Research Output 1989 2020

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2019

Measurement Technologies

Yanes, O., Hollywood, K., Mumm, R., Vinaixa, M., Rankin, N., Wehrens, H. R. M. J. & Salek, R., 19 Aug 2019, Metabolomics: Practical Guide to Design and Analysis. Wehrens, R. & Salek, R. (eds.). 1st ed. New York: Chapman and Hall, 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Mass spectrometry
Capillary electrophoresis
Liquid chromatography
Metabolites
Ultraviolet spectroscopy
2018
3 Citations (Scopus)

3C in maize and arabidopsis

Weber, B., Jamge, S. & Stam, M., 2018, Plant Chromatin Dynamics: Methods and Protocols. Humana Press Inc., p. 247-270 (Methods in Molecular Biology; vol. 1675).

Research output: Chapter in Book/Report/Conference proceedingChapter

Arabidopsis
Zea mays
Chromosomes
Genome
Research
2 Citations (Scopus)

Identification of in planta protein–protein interactions using IP-MS

Jamge, S., Angenent, G. & Bemer, M., 2018, Plant Chromatin Dynamics: Methods and Protocols. Humana Press Inc., p. 315-329 (Methods in Molecular Biology; vol. 1675).

Research output: Chapter in Book/Report/Conference proceedingChapter

Immunoprecipitation
Chromatin
Mass Spectrometry
Transcription Factors
Protein Interaction Maps
3 Citations (Scopus)

Laser ablation electrospray ionization-mass spectrometry imaging (LAESI-MS) for spatially resolved plant metabolomics

Etalo, D. W., Díez-Simón, C., de Vos, R. C. H. & Hall, R. D., 15 May 2018, Plant Metabolomics: Methods and Protocols. António, C. (ed.). New York: Humana Press Inc., p. 253-267 (Methods in Molecular Biology; vol. 1778).

Research output: Chapter in Book/Report/Conference proceedingChapter

Metabolomics
Electrospray Ionization Mass Spectrometry
Laser Therapy
Vacuum

Organic seed production, certification and availability: Corp Breeding and cultivation:

Groot, S. P. C. & Raaijmakers, M. H. J. E., 2018, Improving organic crop cultivation. Köpke, U. (ed.). Cambridge, UK: Burleigh Dodds Science Publishing Limited

Research output: Chapter in Book/Report/Conference proceedingChapter

seed crop production
certification
breeding
seeds
seed quality
5 Citations (Scopus)

Profiling nucleosome occupancy by MNase-seq: Experimental protocol and computational analysis

Pajoro, A., Muiño, J. M., Angenent, G. C. & Kaufmann, K., 2018, Plant Chromatin Dynamics: Methods and Protocols. Humana Press Inc., p. 167-181 (Methods in Molecular Biology; vol. 1675).

Research output: Chapter in Book/Report/Conference proceedingChapter

Micrococcal Nuclease
Nucleosomes
Genome
Chromatin
Digestion
3 Citations (Scopus)

Unraveling the complex epigenetic mechanisms that regulate gene activity

Bemer, M., 2018, Plant Chromatin Dynamics. Humana Press Inc., p. 205-231 (Methods in Molecular Biology; vol. 1675).

Research output: Chapter in Book/Report/Conference proceedingChapter

Epigenomics
Genes
Transcription Factors
Histone Code
Nucleic Acid Conformation
2017

Biosynthesis, localization and ecological role of pyrethrins and linked secondary metabolites in pyrethrum

Jongsma, M. A. & Ramirez, A., 2017, 2nd International Symposium on Pyrethrum. International Society for Horticultural Science, Vol. 1169. p. 101-111 (Acta Horticulturae; vol. 1169).

Research output: Chapter in Book/Report/Conference proceedingChapter

Tanacetum
pyrethrins
secondary metabolites
biosynthesis
metabolites

Prunus fruit juices

Toydemir, G., Boyacioglu, D., Hall, R. D., Beekwilder, M. J. & Capanoglu, E., 26 May 2017, Innovative Technologies in Beverage Processing. Aguiló-Aguayo, I. & Plaza, L. (eds.). Chichester UK: Wiley, p. 59-77

Research output: Chapter in Book/Report/Conference proceedingChapter

Prunus
fruit juices
Prunus cerasus
Prunus avium
pasteurization

Robust and confident predictor selection in metabolomics

Hageman, J. A., Engel, B., de Vos, C. H., Mumm, R., Hall, R. D., Jwanro, H., Crouzillat, D., Spadone, C. & van Eeuwijk, F. A., 2017, Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry; Frontiers in Probability and the Statistical Sciences. Datta, S. & Mertens, B. J. A. (eds.). Springer, p. 239-257 (Frontiers in Probability and the Statistical Sciences).

