & Klau, G. W., 5 Feb 2019, In : Algorithms for Molecular Biology. 14, 1, p. 1-10 10 p., 1.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Knapsack
Drugs
Assignment
Charge
Molecules

A Variational Approach to London Dispersion Interactions without Density Distortion

Kooi, D. P. & Gori-Giorgi, P., 4 Apr 2019, In : Journal of Physical Chemistry Letters. 10, 7, p. 1537-1541 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Monomers
Atoms
monomers
interactions
Wave functions

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Groenenboom, A. E., Parker, M. E., De Vries, A., De Groot, S., Zobrist, S., Mansen, K., Milani, P., Kort, R., Smid, E. J. & Schoustra, S. E., 10 May 2019, In : PLoS ONE. 14, 5, e0215658.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Senegal
Probiotics
bacterial communities
Fermentation
probiotics

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 30 Oct 2019, In : Ecotoxicology and Environmental Safety. 182, p. 1-10 10 p., 109414.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chemostats
Metformin
Biodegradability
Biodegradation
Sewage

Bioinformatics in the Netherlands: The value of a nationwide community

Van Gelder, C. W. G., Hooft, R. W. W., Van Rijswijk, M. N., Van Den Berg, L., Kok, R. G., Reinders, M., Mons, B. & Heringa, J., 22 Mar 2019, In : Briefings in bioinformatics. 20, 2, p. 375-383 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bioinformatics
Computational Biology
Netherlands
Biological Science Disciplines
Research
Open Access
Histamine H3 Receptors
histamines
Bioluminescence
bioluminescence
Energy Transfer

Body size as emergent property of metabolism

Lika, K., Augustine, S. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 8-17 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

body size
metabolism
assimilation (physiology)
body mass
breathing

Brominated and organophosphorus flame retardants in South African indoor dust and cat hair

Brits, M., Brandsma, S. H., Rohwer, E. R., De Vos, J., Weiss, J. M. & de Boer, J., 5 Jul 2019, In : Environmental Pollution. 253, p. 120-129 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Flame Retardants
Flame retardants
Dust
Hair
Phosphates

Carbon monoxide insertion at a heavy p-block element: unprecedented formation of a cationic bismuth carbamoyl

Ramler, J., Poater, J., Hirsch, F., Ritschel, B., Fischer, I., Bickelhaupt, F. M. & Lichtenberg, C., 21 Apr 2019, In : Chemical Science. 10, 15, p. 4169-4176 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Bismuth
Carbon Monoxide
X ray analysis
Substrates
Ultraviolet spectroscopy

Cation affinities throughout the periodic table

Boughlala, Z., Fonseca Guerra, C. & Bickelhaupt, F. M., 2019, Computational Chemistry. van Eldik, R. & Puchta, R. (eds.). Academic Press Inc., p. 123-158 36 p. (Advances in Inorganic Chemistry; vol. 73).

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

Cations
Lewis Bases
Alkali Metals
Molecular orbitals
Hydrides

CE-MS for metabolomics: Developments and applications in the period 2016–2018

Ramautar, R., Somsen, G. W. & de Jong, G. J., 1 Jan 2019, In : Electrophoresis. 40, 1, p. 165-179 15 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Metabolomics
Metabolites
Electrophoresis
Coatings

CE-SDS method development, validation and best practice - an overview

Sänger-van de Griend, C. E., 29 May 2019, In : Electrophoresis.

Research output: Contribution to JournalReview articleAcademicpeer-review

Licensure
Practice Guidelines
Industry
Proteins
Therapeutics

Chaperones and substrate specificity, type VII secretion systems reconnected

Phan, T. H., 2019, 194 p.

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

Open Access
File
Open Access
Sulfaphenazole
Floxacillin
Cytochrome P-450 CYP3A
Cytochromes
Hydroxylation

Characterization of Non-covalent Interactions in Self-assembling Systems

Petelski, A. N., 2019, 200 p.

