• 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

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

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

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., 4 Apr 2019, In : Toxicology in Vitro. 59, p. 44-50 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Chemical Safety
Ontology
Toxicity
Education
Cosmetics

Analysis of a predator–prey model with specific time scales: a geometrical approach proving the occurrence of canard solutions

Poggiale, J. C., Aldebert, C., Girardot, B. & Kooi, B. W., 20 Feb 2019, In : Journal of Mathematical Biology. p. 1-22 22 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Canard
Predator-prey Model
Time Scales
Predator
Prey

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

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

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

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

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

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

Bioinformatics
Computational Biology
Netherlands
Biological Science Disciplines
Research

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

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

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
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

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

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

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., 15 May 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 life

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

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

Open Access
File

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 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
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

Surface defects
Nanorods
Perovskite
Nanoparticles
Solar cells

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

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

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model

Visscher, K. M. & Geerke, D. P., 14 Feb 2019, In : Journal of Chemical Theory and Computation. 15, 3, p. 1875–1883 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

field theory (physics)
inclusions
Molecular mechanics
Alkanes
Dipole moment

Design, synthesis, and: In vitro and in vivo characterization of 1-{4-[4-(substituted)piperazin-1-yl]butyl}guanidines and their piperidine analogues as histamine H 3 receptor antagonists

Staszewski, M., Stasiak, A., Karcz, T., McNaught Flores, D., Fogel, W. A., Kieć-Kononowicz, K., Leurs, R. & Walczyński, K., Feb 2019, In : MedChemComm. 10, 2, p. 234-251 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Guanidines
Histamine
Guanidine
Rats
Histamine Receptors

Design and evaluation of a multiplexed angular-scanning surface plasmon resonance system employing line-laser optics and CCD detection in combination with multi-ligand sensor chips

Lakayan, D., Tuppurainen, J., Eemeli Suutari, T., van Iperen, D. J., Somsen, G. W. & Kool, J., 1 Mar 2019, In : Sensors and Actuators, B: Chemical. 282, p. 243-250 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Laser optics
Surface plasmon resonance
surface plasmon resonance
Charge coupled devices
charge coupled devices

Designing Self-Assembled Rosettes: Why Ammeline is a Superior Building Block to Melamine

Petelski, A. N. & Fonseca Guerra, C., Feb 2019, In : ChemistryOpen. 8, 2, p. 135-142 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Hydrogen bonds
Supramolecular chemistry
Molecular orbitals
Discrete Fourier transforms
Density functional theory

Designing Self-Assembled Rosettes: Why Ammeline is a Superior Building Block to Melamine

Petelski, A. N. & Fonseca Guerra, C., 1 Feb 2019, In : ChemistryOpen. 8, 2, p. 134-134 1 p.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Pallets
Hydrogen
Gases
Water
ammeline

Development of a neurotoxicity assay that is tuned to detect mitochondrial toxicants

Delp, J., Funke, M., Rudolf, F., Cediel, A., Bennekou, S. H., van der Stel, W., Carta, G., Jennings, P., Toma, C., Gardner, I., van de Water, B., Forsby, A. & Leist, M., 1 Jan 2019, In : Archives of Toxicology.

Research output: Contribution to JournalArticleAcademicpeer-review

Galactose
Assays
Electron Transport
Toxicity
Electron Transport Complex I

Diels-Alder reactivities of cycloalkenediones with tetrazine

Levandowski, B. J., Hamlin, T. A., Eckvahl, H. J., Bickelhaupt, F. M. & Houk, K. N., Feb 2019, In : Journal of Molecular Modeling. 25, 2, p. 1-5 5 p., 33.

Research output: Contribution to JournalArticleAcademicpeer-review

Coulomb interactions
Cycloparaffins
reactivity
electrostatics
interactions

Differential Salt Sensitivity in Potato Cultivars: The Role of Na+ Tissue Distribution and Vacuolar Na+ Sequestration

Jaarsma, R., 2019, 113 p.

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

Open Access
File
Open Access
Creativity
Self Efficacy
Workplace
Employee creativity
Efficacy

Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays

Otvos, R. A., Still, K. B. M., Somsen, G. W., Smit, A. B. & Kool, J., 1 Mar 2019, In : SLAS Discovery. 24, 3, p. 362-385 24 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Nicotinic Receptors
Drug Discovery
Biological Products
Ion Channels
Libraries