Research output: Chapter in Book/Report/Conference proceedingChapter

metabolomics
metabolites
chocolate liquor
biomarkers
foods
3 Citations (Scopus)

SELEX-seq: A method to determine DNA binding specificities of plant transcription factors

Smaczniak, C., Angenent, G. C. & Kaufmann, K., 2017, Plant gene regulatory networks: Methods and protocols. Kaufmann, K. & Mueller-Roeber, B. (eds.). Humana Press Inc., Vol. 1629. p. 67-82 (Methods in Molecular Biology - Springer Protocols; vol. 1629).

Research output: Chapter in Book/Report/Conference proceedingChapter

SELEX Aptamer Technique
Transcription Factors
DNA
High-Throughput Nucleotide Sequencing
Nucleotide Motifs

Species-specific genome sequence databases: A practical review

van Dijk, A-J., 2017, Plant genomics databases: Methods and Protocols. van Dijk, A. D. J. (ed.). Humana Press Inc., p. 173-181 (Methods in Molecular Biology; vol. 1533).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
Databases
Proteins
2016

Cherry Juice

Toydemir, G., Boyacioglu, D., Beekwilder, M. J., Hall, R. D. & Capanoglu, E., 2016, Handbook of Functional Beverages and Human Health. CRC Press, p. 175-185

Research output: Chapter in Book/Report/Conference proceedingChapter

Strategies to reduce or prevent wheat coeliacimmunogenicity and wheat sensitivity through food

Gilissen, L. J. W. J., van der Meer, I. M. & Smulders, M. J. M., 2016, Proceedings of the 29th Meeting, WORKING GROUP on PROLAMIN ANALYSIS and TOXICITY. Koehler, P. (ed.). Freising: Verlag Deutsche Forschungsanstalt für Lebensmittelchemie, p. 41-55

Research output: Chapter in Book/Report/Conference proceedingChapter

food allergies
gluten
wheat
gluten-free diet
disease prevention

Strategies to reduce or prevent wheat coeliac- immunogenicity and wheat sensitivity through food

Gilissen, L. J. W. J., van der Meer, I. M. & Smulders, M. J. M., 2016, Proceedings of the 29th Meeting Working Group on Prolamin Analysis and Toxicity (PWG). Koehler, P. (ed.). Tulln, Austria: WGPAT

Research output: Chapter in Book/Report/Conference proceedingChapter

food allergies
gluten
abdomen
immune response
wheat
2015
7 Citations (Scopus)

Bacillus thuringiensis-based Products for Insect Pest Control

de Maagd, R. A., 2015, Principles of Plant-Microbe Interactions : Microbes for Sustainable Agriculture. Lugtenberg, B. (ed.). Springer, p. 185-192 185 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

pest control
Bacillus thuringiensis
insect pests
toxins
crystals
7 Citations (Scopus)

Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: Experimental protocol and computational analysis

Van Mourik, H., Muiño, J. M., Pajoro, A., Angenent, G. C. & Kaufmann, K., 2015, Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York LLC, p. 93-121

Research output: Chapter in Book/Report/Conference proceedingChapter

Transcription Factors
transcription factors
DNA
Proteins
proteins

Health Management for Seeds and Other Organic Propagation Material

Koch, E. & Groot, S. P. C., 2015, Plant Diseaes and Their Management in Organic Agriculture. Finckh, M. R., van Bruggen, A. H. C. & Tamm, L. (eds.). Minnesota: The American Phytopathological Society, p. 189-203

Research output: Chapter in Book/Report/Conference proceedingChapter

propagation materials
seeds
organic production
seed tubers
plant cuttings

Literatuurstudie naar het effect van zoutstress op plantenstoffen en de potentiële toegevoegde waarde

van Arkel, J. & van der Meer, I. M., 2015, Zilt Perspectief : kennis en kansen voor teelt en verwerking van gewassen op zilte landbouwgrond rond de Wadden, afgestemd op de unieke natuurlijke en landschappelijke kwaliteiten met aandacht voor educatie en kennisverspreiding: eindverslag. Vos, A. C., Rijsselberghe, A. M. J. & Kieft, H. (eds.). Den Burg: Stichting Ziltperspectief, p. 64-70 81 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Pepper, Sweet (Capsicum annuum)

Heidmann, I. & Boutilier, K. A., 2015, Agrobacterium Protocols: Volume 1 (third edition). Wang, K. (ed.). New York, p. 321-334 368 p. (Methods in Molecular Biology; no. 1223).

