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Research Output 2000 2019

2019
1 Citation (Scopus)

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S. A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 2019, In : Scientific Data. 6, 6.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access
Data Management
Information management
management
Stewardship
Data management
4 Citations (Scopus)

BrAPI-an application programming interface for plant breeding applications

Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O. E., Birkett, C., Calaminos, V. C., Carceller, P., Cornut, G., Vasques Costa, B., Edwards, J. D., Finkers, R., Yanxin Gao, S., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., König, P. & 30 others, Lagare, J. E. B., Lange, M., Laporte, M. A., Larmande, P., LeBauer, D. S., Lyon, D. A., Marshall, D. S., Matthews, D., Milne, I., Mistry, N., Morales, N., Mueller, L. A., Neveu, P., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Pommier, C., Ramírez-González, R. H., Rathore, A., Raquel, A. M., Raubach, S., Rife, T., Robbins, K., Rouard, M., Sarma, C., Scholz, U., Sempéré, G., Shaw, P. D., Simon, R. & Verouden, M., 15 Oct 2019, In : Bioinformatics (Oxford, England). 35, 20, p. 4147-4155

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Application programming interfaces (API)
Breeding
Programming
Specifications
Specification

Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads

Motazedi, E., Maliepaard, C., Finkers, R., Visser, R. & De Ridder, D., 16 Apr 2019, In : Frontiers in Genetics. 10, MAR, 335.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Polyploidy
Haplotypes
Alleles
Genotype
Population

Haplotype assembly of autotetraploid potato using integer linear programing

Siragusa, E., Haiminen, N., Finkers, R., Visser, R. & Parida, L., 15 Sep 2019, In : Bioinformatics (Oxford, England). 35, 18, p. 3279-3286 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Linear Programming
Haplotype
Potato
Solanum tuberosum
Haplotypes
6 Citations (Scopus)

UAV based soil salinity assessment of cropland

Ivushkin, K., Bartholomeus, H., Bregt, A. K., Pulatov, A., Franceschini, M. H. D., Kramer, H., van Loo, E. N., Jaramillo Roman, V. & Finkers, R., 2019, In : Geoderma. 338, p. 502-512 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

soil salinity
lidar
salt
salts
remote sensing
2018

Breeding API

Finkers, H. J., 12 Dec 2018. 1 p.

Research output: Contribution to conferenceAbstractAcademic

Open Access

Designing plant varieties with information technology

Visser, R. G. F. & Finkers, H. J., 2018, In : Prophyta - Focus on Europe. p. 28-30

Research output: Contribution to journalArticleProfessional

Open Access
Bioinformatics
Information technology
5 Citations (Scopus)

Efficient algorithms for polyploid haplotype phasing

He, D., Saha, S., Finkers, R. & Parida, L., 9 May 2018, In : BMC Genomics. 19, Supplement 2, 110.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Polyploidy
Haplotypes
Diploidy
11 Citations (Scopus)

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

Motazedi, E., Finkers, H. J., Maliepaard, C. A. & de Ridder, D., May 2018, In : Briefings in Bioinformatics. 19, 3, p. 387-403

Research output: Contribution to journalArticleAcademicpeer-review

Polyploidy
Nucleotides
Haplotypes
Ploidies
Polymorphism
2 Citations (Scopus)

Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties

Dinh, Q. D., Finkers, R., Westphal, A. H., van Dongen, W. M. A. M., Visser, R. G. F. & Trindade, L. M., 29 Oct 2018, In : PLoS ONE. 13, 10, e0206636.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
sucrose synthase
Lycopersicon esculentum
Haplotypes
Sucrose
haplotypes

Farm Data Train

Finkers, H. J., 12 Dec 2018. 1 p.

Research output: Contribution to conferenceAbstractAcademic

Open Access

Linked Data Platform for Plant Breeding and Genomics

Kuzniar, A., Singh, G., Martinez-Ortiz, C., Visser, R. G. F. & Finkers, H. J., 12 Dec 2018. 1 p.

