Research Output 1951 2020

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2019

Scalable workflows and reproducible data analysis for genomics

Strozzi, F., Janssen, R., Wurmus, R., Crusoe, M. R., Githinji, G., Di Tommaso, P., Belhachemi, D., Möller, S., Smant, G., de Ligt, J. & Prins, P., 6 Jul 2019, Evolutionary Genomics: Statistical and Computational Methods. Humana Press Inc., p. 723-745 (Methods in Molecular Biology; vol. 1910).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
Workflow
Genomics
Software
Language
Gene Expression Profiling

Systems genetics for evolutionary studies

Prins, P., Smant, G., Arends, D., Mulligan, M. K., Williams, R. W. & Jansen, R. C., 6 Jul 2019, Evolutionary Genomics: Statistical and Computational Methods. Anisimova, M. (ed.). New York: Humana Press Inc., p. 635-652 (Methods in Molecular Biology; vol. 1910).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
Quantitative Trait Loci
Proteins
RNA
Gene Expression
High-Throughput Nucleotide Sequencing
2017

Soil Biodiversity and Ecosystem Functioning

Bardgett, R. D., De Vries, F. T. & van der Putten, W. H., Apr 2017, Microbial Biomass: A Paradigm Shift in Terrestrial Biochemistry. Tate, K. T. (ed.). London, UK: World Scientific Publishing, p. 119-140

Research output: Chapter in Book/Report/Conference proceedingChapter

2015

Ecosystem Services Provided by Soil Life

van der Putten, W. H. & Wall, D. H., 2015, Routledge Handbook of Ecosystem Services. Potschin, M., Haines-Young, R., Fish, R. & Turner, K. (eds.). London and New York: Routledge, p. 415-420 640 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Phytopathogenic Nematodes

Helder, J., Vervoort, M. T. W., van Megen, H. H. B., Rybarczyk-Mydlowska, K., Quist, C. W., Smant, G. & Bakker, J., 2015, Principles of Plant-Microbe Interactions. Lugtenberg, B. (ed.). Springer, 443 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

plant parasitic nematodes
Nematoda
soil
parasites
rhizosphere
2014

Netwerk van metingen brengt bodemaaltjes in beeld

Beitema, N. & Vervoort, M. T. W., 2014, ERGO: een terugblik. Reflecties van onderzoekers en van andere betrokkenen op het onderzoeksprogramma Ecologie Rond Genetisch Gemodificeerde Organismen 2006-2012. Beintema, N. (ed.). Den Haag: NWO, p. 31-33

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
2013

Bodemleven op Planken Wambuis

van der Putten, W. H. & Bezemer, T. M., 2013, Wild en Bijster Land: Planken Wambuis:. Abels, P., Bosch, M., Crans, A. & Frijns, M. (eds.). Enschede/Doetinchem: AFdH, p. 362-383 448 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access

Root-knot nematodes

Karssen, G., Wesemael, W. M. L. & Moens, M., 2013, Plant Nematology. Perry, R. N. & Moens, M. (eds.). Wallingford, UK, p. 73-108 512 p. (2).

Research output: Chapter in Book/Report/Conference proceedingChapter

nematode biology
root-knot nematodes
plant protection
Nematoda
nematode control
2012

Bodemleven

van der Putten, W. H., 2012, Eco-engineering: een symbiose van harde en zachte systemen. van Bohemen, H. (ed.). Delft: VSSD, p. 112-114 254 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Environmental Impact of Chemicals, Biobased Molecules & Processes (interview met dr. ir. J. Helder)

van de Graaf, A. & Helder, J., 2012, BE-Basic Annual report 2011. de Nobel, N. & Brouwer, B. (eds.). p. 16-17

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
2 Citations (Scopus)

Genetical Genomics for Evolutionary Studies

Prins, J. C. P., Smant, G. & Jansen, R. C., 2012, Evolutionary Genomics. Statistical and Computational Methods, Volume 2. Anisimova, M. (ed.). p. 469-485 556 p. (Methods in Molecular Biology; no. 856).