Research output: Chapter in Book/Report/Conference proceedingChapter

sweet peppers
Capsicum annuum
Agrobacterium
genetically modified organisms
Capsicum

Research tools: Ethylene detection

Cristescu, S. M., Woltering, E. J., Hermans, C., Harren, F. J. M. & te Lintel Hekkert, B., 2015, Ethylene in plants. Wen, C. K. (ed.). Dordrecht: Springer, p. 263-285

Research output: Chapter in Book/Report/Conference proceedingChapter

2014
2 Citations (Scopus)

Fructan Biosynthesis Regulation and the Production of Tailor-Made Fructan in Plants

van Arkel, J., Sévenier, R., Hakkert, J. C., Bouwmeester, H. J., Koops, A. J. & van der Meer, I. M., 2014, Polysaccharides : Natural Fibers in Food and Nutrition. Benkeblia, N. (ed.). CRC Press, p. 1 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2013

Biological containment strategies for transgenic crops

de Maagd, R. A. & Boutilier, K. A., 2013, Genetically modified and non-genetically modified food supply chains: Co-existence and traceability. Bertheau, Y. (ed.).

Research output: Chapter in Book/Report/Conference proceedingChapter

biocontainment
genetically modified organisms
crops
transgenes
plant development
6 Citations (Scopus)

Hemiterpenoids and Pyrazines in the Odoriferous Urine of the Maned Wolf

Goodwin, T. E., Songsasen, N., Broederdorf, L. J., Burkert, B. A., Joi Chen, C., Jackson, S. R., Keplinger, K. B., Rountree, M. E., Waldrip, Z. J., Wedell, M. E., Desrochers, L. P., Baker, W. K. & Helsper, J. P. F. G., 2013, Chemical Signals in Vertebrates 12. East, M. L. & Dehnhard, M. (eds.). New York [etc.]: Springer, p. 171-184

Research output: Chapter in Book/Report/Conference proceedingChapter

pyrazines
urine
pheromones
insect pheromones
odors
13 Citations (Scopus)

Induction of Germination

Yoneyama, K., Ruyter-Spira, C. P. & Bouwmeester, H. J., 2013, Parasitic Orobanchaceae: Parasitic Mechanisms and Control Strategies. Joel, D. M. & Gressel, J. (eds.). Berlin: Springer Verlag, p. 167-194

Research output: Chapter in Book/Report/Conference proceedingChapter

germination
carotenoids
Orobanchaceae
parasitic plants
isomerases
2 Citations (Scopus)

Strigolactone Biosynthesis and Biology

Zhang, Y., Haider, I., Ruyter-Spira, C. P. & Bouwmeester, H. J., 2013, Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2. de Bruijn, F. J. (ed.). Singapore: Wiley, p. 355-371 1328 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

biosynthesis
Biological Sciences
plant hormones
mechanism of action
rhizosphere

The Large Scale Identification and Quantification of Conjugates of Intact and Gut Microbial Bioconversion Products of Polyphenols.

van der Hooft, J. J. J., de Vos, C. H., Bino, R. J., Mihaleva, V. V., Ridder, L. O., de Roo, N., Jacobs, D. M., van Duynhoven, J. P. M. & Vervoort, J., 2013, Magnetic Resonance in Food Science. Duynhoven, J., Belton, P. S., Webb, G. A. & As, H. (eds.). CBSG/NMC, p. 177-182

Research output: Chapter in Book/Report/Conference proceedingChapter

Bioconversion
Polyphenols
Flavonoids
Metabolites
Cocoa
2012

Acceptance of Natural and Genetically Modified Hypoallergenic Apples by Consumers with an Oral Allergy Syndrome (OAS).

van der Meer, I. M., Schenk, M. F., Fischer, A. R. H., Frewer, L. J., van der Maas, M. P., Smulders, M. J. M. & Gilissen, L. J. W. J., 2012, Multidisciplinary Approaches to Allergies. Gao, Z. S., Shen, H. H., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Zhejiang University Press, p. 401-408 480 p. (Advanced topics in science and technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

Allergen Protein Families and Cross- Reactivity

Gilissen, L. J. W. J. & Gao Zhongshan, 2012, Multidisciplinary Approaches to Allergies. Gao, Z. S., Shen, H. H., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Zhejiang University Press, p. 81-90 480 p. (Advanced topics in science and technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

19 Citations (Scopus)

Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach.