Research output: Contribution to conferenceAbstractAcademic

Open Access
2 Citations (Scopus)

QTLTableMiner++: Semantic mining of QTL tables in scientific articles

Singh, G., Kuzniar, A., van Mulligen, E. M., Gavai, A., Bachem, C. W., Visser, R. G. F. & Finkers, R., 25 May 2018, In : BMC Bioinformatics. 19, 183.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Quantitative Trait Loci
Semantics
Ontology
Tables
Mining
2 Citations (Scopus)

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Motazedi, E., de Ridder, D., Finkers, R., Baldwin, S., Thomson, S., Monaghan, K. & Maliepaard, C., 15 Nov 2018, In : Bioinformatics. 34, 22, p. 3864-3872

Research output: Contribution to journalArticleAcademicpeer-review

Polyploidy
Haplotype
Haplotypes
Sequencing
Chromosomes
2017
1 Citation (Scopus)

Managing Variant Calling Files the Big Data Way: Using HDFS and Apache Parquet

Boufea, A., Finkers, H. J., van Kaauwen, M. P. W., Kramer, M. R. & Athanasiadis, I. N., 2017, BDCAT '17 Proceedings of the Fourth IEEE/ACM International Conference on Big Data Computing, Applications and Technologies. ACM, p. 219-226

Research output: Chapter in Book/Report/Conference proceedingChapter

Open Access
Electric sparks
Big data

Toward better data sharing methods for genebanks

Papoutsoglou, E., Kaliyaperumal, R., Van Hintum, T., Visser, R. G. F., Athanasiadis, I. N. & Finkers, R., 2017. 6 p.

Research output: Contribution to conferencePaperAcademicpeer-review

Open Access
Data integration
Electronic data interchange
User interfaces
Crops
Conservation
2016

Improved utilization of crop diversity for rationalized breeding using data interoperability

Finkers, H. J., 2016, Enhancing crop genepool use: capturing wild relative and landrace diversity for crop improvement. Maxted, N., Dulloo, M. E. & Ford-Lloyd, M. V. (eds.). CAB International, p. 436-440

Research output: Chapter in Book/Report/Conference proceedingChapter

gene banks
plant breeders
wild relatives
food crops
plant breeding
1139 Citations (Scopus)

The FAIR Guiding Principles for scientific data management and stewardship: Comment

Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., Da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S. A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 2016, In : Scientific Data. 3, 160018.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Reusability
Data Management
Information management
management
Reuse

Using phenomics and genomics to unlock landrace and wild relative diversity for crop improvement

Vosman, B., Pelgrom, K. T. B., Sharma, G., Voorrips, R. E., Broekgaarden, C., Pritchard, J., May, S., Adobor, S., Castellanos-Uribe, M., van Kaauwen, M. P. W., Finkers, H. J., Janssen, B., van Workum, W. & Ford-Lloyd, B., 2016, Enhancing crop genepool use: capturing wild relative and landrace diversity for crop improvement. Maxted, N., Dulloo, M. E. & Ford-Lloyd, B. V. (eds.). CABI, p. 1-9

Research output: Chapter in Book/Report/Conference proceedingChapter

wild relatives
Aleyrodidae
landraces
Brevicoryne brassicae
plant genetic resources

Utilizing low-coverage sequence data in tomato recombinant inbred lines (S. lycopersicum x S. pimpinellifolium)

van Binsbergen, R., Bink, M. C. A. M., Finkers, H. J., Calus, M. P. L., Veerkamp, R. F. & van Eeuwijk, F. A., 2016, Plant Breeding: the art of bringing science to life - Abstracts of the 20th EUCARPIA General Congress. Kölliker, R. & Boller, B. (eds.). Agroscope, Institute for Sustainability Sciences ISS, p. 19 1 p.