Research output: Chapter in Book/Report/Conference proceedingChapter

quantitative trait loci
genomics
gene expression
explosions
protein-protein interactions

Introduction to section 1 - The living soil and ecosystem services

Ritz, K. & van der Putten, W. H., 2012, Soil ecology and ecosystem services. Bardgett, R. D., Wall, D. H., Behan-Pelletier, V., Herrick, J. E., Jones, T. H., Ritz, K., Six, J., Strong, D. R. & van der Putten, W. H. (eds.). Oxford: Oxford University Press, p. 5-6

Research output: Chapter in Book/Report/Conference proceedingChapter

Introduction to section 2 - From genes to ecosystem services

van der Putten, W. H. & Ritz, K., 2012, Soil ecology and ecosystem services. Bardgett, R. D., Wall, D. H., Behan-Pelletier, V., Herrick, J. E., Jones, T. H., Ritz, K., Six, J., Strong, D. R. & van der Putten, W. H. (eds.). Oxford: Oxford University Press, p. 63-64

Research output: Chapter in Book/Report/Conference proceedingChapter

23 Citations (Scopus)

Nematode Effector Proteins: Targets and Functions in Plant Parasitism

Rosso, M. N., Hussey, R. S., Davis, E. L., Smant, G., Baum, T. J., Abad, P. & Mitchum, M. G., 2012, Effectors in Plant-Microbe Interactions. Martin, F. & Kamoun, S. (eds.). John Wiley and Sons, p. 327-354 426 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Citations (Scopus)

Scalable Computing for Evolutionary Genomics

Prins, J. C. P., Belhachemi, D., Möller, S. & Smant, G., 2012, Evolutionary Genomics. Statistical and Computational Methods, Volume 2. Anisimova, M. (ed.). p. 529-545 556 p. (Methods in Molecular Biology; no. 856).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bioinformatics
Computer operating systems
Software packages
Pipelines
Cluster computing
2 Citations (Scopus)

Sharing Programming Resources Between Bio* Projects Through Remote Procedure Call and Native Call Stack Strategies

Prins, J. C. P., Goto, N., Yates, A., Gautier, L., Willis, S., Fields, C. & Katayama, T., 2012, Evolutionary Genomics. Statistical and Computational Methods, Volume 2. Anisimova, M. (ed.). p. 513-527 556 p. (Methods in Molecular Biology; no. 856).

Research output: Chapter in Book/Report/Conference proceedingChapter

Computer programming languages
Interfaces (computer)
Windows operating system
Computer software reusability
Ruby

Synthesis of section 1 - The living soil and ecosystem services

Ritz, K. & van der Putten, W. H., 2012, Soil ecology and ecosystem services. Bardgett, R. D., Wall, D. H., Behan-Pelletier, V., Herrick, J. E., Jones, T. H., Ritz, K., Six, J., Strong, D. R. & van der Putten, W. H. (eds.). Oxford: Oxford University Press, p. 59-60

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthesis of section 2 - From genes to ecosystem services

van der Putten, W. H. & Ritz, K., 2012, Soil ecology and ecosystem services. Wall, D. H., Behan-Pelletier, V., Herrick, J. E., Jones, T. H., Ritz, K., Six, J., Strong, D. R., van der Putten, W. H. & Bardgett, R. D. (eds.). Oxford: Oxford University Press, p. 111-112

Research output: Chapter in Book/Report/Conference proceedingChapter

2011

Microbial ecology and nematode control in natural ecosystems. Building coherence between microbial ecology and molecular mechanisms

Costa, S. R., van der Putten, W. H. & Kerry, B. R., 2011, Biological control of plant-parasitic nematodes: Building coherence between microbial ecology and molecular mechanisms. Davies, K. & Spiegel, Y. (eds.). p. 39-64 311 p. (Progress in Biological Control; no. 11).

