• 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

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

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, p. e0215658

Research output: Contribution to JournalArticleAcademicpeer-review

Senegal
Probiotics
bacterial communities
Fermentation
probiotics

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

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

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

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

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., Tytgat, H., 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

Control of Surface Defects in ZnO Nanorod Arrays with thermally-deposited Au nanoparticles for Perovskite Photovoltaics

Tulus, ., Olthof, S., Marszalek, M., Peukert, A., Muscarella, L. A., Ehrler, B., Vukovic, O., Galagan, Y., Boehme, S. C. & von Hauff, E., 26 Apr 2019, In : ACS Applied Energy Materials. p. acsaem.9b00452

Research output: Contribution to JournalArticleAcademicpeer-review

surface defects
nanorods
solar cells
nanoparticles
photoelectron spectroscopy

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., 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

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

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

Cycloparaffins
Coulomb interactions
reactivity
Electrostatics
electrostatics

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

Drug-receptor binding kinetics in drug discovery: Sticking around at the histamine H1 receptor

Bosma, R., 2019, 177 p.

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

Open Access
File

Een praktische gids voor probiotica ter preventie van antibiotica-gerelateerde diarree in Nederland

Agamennone, V., Krul, C., Rijkers, G. & Kort, R., 8 Feb 2019, In : Pharmaceutisch Weekblad. 154, 6, p. 17-24 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Probiotics
Netherlands
Diarrhea
Anti-Bacterial Agents
Lactobacillus rhamnosus

Effects of 25 thyroid hormone disruptors on zebrafish embryos: A literature review of potential biomarkers

Spaan, K., Haigis, A. C., Weiss, J. & Legradi, J., 15 Mar 2019, In : Science of the Total Environment. 656, p. 1238-1249 12 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Biomarkers
Thyroid Hormones
literature review
hormone
biomarker
Electron correlations
space density
Density functional theory
density functional theory
Carbon Monoxide

Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions

Hamlin, T. A., Svatunek, D., Yu, S., Ridder, L., Infante, I., Visscher, L. & Bickelhaupt, F. M., 23 Jan 2019, In : European Journal of Organic Chemistry. 2019, 2, p. 378-386 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Cycloaddition
cycloaddition
reactivity
trends
Chemical activation

Enantioselective Bio-Hydrolysis of Geranyl-Derived rac-Epoxides: A Chemoenzymatic Route to trans-Furanoid Linalool Oxide

van Lint, M. J., Gümüs, A., Ruijter, E., Faber, K., Orru, R. V. A. & Hall, M., 1 Jan 2019, (Accepted/In press) In : Advanced Synthesis and Catalysis. 361, 4, p. 813-825

Research output: Contribution to JournalArticleAcademicpeer-review

Epoxide Hydrolases
Hydrolases
Enzymatic hydrolysis
Epoxy Compounds
Hydrolysis

Enlightening developments in 1,3-P,N-ligand-stabilized multinuclear complexes: A shift from catalysis to photoluminescence

Rong, M. K., Holtrop, F., Slootweg, J. C. & Lammertsma, K., 1 Mar 2019, In : Coordination Chemistry Reviews. 382, p. 57-68 12 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Catalysis
catalysis
Photoluminescence
Coinage
Metals

Erratum for den Blaauwen and Luirink, "Checks and Balances in Bacterial Cell Division"

den Blaauwen, T. & Luirink, J., 16 Apr 2019, In : mBio. 10, 2

Research output: Contribution to JournalComment / Letter to the editorAcademic

Experimental design and measurement uncertainty in ligand binding studies by affinity capillary electrophoresis

Stein, M., Haselberg, R., Mozafari-Torshizi, M. & Wätzig, H., 14 Jan 2019, In : Electrophoresis. p. 1-14

Research output: Contribution to JournalArticleAcademicpeer-review

Capillary electrophoresis
Capillary Electrophoresis
Design of experiments
Uncertainty
Research Design

Fire

de Boer, J., Feb 2019, In : Chemosphere. 217, p. A1-A2 2 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

First detection of short-chain chlorinated paraffins (SCCPs) in humpback whales (Megaptera novaeangliae) foraging in Antarctic waters

Casà, M. V., van Mourik, L. M., Weijs, L., Mueller, J. & Nash, S. B., 25 Apr 2019, In : Environmental Pollution. 250, p. 953-959 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Humpback Whale
Whales
Paraffin
Paraffins
Water