Kastritis, P. L., van Dijk, A. D. J. & Bonvin, A. M., 2012, Computational Drug Discovery and Design . Baron, R. (ed.). New York: Springer Science + Business Media, p. 355-374 (Methods in Molecular Biology ; vol. 819).

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecules
Water
Proteins
Hydrogen bonds
Crystal structure

Fruit Allergy and Genetic and Genomic Tools to select Hypoallergenic Fruit Cultivars

Gao Zhongshan, Yang, Z. W. & Gilissen, L. J. W. J., 2012, Multidisciplinary Approaches to Allergies. Gao, Z. S., Shen, H. H., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Zhejiang University Press, p. 359-383 480 p. (Advanced topics in science and technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)

High-Performance Liquid Chromatography–Mass Spectrometry Analysis of Plant Metabolites in Brassicaceae

de Vos, C. H., Schipper, A. & Hall, R. D., 2012, Plant metabolomics : methods and protocols. Hardy, N. G. & Hall, R. D. (eds.). p. 111-128 (Methods in molecular biology; no. 860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Brassicaceae
spectroscopy
metabolites
liquids
Brassica napus
1 Citation (Scopus)

Immunomodulation by Food

van der Meer, I. M., Mes, J. J., Weijn, A. & Wichers, H. J., 2012, Multidisciplinary Approaches to Allergies. Gao, Z. S., Shen, H. H., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Zhejiang University Press, p. 303-313 480 p. (Advanced topics in science and technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

In Search of Hypoallergenic Birch Trees: Characterization of PR-10 Genes from Eight Betula Species and Detection of Bet v 1 Isoforms in Birch Pollen Using a Combined Genomics-Proteomics Approach

Smulders, M. J. M., Schenk, M. F. & Gilissen, L. J. W. J., 2012, Multidisciplinary Approaches to Allergies. Shen, H. H., Gao, Z. S., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Zhejiang University Press, p. 335-346 480 p. (Advanced topics in science and technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

Betula
proteomics
pollen
Betula pendula
genomics

Kennisbasisthema 7. Technologische ontwikkeling

Janssen, S. J. C. & Angenent, G. C., 2012, Jaarrapportage Kennisbasisonderzoek 2011. [S.l.]: S.n., p. 99-110

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
1 Citation (Scopus)

Multidisciplinary Approaches to Allergy Prevention

Gilissen, L. J. W. J., Gao Zhongshan & Chen, Z., 2012, Multidisciplinary Approaches to Allergies. Gao, Z. S., Shen, H. H., Zheng, M., Frewer, L. J. & Gilissen, L. J. W. J. (eds.). Berlin: Springer, p. 33-55 480 p. (Advanced Topics in Science and Technology in China).

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)

Practical Applications of Metabolomics in Plant Biology

Hall, R. D. & Hardy, N. W., 2012, Plant metabolomics. Hardy, N. G. & Hall, R. D. (eds.). London, p. 1-10 (Methods in molecular biology; no. 860).

Research output: Chapter in Book/Report/Conference proceedingChapter

plant biology
metabolomics
infancy
pasteurization
boiling
9 Citations (Scopus)

Solid Phase Micro-Extraction GC–MS Analysis of Natural Volatile Components in Melon and Rice

Verhoeven, H. A., Jonker, H. H., de Vos, C. H. & Hall, R. D., 2012, Plant metabolomics. Hardy, N. G. & Hall, R. D. (eds.). London, p. 85-99 (Methods in molecular biology; no. 860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Fragrances
Crops
Gas chromatography
Mass spectrometry
Flavors

Strigolactones: A Cry for Help Results in Fatal Attraction. Is Escape Possible?

Ruyter-Spira, C. P., Lopez-Raez, J. A., Cardoso, C., Charnikhova, T., Matusova, R., Kohlen, W., Jamil, M., Bours, R., Verstappen, F. & Bouwmeester, H. J., 2012, Isoprenoid Synthesis in Plants and Microorganisms. Bach, T. J. & Rohmer, M. (eds.). New York: Springer Science + Business Media, p. 199-211

Research output: Chapter in Book/Report/Conference proceedingChapter

parasitic plants
mycorrhizal fungi
phosphates
ecological balance
isoprenoids
2011
3 Citations (Scopus)

Breeding of Hypoallergenic Fruits

Gao, Z. S. & Gilissen, L. J. W. J., 2011, Breeding for Fruit Quality. Jenks, M. A. & Bebeli, P. J. (eds.). Hoboken, NJ, USA: John Wiley and Sons, p. 105-126

Research output: Chapter in Book/Report/Conference proceedingChapter

21 Citations (Scopus)

Crops and food – a role for metabolomics?