Research output: Chapter in Book/Report/Conference proceedingChapter

microbial ecology
nematode
ecosystem
parasitic plant
food web

Phylogency and Evolution of Nematodes

Bert, W., Karssen, G. & Helder, J., 2011, Genomics and Molecular Genetics of Plant-Nematode Interactions. Jones, J., Fenoll, C. & Gheysen, G. (eds.). Londen: Springer, p. 45-59

Research output: Chapter in Book/Report/Conference proceedingChapter

Pratylenchus
Meloidogyne
plant parasitic nematodes
root-knot nematodes
Globodera

Suppression of Plant Defences by Nematodes

Smant, G. & Jones, J., 2011, Genomics and Molecular Genetics of Plant-Nematode Interactions. Jones, J., Fenoll, C. & Gheysen, G. (eds.). Londen: Springer, p. 273-286

Research output: Chapter in Book/Report/Conference proceedingChapter

Nematoda
plant parasitic nematodes
microbial detection
animal parasitic nematodes
parasites
4 Citations (Scopus)

Survival of Plant-parasitic Nematodes inside the Host

Lozano, J. & Smant, G., 2011, Molecular and Physiological Basis of Nematode Survival. Perry, R. N. & Wharton, D. A. (eds.). Londen: CABI, p. 28-65 320 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

The Role of Plant Hormones in Nematode Feeding Cell Formation

Goverse, A. & Bird, D., 2011, Genomics and Molecular Genetics of Plant-Nematode Interactions. Jones, J., Fenoll, C. & Gheysen, G. (eds.). Londen: Springer, p. 325-347

Research output: Chapter in Book/Report/Conference proceedingChapter

plant hormones
Nematoda
cells
nematode infections
root-knot nematodes
2010

Biological Invasions and Soil Biodiversity

van der Putten, W. H. & Hol, W. H. G., 2010, European Atlas Of Soil Biodiversity. Luxemburg: European Union, p. 58-59 128 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access

Invasieve exoten in bossen

Vanhellemont, M., van der Putten, W. H. & Verheyen, K., 2010, Bosecologie en bosbeheer. ACCO, p. 469-476

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access

Nematode-Nematoden

Karssen, G., Gremers, H. J. W. M. & Bongers, A. M. T., 2010, De Nederlandse Biodiversiteit -Nederlandse fauna 10. Noordwijk, J., Kleukers, R. M. J. C., van Nieukerken, E. J. & van Loon, A. J. (eds.). Leiden: Nederlands Centrum voor Biodiversiteit Naturalis & European Invertebrate Survey, p. 153-156 510 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2009

Applications of community ecology approaches in terrestrial ecosystems: local problems, remote causes

van der Putten, W. H., 2009, Community Ecology. Processes, Models, and Applications. Verhoef, H. A. & Morin, P. J. (eds.). Oxford: University Press, 288 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Een nieuwe iepenwortelparasiet

Karssen, G., 2009, Iep of Olm, karakterboom van de Lage Landen. Heybroek, H. M., Goudswaard, L. & Kaljee, H. (eds.). Zeist: KNNV uitgeverij, p. 132 272 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Exoten en invasieve soorten: nieuwe uitdagingen voor het natuurbeheer

Quist, C. W. & Weeda, E. J., 2009, Natuur als nooit tevoren. Beschouwingen over natuurbeheer in Nederland. Schaminée, J. & Weeda, E. (eds.). Zeist, p. 167-187 190 p. (Vegetatiekundige monografieën; no. 2).

