Research Output 2005 2020

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2020

Development and evaluation of two TaqMan assays for generic detection of Dickeya species

Zijlstra, C., De Haas, L. G., Krijger, M., Verstappen, E., Warris, S., de Haan, E. & van der Wolf, J., Jan 2020, In : European Journal of Plant Pathology. 156, p. 311-316 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Dickeya
assays
DNA
Erwinia chrysanthemi
potatoes
2019
3 Citations (Scopus)

Comparative analysis of repetitive sequences among species from the potato and the tomato clades

Gaiero Guadagna, P., Vaio, M., Peters, S. A., Schranz, M. E., de Jong, J. H. S. G. M. & Speranza, P. R., 15 Feb 2019, In : Annals of Botany. 123, 3, p. 521-532

Research output: Contribution to journalArticleAcademicpeer-review

repetitive sequences
tomatoes
potatoes
genome
Solanum etuberosum
2 Citations (Scopus)

Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum

van de Vossenberg, B. T. L. H., Warris, S., Nguyen, H. D. T., van Gent-Pelzer, M. P. E., Joly, D. L., van de Geest, H. C., Bonants, P. J. M., Smith, D. S., Lévesque, A. C. & van der Lee, T. A. J., 17 Jun 2019, In : Scientific Reports. 9, 1, 8672.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Synchytrium endobioticum
Chytridiomycota
lifestyle
genomics
fungi
3 Citations (Scopus)

Comprehensive phenotyping reveals interactions and functions of Arabidopsis thaliana TCP genes in yield determination

van Es, S. W., van der Auweraert, E., Rodrigues da Silveira, S., Angenent, G. C., van Dijk, A. D. J. & Immink, G. H., 22 Mar 2019, In : The Plant Journal.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Arabidopsis
seed yield
Arabidopsis thaliana
vegetative growth
phenotype
3 Citations (Scopus)

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

Lind, A. L., Lai, Y. Y. Y., Mostovoy, Y., Holloway, A. K., Iannucci, A., Mak, A. C. Y., Fondi, M., Orlandini, V., Eckalbar, W. L., Milan, M., Rovatsos, M., Kichigin, I. G., Makunin, A. I., Johnson Pokorná, M., Altmanová, M., Trifonov, V. A., Schijlen, E., Kratochvíl, L., Fani, R., Velenský, P. & 10 others, Rehák, I., Patarnello, T., Jessop, T. S., Hicks, J. W., Ryder, O. A., Mendelson, J. R., Ciofi, C., Kwok, P. Y., Pollard, K. S. & Bruneau, B. G., 29 Jul 2019, In : Nature Ecology and Evolution. 3, 8, p. 1241-1252

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
lizard
lizards
genome
reptile
anticoagulant

Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing

Zwart, M. P., Ali, G., van Strien, E. A., Schijlen, E. G. W. M., Wang, M., van der Werf, W. & Vlak, J. M., 17 Sep 2019, In : Viruses. 11, 9, 872.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biological Control Agents
Central Asia
Nucleopolyhedrovirus
High-Throughput Nucleotide Sequencing
Spodoptera
1 Citation (Scopus)
Protein-protein Interaction
Contact
Proteins
Protein
Mutation

maTE: discovering expressed interactions between microRNAs and their targets

Yousef, M., Abddallah, L. & Allmer, J., 15 Oct 2019, In : Bioinformatics. 35, 20, p. 4020-2028 btz204.

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA
MicroRNAs
Gene expression
Classifiers
Genes

Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)

Linsmith, G., Rombauts, S., Montanari, S., Deng, C. H., Celton, J. M., Guérif, P., Liu, C., Lohaus, R., Zurn, J. D., Cestaro, A., Bassil, N. V., Bakker, L. V., Schijlen, E., Gardiner, S. E., Lespinasse, Y., Durel, C. E., Velasco, R., Neale, D. B., Chagné, D., Van de Peer, Y. & 2 others, Troggio, M. & Bianco, L., Dec 2019, In : GigaScience. 8, 12, giz138.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Pyrus
Haploidy
Chromosomes
Genes
Genome
1 Citation (Scopus)

Spatial distribution of soil nematodes relates to soil organic matter and life strategy

Quist, C. W., Gort, G., Mooijman, P., Brus, D. J., van den Elsen, S., Kostenko, O., Vervoort, M., Bakker, J., van der Putten, W. H. & Helder, J., 1 Sep 2019, In : Soil Biology and Biochemistry. 136, 107542.