Stewart, D. W., Hall, R. D. & Fraser, P., 2011, The biology of plant metabolomics. Oxford: Blackwell/Wiley, p. 181-217 405 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Citations (Scopus)

Metabolic Pathway Inference from Time Series Data: A Non Iterative Approach

Astola, L. J., Groenenboom, M. A. C., Gomez Roldan, M. V., van Eeuwijk, F. A., Hall, R. D., Bovy, A. G. & Molenaar, J., 2011, Pattern Recognition in Bioinformatics : 6th IAPR International Conference, PRIB 2011, Delft, The Netherlands, 2-4 November 2011. Loog, M. & Wessels, L. (eds.). Berlin [etc.], p. 97-108 (Lecture notes in computer science; no. 7036).

Research output: Chapter in Book/Report/Conference proceedingChapter

time series
reaction rate
method
secondary metabolite
metabolite
17 Citations (Scopus)

Metabolomics of a model fruit: tomato

de Vos, R. C. H., Hall, R. D. & Moing, A., 2011, The Biology of Plant Metabolomics . Annual Plant Reviews. Oxford: Blackwell/Wiley, p. 109-156 405 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

metabolomics
tomatoes
fruits
phenotype
plant physiology
4 Citations (Scopus)

Microarray-Based Identification of Transcription Factor Target Genes

Gorte, M., Horstman, A., Page, R. B., Heidstra, R., Stromberg, A. & Boutilier, K. A., 2011, Plant Transcription Factors: Methods and Protocols.. Yuan, L. & Perry, S. E. (eds.). p. 119-141 347 p. (Methods in Molecular Biology; no. 754).

Research output: Chapter in Book/Report/Conference proceedingChapter

transcription factors
statistical analysis
genes
DNA
plant identification
49 Citations (Scopus)

Plant Metabolomics and Its Potential for Systems Biology Research: Background Concepts, Technology, and Methodology

Allwood, J. W., de Vos, C. H., Moing, A., Deborde, C., Erban, A., Kopka, J., Goodacre, R. & Hall, R. D., 2011, Methods in Systems Biology. Jameson, D., Verma, M. & Westerhoff, H. V. (eds.). p. 299-336 (Methods in Enzymology; no. 500).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mass spectrometry
Throughput
Liquid chromatography
Metabolites
Gene expression
30 Citations (Scopus)

Plant Metabolomics in a nutshell: Potential and Future Challenges

Hall, R. D., 2011, The biology of plant metabolomics. hall, R. D. (ed.). Oxford: Blackwell/Wiley, Vol. 43. p. 1-24

Research output: Chapter in Book/Report/Conference proceedingChapter

metabolomics
travel
roads
chemical composition
metabolites

The role of metabolomics in plant studies – views on sampling and data acquisition

Allwood, J. W., Moing, A., de Vos, C. H., Deborde, C., Kokpa, J. & Hall, R. D., 2011, Methods in Systems Biology. Westerhoff, H., Verma, M. & Jameson, D. (eds.). (Methods in Systems Biology; no. 500).

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Citations (Scopus)

Visualizing and characterizing In Vivo DNA-Binding Events and Direct Target Genes of Plant Transcription Factors.

Muino, J. M., Angenent, G. C. & Kaufmann, K., 2011, Plant Transcription Factors, Methods in Molecular Biology. Yuan, L. & Perry, S. E. (eds.). p. 293-305 13 p. (754; no. 17).

Research output: Chapter in Book/Report/Conference proceedingChapter

Plant Genes
Transcription Factors
Genome
DNA
Computational Biology
27 Citations (Scopus)

Yeast Protein–Protein Interaction Assays and Screens

de Folter, S. & Immink, G. H., 2011, Plant Transcription Factors, Methods in Molecular Biology. Yuan, L. & Perry, S. E. (eds.). p. 145-165 21 p. (Methods in Molecular Biology; no. 754).

Research output: Chapter in Book/Report/Conference proceedingChapter

Yeasts
Proteins
Transcription Factors
Reporter Genes
2010
19 Citations (Scopus)

Strategies to optimise the flavonoid content of tomato fruit

Bovy, A. G., Gomez-Roldan, M. V. & Hall, R. D., 2010, The Handbook of Polyphenols. Santos-Buelga, C., Escribano-Bailon, M. T. & Lattanzio, V. (eds.). p. 138-162 252 p.

Research output: Chapter in Book/Report/Conference proceedingChapter