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

Open Access
File

Characterizing export of land-based microplastics to the estuary - Part I: Application of integrated geospatial microplastic transport models to assess tire and road wear particles in the Seine watershed

Unice, K. M., Weeber, M. P., Abramson, M. M., Reid, R. C. D., van Gils, J. A. G., Markus, A. A., Vethaak, A. D. & Panko, J. M., 1 Jan 2019, In : Science of the Total Environment. 646, p. 1639-1649 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

tire
Estuaries
Watersheds
Tires
Wear of materials

Characterizing export of land-based microplastics to the estuary - Part II: Sensitivity analysis of an integrated geospatial microplastic transport modeling assessment of tire and road wear particles

Unice, K. M., Weeber, M. P., Abramson, M. M., Reid, R. C. D., van Gils, J. A. G., Markus, A. A., Vethaak, A. D. & Panko, J. M., 1 Jan 2019, In : Science of the Total Environment. 646, p. 1650-1659 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

tire
Estuaries
Tires
Sensitivity analysis
sensitivity analysis

Checks and balances in bacterial cell division

Den Blaauwen, T. & Luirink, J., 1 Jan 2019, In : mBio. 10, 1, e00149-19.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access
Peptidoglycan
Cell Division
Gram-Positive Bacteria
Proteins
Anti-Bacterial Agents

Chemoselectivity of Tertiary Azides in Strain-Promoted Alkyne-Azide Cycloadditions

Svatunek, D., Houszka, N., Hamlin, T. A., Bickelhaupt, F. M. & Mikula, H., 14 Jan 2019, In : Chemistry - A European Journal. 25, 3, p. 754-758 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Alkynes
Azides
Cycloaddition
Computational methods
Reaction kinetics

Child development, growth and microbiota: follow-up of a randomized education trial in Uganda

Atukunda, P., Muhoozi, G. K. M., van den Broek, T. J., Kort, R., Diep, L. M., Kaaya, A. N., Iversen, P. O. & Westerberg, A. C., Jun 2019, In : Journal of global health. 9, 1, p. 1-11 11 p., 010431.

Research output: Contribution to JournalArticleAcademicpeer-review

Uganda
Microbiota
Child Development
Mothers
Education

Chiral Discrimination of DL-Amino Acids by Trapped Ion Mobility Spectrometry after Derivatization with (+)-1-(9-Fluorenyl)ethyl Chloroformate

Pérez-Míguez, R., Bruyneel, B., Castro-Puyana, M., Marina, M. L., Somsen, G. W. & Domínguez-Vega, E., 5 Mar 2019, In : Analytical Chemistry. 91, 5, p. 3277-3285 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Trapped ions
Spectrometry
Amino Acids
Enantiomers
1-(9-fluorenyl)ethyl chloroformate

Chlorinated paraffins in indoor dust from Australia: Levels, congener patterns and preliminary assessment of human exposure

He, C., Brandsma, S. H., Jiang, H., O'Brien, J. W., van Mourik, L. M., Banks, A. P., Wang, X., Thai, P. K. & Mueller, J. F., 10 Sep 2019, In : Science of the Total Environment. 682, p. 318-323 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Paraffin
Paraffins
Dust
dust
alkane

Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations

Patty, C. H. L., Ariese, F., Buma, W. J., ten Kate, I. L., van Spanning, R. J. M. & Snik, F., May 2019, In : Photosynthesis Research. 140, 2, p. 129-139

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Circular spectropolarimetric sensing of life

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

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

Open Access
File

Circular Spectropolarimetric Sensing of Vegetation in the Field: Possibilities for the Remote Detection of Extraterrestrial Life

Patty, C. H. L., Ten Kate, I. L., Buma, W. J., van Spanning, R. J. M., Steinbach, G., Ariese, F. & Snik, F., 30 Jul 2019, In : Astrobiology.

Research output: Contribution to JournalArticleAcademicpeer-review

Exobiology
Forestry
Agriculture
Lighting
Light

Closed-open innovation strategy for autonomous vehicle development

Blankesteijn, M., De Jong, F. & Bossink, B., 7 Mar 2019, In : International Journal of Automotive Technology and Management. 19, 1/2, p. 74-103 30 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Innovation
Railroad cars
Innovation strategy
Open innovation
Automotive industry

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, 1 Dec 2019, In : Nature Communications. 10, 1, 2674.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Pharmacogenetics
Drug Combinations
drugs
cancer
predictions

Comparative characterization of human induced pluripotent stem cells (hiPSC) derived from patients with schizophrenia and autism