Research output: Contribution to journalArticleAcademicpeer-review

soil nematodes
nematode
soil organic matter
Soil
Nematoda
1 Citation (Scopus)

Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae)

Bogdanovic, M., Cankar, K., Todorovic, S., Dragicevic, M., Simonovic, A., van Houwelingen, A. M. M. L., Schijlen, E. G. W. M., Schipper, A., Gagneul, D., Hendriks, T., Quillet, M-C., Bouwmeester, H. J., Bosch, H. J. & Beekwilder, M. J., Mar 2019, In : Industrial Crops and Products. 129, p. 253-260

Research output: Contribution to journalArticleAcademicpeer-review

Cichorium intybus
chicory
sesquiterpenoid lactones
Asteraceae
biosynthesis
2018
33 Citations (Scopus)

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., van de Geest, H., Hesselink, T., Van Laere, K., Debray, K., Balzergue, S., Thouroude, T., Chastellier, A., Jeauffre, J., Voisine, L., Gaillard, S. & 21 others, Borm, T. J. A., Arens, P., Voorrips, R. E., Maliepaard, C., Neu, E., Linde, M., Le Paslier, M. C., Bérard, A., Bounon, R., Clotault, J., Choisne, N., Quesneville, H., Kawamura, K., Aubourg, S., Sakr, S., Smulders, M. J. M., Schijlen, E., Bucher, E., Debener, T., De Riek, J. & Foucher, F., 2018, In : Nature Plants. 4, p. 473-484

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Rosa chinensis
Rosa
genome
plant spines
doubled haploids
4 Citations (Scopus)

Comparative analysis of binding patterns of MADS-domain proteins in Arabidopsis thaliana

Aerts, N., de Bruijn, S., van Mourik, H., Angenent, G. C. & van Dijk, A. D. J., 25 Jun 2018, In : BMC Plant Biology. 18, 1, 131.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Arabidopsis thaliana
transcription factors
DNA-binding domains
protein binding
ecotypes
38 Citations (Scopus)

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

van Velzen, R., Holmer, R., Bu, F., Rutten, L. J. J., van Zeijl, A. L., Liu, W., Santuari, L., Cao, Q., Sharma, T., Shen, D., Purwana Roswanjaya, Y., Wardhani, T., Seifi Kalhor, M., Jansen, J., van den Hoogen, D. J., Güngör, B., Hartog, M. V., Hontelez, J., Verver, J., Yang, W-C. & 11 others, Schijlen, E. G. W. M., Repin, R., Schilthuizen, M., Schranz, M. E., Heidstra, R., Miyata, K., Fedorova, E., Kohlen, W., Bisseling, A. H. J., Smit, S. & Geurts, R., 15 May 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 20, p. E4700-E4709

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Parasponia
Rhizobium
symbiosis
nodulation
genomics
1 Citation (Scopus)

Correcting palindromes in long reads after whole-genome amplification

Warris, S., Schijlen, E. G. W. M., van de Geest, H. C., Vegesna, R., Hesselink, T., te Lintel Hekkert, B., Sanchez Perez, G. F., Medvedev, P., Makova, K. D. & de Ridder, D., 6 Nov 2018, In : BMC Genomics. 19, 798.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genome
DNA
Chromosomes
Technology
1 Citation (Scopus)

Development of Simple Sequence Repeat Markers in Hazelnut (Corylus avellana L.) by Next-Generation Sequencing and Discrimination of Turkish Hazelnut Cultivars

Öztürk, S. C., Göktay, M., Allmer, J., Doğanlar, S. & Frary, A., Dec 2018, In : Plant Molecular Biology Reporter. 36, 5-6, p. 800–811

Research output: Contribution to journalArticleAcademicpeer-review

Corylus colurna
Corylus
Corylus avellana
hazelnuts
Microsatellite Repeats
2 Citations (Scopus)

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom

Demirci, S., Peters, S. A., de Ridder, D. & van Dijk, A. D. J., 1 Aug 2018, In : Plant Journal. 95, 4, p. 686-699 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lycopersicon esculentum
Zea mays
Arabidopsis
nucleotide sequences
tomatoes
3 Citations (Scopus)
cauliflower
ambient temperature
gene
curds (plant)
flowering
11 Citations (Scopus)