Research output: Chapter in Book/Report/Conference proceedingChapter

34 Citations (Scopus)

Indices Developed Specifically for analysis of Nematode Assemblages

Ferris, H. & Bongers, A. M. T., 2009, Nematodes as Environmental Indicators. Wilson, M. J. & Kakouli-Duarte, T. (eds.). CAB International, p. 124-145 326 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Influencia de los insectos de suelo sobre las relaciones planta-herbivoro-parasitoide

Soler, R., Bezemer, T. M. & Harvey, J. A., 2009, Relaciones entre organismos en los sistemas hosepederos-parasitoides simbiontes. Basso, C. & Grille, G. (eds.). Montevideo Uruguay: Universidad De La Republica, p. 81-108 226 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Microbial biodiversity and ecosystems funtioning under controlled conditions in the wild

Bell, T. G., Gessner, M. O., Griffiths, R. I., McLaren, J. R., Morin, P. J., Heijden, M. & van der Putten, W. H., 2009, Biodiversity, Ecosystem Functioning, and Human Wellbeing: An Ecological and Economic Perspective. Naeem, S., Bunker, D. E., Hector, A., Loreau, M. & Perrings, C. (eds.). Oxford: Oxford University Press, p. 121-133 384 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

8 Citations (Scopus)

Molecular Tools for Analysing Nematode Assemblages

Neilson, R., Donn, S., Griffiths, B., Daniell, T., Rybarczyk-Mydlowska, K. D., van den Elsen, S. J. J., Mooijman, P. J. W. & Helder, J., 2009, Nematodes as Environmental Indicators. Wilson, M. & Khakouli-Duarte, T. (eds.). CAB International, p. 188-207 326 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

12 Citations (Scopus)

Resistant Plant Responses

Finkers-Tomczak, A. M., Koropacka, K. B., Smant, G., Goverse, A. & Bakker, E. H., 2009, Cell biology of plant nematode parasitism. Berg, R. H. & Taylor, C. G. (eds.). Berlin Heidelberg, p. 83-113 (Plant cell monographs; no. 15).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
plant response
Nematoda
pathogens
coevolution
plant protection
42 Citations (Scopus)

Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism Among Nematodes

Mitreva, M., Smant, G. & Helder, J., 2009, Horizon Gene Transfer: Genomes in Flux. Gogarten, M. B., Gogarten, J. P. & Olendzenski, L. C. (eds.). p. 517-535 551 p. (Methods in Molecular Biology; no. 532).

Research output: Chapter in Book/Report/Conference proceedingChapter

parasitism
cellulases
Nematoda
soil bacteria
plant parasitic nematodes
52 Citations (Scopus)

The Role of Nematodes in Ecosystems

Yeates, G. W., Ferris, H., Moens, T. & van der Putten, W. H., 2009, Nematodes as Environmental Indicators. Wilson, M. J. & Kakouli-Duarte, T. (eds.). CAB International, p. 1-44 326 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2008

Getting Plant-Soil Feedback out of the Greenhouse: Experimental and Conceptual Approaches

Kulmatiski, A. & Kardol, P., 2008, Progress in Botany. Lüttige, U., Beyschlag, W. & Murata, J. (eds.). Heidelberg, 480 p. (Progress in Botany; no. 69).

Research output: Chapter in Book/Report/Conference proceedingChapter

24 Citations (Scopus)

Linking above- and belowground herbivory

Johnson, S. N., Bezemer, T. M. & Jones, T. H., 2008, Root Feeders an Ecosystem Perspective. Johnson, S. N. & Murray, P. J. (eds.). Trowbridge: CABI, p. 153-170

Research output: Chapter in Book/Report/Conference proceedingChapter

Meloidogyne minor - Gele plek wortelknobbelnematode

Mulder, A. & Karssen, G., 2008, Aardappel ziektenboek. Mulder, A. & Turkensteen, L. J. (eds.). Den Haag: Aardappelwereld, p. 178-179 390 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2007

Metals affect secondary stress sensitivity of nematode field populations

van der Wurff, A. W. G., Kools, S. A. E., Boivin, M. E. Y., van den Brink, P. J., van Megen, H. H. B., Riksen, J. A. G., Doroszuk, A. & Kammenga, J. E., 2007, Exposure and ecological effects of toxic mixtures at field-relevant concentrations: Model validation and integration of the SSEO programme. posthuma, L. & Vijver, M. G. (eds.). Bilthoven, p. 115-117 199 p. (RIVM Rapporten; no. 860706002/2007).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
2006

Chemical communication between roots and shoots: Towards an integration of aboveground and belowground induced responses in plants

van Dam, N. M. & Bezemer, T. M., 2006, Chemical ecology : from gene to ecosystem: Proceedings of the Frontis Workshop on Chemical Ecology: from Gene to Ecosystem, Wageningen, The Netherlands 19-23 March 2005. Dicke, M. & Takken, W. (eds.). Nederland, p. 127-143 (Wageningen UR Frontis Series; no. 16).