Grunwald, L. M., Stock, R., Haag, K., Buckenmaier, S., Eberle, M. C., Wildgruber, D., Storchak, H., Kriebel, M., Weißgraeber, S., Mathew, L., Singh, Y., Loos, M., Li, K. W., Kraushaar, U., Fallgatter, A. J. & Volkmer, H., 1 Dec 2019, In : Translational Psychiatry. 9, 1, 179.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Induced Pluripotent Stem Cells
Autistic Disorder
Schizophrenia
Neurons
Gene Expression Profiling

Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity

Wels, M., Siezen, R., Van Hijum, S., Kelly, W. J. & Bachmann, H., 31 Jan 2019, In : Frontiers in Microbiology. 10, January, p. 1-18 18 p., 4.

Research output: Contribution to JournalArticleAcademicpeer-review

Lactococcus lactis
Genotype
Genome
Phenotype
Dairying

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

Van Der Veer, C., Hertzberger, R. Y., Bruisten, S. M., Tytgat, H. L. P., Swanenburg, J., De Kat Angelino-Bart, A., Schuren, F., Molenaar, D., Reid, G., De Vries, H. & Kort, R., 29 Mar 2019, In : Microbiome. 7, 1, p. 1-14 14 p., 49.

Research output: Contribution to JournalArticleAcademicpeer-review

File
Microbiota
Genomics
Glycogen
Glycosylation
Lactobacillus

Comparative physiological energetics of Mediterranean and North Atlantic loggerhead turtles

Marn, N., Jusup, M., Catteau, S., Kooijman, S. A. L. M. & Klanjšček, T., Jan 2019, In : Journal of sea research. 143, p. 100-118 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Caretta caretta
energy budget
turtle
energetics
sexual maturity
space density
Density functional theory
prototypes
density functional theory
Molecules
Hydrophobic and Hydrophilic Interactions
Liquid chromatography
Liquid Chromatography
Glycoproteins
Liquids

Contingent use of rational, intuitive and political decision-making in R&D

Kolbe, L. M., Bossink, B. & de Man, A. P., 2019, (Accepted/In press) In : Management Decision.

Research output: Contribution to JournalArticleAcademicpeer-review

Decision making
Innovation
Decision-making process
Innovation process
Interaction

Control of Surface Defects in ZnO Nanorod Arrays with Thermally Deposited Au Nanoparticles for Perovskite Photovoltaics

Tulus, T., Olthof, S., Marszalek, M., Peukert, A., Muscarella, L. A., Ehrler, B., Vukovic, O., Galagan, Y., Boehme, S. C. & Von Hauff, E., 28 May 2019, In : ACS Applied Energy Materials. 2, 5, p. 3736-3748 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Surface defects
Nanorods
Perovskite
Nanoparticles
Solar cells

Corrigendum: Investigation of Nrf2, AhR and ATF4 activation in toxicogenomic databases (Frontiers Media S.A. (2018) 9 (429) DOI: 10.3389/fgene.2018.00429)

Zgheib, E., Limonciel, A., Jiang, X., Wilmes, A., Wink, S., Van De Water, B., Kopp-Schneider, A., Bois, F. Y. & Jennings, P., 1 Jan 2019, In : Frontiers in Genetics. 10, JUN, 517.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access
Toxicogenetics
Databases
Gift Giving
Organized Financing
European Union

Corrigendum: Investigation of Nrf2, AhR and ATF4 Activation in Toxicogenomic Databases

Zgheib, E., Limonciel, A., Jiang, X., Wilmes, A., Wink, S., van de Water, B., Kopp-Schneider, A., Bois, F. Y. & Jennings, P., 2019, In : Frontiers in Genetics. 10, p. 517

Research output: Contribution to JournalArticleAcademic

Open Access
Toxicogenetics
Databases
corrigendum

De hygiënehypothese onder de loep

Croon, S., Rijkers, G., Budding, A., de Jong, E., Knol, E., Smits, H., Tool, B. & Kort, R., May 2019, In : Dutch Journal of Allergy, Asthma & Clinical Immunology (NTvAAKI). 19, p. 55-60 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Hygiene Hypothesis
Immune System
Hypersensitivity
Eczema
Immune System Diseases