Engineering de novo anthocyanin production in Saccharomyces cerevisiae

Levisson, M., Patinios, C., Hein, S., de Groot, P. A., Daran, J. M., Hall, R. D., Martens, S. & Beekwilder, J., 3 Jul 2018, In : Microbial Cell Factories. 17, 1, 103.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Anthocyanins
Yeast
Saccharomyces cerevisiae
Glucosides
Yeasts
18 Citations (Scopus)

Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Zeng, T., Holmer, R., Hontelez, J., te Lintel-Hekkert, B., Marufu, L., de Zeeuw, T., Wu, F., Schijlen, E., Bisseling, T. & Limpens, E., May 2018, In : The Plant Journal. 94, 3, p. 411-425

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
mycorrhizal fungi
Fungi
symbiosis
Symbiosis
host plants
1 Citation (Scopus)

Intact DNA purified from flow-sorted nuclei unlocks the potential of next-generation genome mapping and assembly in Solanum species

Gaiero, P., Šimková, H., Vrána, J., Santiñaque, F. F., López-Carro, B., Folle, G. A., van de Belt, J., Peters, S. A., Doležel, J. & de Jong, H., 1 Jan 2018, In : MethodsX. 5, p. 328-336

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Solanum
Chromosome Mapping
Genes
DNA
Molecular Weight
24 Citations (Scopus)

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity

Mommer, L., Cotton, A., Raaijmakers, J. M., Termorshuizen, A. J., van Ruijven, J., Hendriks, M., van Rijssel, S., van de Mortel, J. E., van der Paauw, J. W. M., Schijlen, E. G. W. M., Smit-Tiekstra, A., Berendse, F., de Kroon, H. & Dumbrell, A. J., Apr 2018, In : New Phytologist. 218, 2, p. 542-553

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Biodiversity
Fungi
Soil
biodiversity
fungi
8 Citations (Scopus)
Open Access
metabolome
Phaeodactylum tricornutum
Bacillariophyceae
proteome
transcriptome
1 Citation (Scopus)

Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition

Cochran, A. T., Bauer, J., Metcalf, J. L., Lovecka, P., de Jong, M. S., Warris, S., Mooijman, P. J. W., van der Meer, I. M., Knight, R. & Pilon-Smits, E. A. H., 2018, In : Phytobiomes Journal. 2, 2, p. 82-91

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
selenium
rhizosphere
species diversity
hyperaccumulators
selenites

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Warris, S., Timal, N. R. N., Kempenaar, M., Poortinga, A. M., van de Geest, H., Varbanescu, A. L. & Nap, J. P., 1 Jan 2018, In : PLoS ONE. 13, 1, e0190279.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Boidae
Python
Sequence Alignment
sequence alignment
Program processors
52 Citations (Scopus)

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Nishiyama, T., Sakayama, H., de Vries, J., Buschmann, H., Saint-Marcoux, D., Ullrich, K. K., Haas, F. B., Vanderstraeten, L., Becker, D., Lang, D., Vosolsobě, S., Rombauts, S., Wilhelmsson, P. K. I., Janitza, P., Kern, R., Heyl, A., Rümpler, F., Villalobos, L. I. A. C., Clay, J. M., Skokan, R. & 40 others, Toyoda, A., Suzuki, Y., Kagoshima, H., Schijlen, E., Tajeshwar, N., Catarino, B., Hetherington, A. J., Saltykova, A., Bonnot, C., Breuninger, H., Symeonidi, A., Radhakrishnan, G. V., Van Nieuwerburgh, F., Deforce, D., Chang, C., Karol, K. G., Hedrich, R., Ulvskov, P., Glöckner, G., Delwiche, C. F., Petrášek, J., Van de Peer, Y., Friml, J., Beilby, M., Dolan, L., Kohara, Y., Sugano, S., Fujiyama, A., Delaux, P. M., Quint, M., Theißen, G., Hagemann, M., Harholt, J., Dunand, C., Zachgo, S., Langdale, J., Maumus, F., Van Der Straeten, D., Gould, S. B. & Rensing, S. A., 12 Jul 2018, In : Cell. 174, 2, p. 448-464.e24

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chara
Embryophyta
Genes
Genome
Charophyceae
6 Citations (Scopus)

Tulipa gesneriana and Lilium longiflorum PEBP Genes and Their Putative Roles in Flowering Time Control

Leeggangers, H. A. C. F., Rosilio-Brami, T., Nadal Bigas, J., Rubin, N., van Dijk, A. D. J., Nunez de Caceres Gonzalez, F. F., Saadon-Shitrit, S., Nijveen, H., Hilhorst, H. W. M., Immink, G. H. & Zaccai, M., Jan 2018, In : Plant and Cell Physiology. 59, 1, p. 90-106