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
4 Citations (Scopus)

Order Mermithida and families incertae sedis (Bastianiidae and Rhabdolaimidae)

Holovachov, O. V. & de Ley, P., 2006, Freshwater nematodes: ecology and taxonomy. Eyualem, A., Traunspurger, W. & Andrássy, I. (eds.). Oxford, UK: CABI Publishing, p. 722-735 752 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Order Plectida

Holovachov, O. V. & de Ley, P., 2006, Freshwater nematodes: ecology and taxonomy. Eyualem, A., Traunspurger, W. & Andrássy, I. (eds.). Oxford, UK: CABI Publishing, p. 611-647 752 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

87 Citations (Scopus)

Root-knot nematodes

Karssen, G. & Moens, M., 2006, Plant Nematology. Perry, R. N. & Moens, M. (eds.). Wallingford: CABI, p. 59-90

Research output: Chapter in Book/Report/Conference proceedingChapter

2005

Identification of pathogenicity-related secretions from root knot and cyst nematodes

Helder, J., 2005, 100 Technology Offers stemming from EU Biotechnology RTD results. Brussel: European Commission, p. 216-219 325 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Linking cDNA-AFLP-based gene expression patterns and ESTs

Qin Ling, Prins, J. C. P. & Helder, J., 2005, Differential display methods and protocols. Totowa, (Methods in molecular biology; no. 317).

Research output: Chapter in Book/Report/Conference proceedingChapter

Mechanisms Involved in Plant Resistance to Nematodes

Bakker, E. H., Dees, R. H. L., Bakker, J. & Goverse, A., 2005, Multigenic and induced systemic resistance in plants. Tuzun, S. & Bent, E. (eds.). Springer, p. 314-334

Research output: Chapter in Book/Report/Conference proceedingChapter

Plant-soil feedback and soil biodiversity affect the compostion of plant communities

van der Putten, W. H., 2005, Biological diversity and function in soils. Bardgett, R. D., Usher, M. B. & Hopkins, D. W. (eds.). Cambridge, p. 250-272 22 p. (Ecological reviews).

Research output: Chapter in Book/Report/Conference proceedingChapter

2004

Cascading effects of deforestation on ecosystem services across soils and freshwater and marine sediments

Ineson, P., Levin, L. A., Kneib, R. T., Hall Jr., R. O., Weslawski, J. M., Bardgett, R. D., Wardle, D. A., Wall, D. H., van der Putten, W. H. & Zadeh, H., 2004, Sustaining biodiversity and ecosystem services in soils and sediments. Washington, p. 225-248 (SCOPE report; no. 64).

Research output: Chapter in Book/Report/Conference proceedingChapter

Ecosystem processes in natural and managed terrestrial soils and the role of soil organisms in the sustainable delivery of ecosystem goods and services

van der Putten, W. H., Anderson, J. M., Bardgett, R. D., Behan-Pelletier, V., Bignell, D. E., Brown, G. G., Brown, V. K., Brussaard, L., Hunt, H. W., Ineson, P., Jones, T. H., Lavelle, P., Paul, E. A., St. John, M., Wardle, D. A., Wojtowicz, T. & Wall, D. H., 2004, Sustaining biodiversity and ecosystem services in soils and sediments. Washington, p. 15-43 (SCOPE report; no. 64).

Research output: Chapter in Book/Report/Conference proceedingChapter