Research output: Contribution to journalArticleAcademicpeer-review

Tulipa
Tulipa gesneriana
Lilium
Lilium longiflorum
Ethanolamine
2017
43 Citations (Scopus)

A footprint of desiccation tolerance in the genome of Xerophyta viscosa

Dias Costa, M. C., Silva Artur, M. A., Maia de Oliveira, J., Jonkheer, E., Derks, M., Nijveen, H., Williams, B., Mundree, S., Jiménez-Gómez, J. M., Hesselink, T., Schijlen, E. G. W. M., Ligterink, W., Oliver, M. J., Farrant, J. M. & Hilhorst, H. W. M., 27 Mar 2017, In : Nature Plants. 3, 10 p., 17038.

Research output: Contribution to journalArticleAcademicpeer-review

desiccation (plant physiology)
genome
dehydration (animal physiology)
seeds
seed maturation
13 Citations (Scopus)

An interactomics overview of the human and bovine milk proteome over lactation

Zhang, L., van Dijk, A-J. & Hettinga, K., 2017, In : Proteome Science. 15, 1.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Human Milk
Proteome
Lactation
Milk
Milk Proteins
13 Citations (Scopus)

Botryococcus braunii strains compared for biomass productivity, hydrocarbon and carbohydrate content

Gouveia, J. D. G., Ruiz, J., van den Broek, B., Hesselink, T., Peters, S. A., Kleinegris, D. M. M., Smith, A. G., van der Veen, D., Barbosa, M. J. & Wijffels, R. H., 2017, In : Journal of Biotechnology. 248, p. 77-86

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Carbohydrates
Hydrocarbons
Biomass
Productivity
Weights and Measures
8 Citations (Scopus)

Categorization of species based on their microRNAs employing sequence motifs, information-theoretic sequence feature extraction, and k-mers

Yousef, M., Nigatu, D., Levy, D., Allmer, J. & Henkel, W., 13 Oct 2017, In : Eurasip Journal on Advances in Signal Processing. 2017, 10 p., 70.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Learning systems
Feature extraction
Proteins
Computational methods
Parameterization
30 Citations (Scopus)

Cross-Family Transcription Factor Interactions: An Additional Layer of Gene Regulation

Bemer, M., van Dijk, A-J., Immink, R. G. H. & Angenent, G. C., 2017, In : Trends in Plant Science. 22, 1, p. 66-80

Research output: Contribution to journalArticleAcademicpeer-review

transcription factors
genes
gene expression
protein-protein interactions
DNA
41 Citations (Scopus)

De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing

Schmidt, M. H. W., Vogel, A., Denton, A. K., Istace, B., Wormit, A., van de Geest, H. C., Bolger, M. E., Alseekh, S., Mass, J., Pfaff, C., Schurr, U., Chetelat, R., Maumus, F., Aury, J-M., Koren, S., Fernie, A. R., Zamir, D., Bolger, A. & Usadel, B., Oct 2017, In : The Plant Cell. 29, 10, p. 2336-2348

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Solanum pennellii
Nanopores
Solanum
Genome
Technology
9 Citations (Scopus)

Disparate gain and loss of parasitic abilities among nematode lineages

Holterman, M., Karegar, A., Mooijman, P., van Megen, H., van den Elsen, S., Vervoort, M. T. W., Quist, C. W., Karssen, G., Decraemer, W., Opperman, C. H., Bird, D. M., Kammenga, J., Goverse, A., Smant, G. & Helder, H., 2017, In : PLoS ONE. 12, 9, 18 p., e0185445.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Aptitude
Nematoda
Biodiversity
Parasites
parasites
15 Citations (Scopus)
Open Access
Euchromatin
Lycopersicon esculentum
inbred lines
cold zones
tomatoes
3 Citations (Scopus)

Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time

van Dijk, A. D. J. & Molenaar, J., 2017, In : PeerJ. 5, 4, 18 p., e3197.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene expression
Cues
Genes
flowering
Gene Expression
3 Citations (Scopus)

Fusarium in the age of genomics

Waalwijk, C., Vanheule, A., Audenaert, K., Zhang, H., Warris, S., van de Geest, H. C. & van der Lee, T. A. J., 2017, In : Tropical Plant Pathology. 42, 3, p. 184-189

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Fusarium
genomics
genome
transposons
chromosomes
152 Citations (Scopus)

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Daccord, N., Celton, J-M., Linsmith, G., Becker, C., Choisne, N., Schijlen, E., van de Geest, H., Bianco, L., Micheletti, D., Velasco, R., Di Pierro, E. A., Gouzy, J., Rees, D. J. G., Guérif, P., Muranty, H., Durel, C. E., Laurens, F., Lespinasse, Y., Gaillard, S., Aubourg, S. & 5 others, Quesneville, H., Weigel, D., van de Weg, E., Troggio, M. & Bucher, E., 2017, In : Nature Genetics. 49, 7, p. 1099-1106

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Malus
Fruit
DNA Transposable Elements
Genome
Pyrus
4 Citations (Scopus)

Identification of methylated GnTI-dependent N-glycans in Botryococcus brauni

Schulze, S., Urzica, E., Reijnders, M. J. M. F., van de Geest, H., Warris, S., Bakker, L. V., Fufezan, C., Martins dos Santos, V. A. P., Schaap, P. J., Peters, S. A. & Hippler, M., 2017, In : New Phytologist. 215, 4, p. 1361-1369

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Botryococcus
Polysaccharides
polysaccharides
Microalgae
microalgae
11 Citations (Scopus)

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere

Schouten, H. J., van de Geest, H., Papadimitriou, S., Bemer, M., Schaart, J. G., Smulders, R., Perez, G. S. & Schijlen, E., Mar 2017, In : Plant Cell Reports. 36, 3, p. 493-504

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
transgenic plants
mutation
DNA
genome
Arabidopsis thaliana
4 Citations (Scopus)

Sequence-based analysis of protein degradation rates

Correa Marrero, M., van Dijk, A-J. & de Ridder, D., 2017, In : Proteins : Structure, Function, and Bioinformatics. 85, 9, p. 1593-1601

Research output: Contribution to journalArticleAcademicpeer-review

Proteolysis
Sequence Analysis
Degradation
Proteins
Proteome

Similarities between plant traits based on their connection to underlying gene functions

Nap, J. P., Sanchez-Perez, G. F. & van Dijk, A-J., 2017, In : PLoS ONE. 12, 8, e0182097.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genes
Phenotype
phenotype
genes
Metabolites
2 Citations (Scopus)

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

Harkes, P., Verhoeven, A., Sterken, M. G., Snoek, B., Van Den Elsen, S. J. J., Mooijman, P. J. W., Quist, C. W., Vervoort, M. T. W. & Helder, H., Dec 2017, In : Oikos. 126, 12, p. 1790-1803

Research output: Contribution to journalArticleAcademicpeer-review

trophic level
food webs
food web
rhizosphere
developmental stage
145 Citations (Scopus)

The genome of Chenopodium quinoa

Jarvis, D. E., Shwen Ho, Y., Lightfoot, D. J., Schmöckel, S. M., Li, B., Borm, T. J. A., Ohyanagi, H., Mineta, K., Mitchell, C. T., Saber, N., Kharbatia, N. M., Rupper, R. R., Sharp, A. R., Dally, N., Boughton, B. A., Woo, Y. H., Gao, G., Schijlen, E. G. W. M., Guo, X., Momin, A. A. & 13 others, Negräo, S., Al-Babili, S., Gehring, C., Roessner, U., Jung, C., Murphy, K., Arold, S. T., Gojobori, T., van der Linden, C. G., van Loo, E. N., Jellen, E. N., Maughan, P. J. & Tester, M., 16 Feb 2017, In : Nature. 542, 7641, p. 307-312

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chenopodium quinoa
genome
genetic improvement
chromosomes
triterpenoid saponins
2016
17 Citations (Scopus)

A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus

Sonnenberg, A. S. M., Gao, W., Lavrijssen, B., Hendrickx, P., Sedaghat-Tellgerd, N., Foulongne-Oriol, M., Kong, W-S., Schijlen, E. G. W. M., Baars, J. J. P. & Visser, R. G. F., 2016, In : Fungal Genetics and Biology. 93, p. 35-45

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Agaricus
Agaricales
Spores
Genetic Recombination
Genome
112 Citations (Scopus)

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D'Andrea, D., Lepore, R., Funk, C. S., Kahanda, I., Verspoor, K. M., Ben-Hur, A., Koo, D. C. E., Penfold-Brown, D., Shasha, D., Youngs, N., Bonneau, R., Lin, A., Sahraeian, S. M. E., Martelli, P. L., Profiti, G., Casadio, R. & 127 others, Cao, R., Zhong, Z., Cheng, J., Altenhoff, A., Skunca, N., Dessimoz, C., Dogan, T., Hakala, K., Kaewphan, S., Mehryary, F., Salakoski, T., Ginter, F., Fang, H., Smithers, B., Oates, M., Gough, J., Törönen, P., Koskinen, P., Holm, L., Chen, C. T., Hsu, W. L., Bryson, K., Cozzetto, D., Minneci, F., Jones, D. T., Chapman, S., BKC, D., Khan, I. K., Kihara, D., Ofer, D., Rappoport, N., Stern, A., Cibrian-Uhalte, E., Denny, P., Foulger, R. E., Hieta, R., Legge, D., Lovering, R. C., Magrane, M., Melidoni, A. N., Mutowo-Meullenet, P., Pichler, K., Shypitsyna, A., Li, B., Zakeri, P., ElShal, S., Tranchevent, L. C., Das, S., Dawson, N. L., Lee, D., Lees, J. G., Sillitoe, I., Bhat, P., Nepusz, T., Romero, A. E., Sasidharan, R., Yang, H., Paccanaro, A., Gillis, J., Sedeño-Cortés, A. E., Pavlidis, P., Feng, S., Cejuela, J. M., Goldberg, T., Hamp, T., Richter, L., Salamov, A., Gabaldon, T., Marcet-Houben, M., Supek, F., Gong, Q., Ning, W., Zhou, Y., Tian, W., Falda, M., Fontana, P., Lavezzo, E., Toppo, S., Ferrari, C., Giollo, M., Piovesan, D., Tosatto, S. C. E., del Pozo, A., Fernández, J. M., Maietta, P., Valencia, A., Tress, M. L., Benso, A., Di Carlo, S., Politano, G., Savino, A., Rehman, H. U., Re, M., Mesiti, M., Valentini, G., Bargsten, J. W., van Dijk, A-J., Gemovic, B., Glisic, S., Perovic, V., Veljkovic, V., Veljkovic, N., Almeida-e-Silva, D. C., Vencio, R. Z. N., Sharan, M., Vogel, J., Kansakar, L., Zhang, S., Vucetic, S., Wang, Z., Sternberg, M. J. E., Wass, M. N., Huntley, R. P., Martin, M. J., O'Donovan, C., Robinson, P. N., Moreau, Y., Tramontano, A., Babbitt, P. C., Brenner, S. E., Linial, M., Orengo, C. A., Rost, B., Greene, C. S., Mooney, S. D., Friedberg, I. & Radivojac, P., 2016, In : Genome Biology. 17, 1, 184.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
protein
prediction
Proteins
proteins
methodology
27 Citations (Scopus)

AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling

Kloth, K. J., Wiegers, G. L., Busscher-Lange, J., van Haarst, J. C., Kruijer, W. T., Bouwmeester, H. J., Dicke, M. & Jongsma, M. A., 23 Apr 2016, In : Journal of Experimental Botany. 67, 1, p. 3383-3396

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Aphids
Salicylic Acid
jasmonic acid
salicylic acid
Aphidoidea
3 Citations (Scopus)

Compact tomato seedlings and plants upon overexpression of a tomato chromatin remodelling ATPase gene

Folta, A., Bargsten, J. W., Bisseling, T., Nap, J. P. H. & Mlynarova, L., 2016, In : Plant Biotechnology Journal. 14, 2, p. 581-591

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chromatin Assembly and Disassembly
Lycopersicon esculentum
Seedlings
adenosinetriphosphatase
chromatin
17 Citations (Scopus)

Gene and transposable element methylation in great tit (Parus major) brain and blood

Derks, M. F. L., Schachtschneider, K. M., Madsen, O., Schijlen, E. G. W. M., Verhoeven, K. J. F. & van Oers, K., 2016, In : BMC Genomics. 17, 332.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
DNA Transposable Elements
Methylation
CpG Islands
Brain
Genes
29 Citations (Scopus)

Genome-wide association mapping and genomic prediction elucidate the genetic architecture of morphological traits in arabidopsis

Kooke, R., Kruijer, W., Bours, R., Becker, F., Kuhn, A., van de Geest, H., Buntjer, J., Doeswijk, T., Guerra, J., Bouwmeester, H., Vreugdenhil, D. & Keurentjes, J. J. B., 2016, In : Plant Physiology. 170, 4, p. 2187-2203

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Arabidopsis
chromosome mapping
Genome
genomics
genome