Research output: Chapter in Book/Report/Conference proceedingAbstract

Open Access
2015
16 Citations (Scopus)

Assessing the genetic variation of Ty-1 and Ty-3 alleles conferring resistance to tomato yellow leaf curl virus in a broad tomato germplasm

Caro Rios, C. M., Verlaan, M. G., Julian, O., Finkers, H. J., Wolters, A. M. A., Hutton, S. F., Scott, J. W., Kormelink, R. J. M., Visser, R. G. F., Diez, M. J., Perez-de-Castro, A. & Bai, Y., 2015, In : Molecular Breeding. 35, 13 p., 132.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Tomato yellow leaf curl virus
Solanum chilense
Lycopersicon esculentum
germplasm
Alleles

candYgene: enabling precision breeding through FAIR Data

Kuzniar, A., Gavai, A. K., Ridder, L. O., Bonino da Silva Santos, L. O., Singh, G., Visser, R. G. F. & Finkers, H. J., 2015.

Research output: Contribution to conferenceAbstractAcademic

Open Access
breeding
genes
prioritization
infrastructure
quantitative trait loci
23 Citations (Scopus)

Combined biotic and abiotic stress resistance in tomato

Kissoudis, C., Chowdhury, R., van Heusden, A. W., van de Wiel, C. C. M., Finkers, H. J., Visser, R. G. F., Bai, Y. & van der Linden, C. G., 2015, In : Euphytica. 202, 2, p. 317-332

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Salt-Tolerance
Disease Resistance
Lycopersicon esculentum
biotic stress
powdery mildew
1 Citation (Scopus)
Metabolomics
Phytochemicals
Transcription
Lycopersicon esculentum
Fruits
4 Citations (Scopus)

Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning

Wolters, A. M. A., Caro Rios, C. M., Dong, S., Finkers, H. J., Gao, J., Visser, R. G. F., Wang, X., Du, Y. & Bai, Y., 2015, In : Theoretical and Applied Genetics. 128, 10, p. 1987-1997

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
genome assembly
Solanum lycopersicum
Lycopersicon esculentum
introgression
Organism Cloning
2 Citations (Scopus)

Genebanks and genomics: how to interconnect data from both communities?

Finkers, H. J., Chibon, P. Y. F. R. P., van Treuren, R., Visser, R. G. F. & van Hintum, T. J. L., 2015, In : Plant genetic resources: characterization and utilization. 13, 1, p. 90-93

Research output: Contribution to journalArticleAcademicpeer-review

world wide web
Access to Information
Genomics
genetic resources
Semantics

Mission erfüllt: Zwiebelgenom entschlüsselt

Jacobsen, T., Scholten, O. E. & Finkers, H. J., 2015, In : Gartenbau Profi. 2, p. 8-10

Research output: Contribution to journalArticleProfessional

SEQUON - Sequencing the Onion Genome

Finkers, H. J., van Workum, W., van Kaauwen, M. P. W., Huits, H., Jungerius, A., Vosman, B. J. & Scholten, O. E., 2015.

Research output: Contribution to conferenceAbstractAcademic

Open Access
onions
genome
Netherlands
tomatoes
genome assembly

The Key to Sufficient Food Production; Big data analysis solves complicated puzzle

Hall, R. D., Finkers, H. J. & Wehrens, H. R. M. J., 2015, In : Prophyta Annual. 2015, p. 28-29 52 p.

Research output: Contribution to journalArticleProfessional

Open Access
food production
biologists
data analysis
crops
2014
1 Citation (Scopus)

A Stringent and Broad Screen of Solanum spp. tolerance Against Erwinia Bacteria Using a Petiole Test

Rietman, H., Finkers, H. J., Evers, L., van der Zouwen, P. S., van der Wolf, J. M. & Visser, R. G. F., 2014, In : American Journal of Potato Research. 91, 2, p. 204-214

Research output: Contribution to journalArticleAcademicpeer-review

Erwinia
Solanum
potatoes
genotype
bacteria
145 Citations (Scopus)
Solanum
Lycopersicon esculentum
tomatoes
Single Nucleotide Polymorphism
Genome
8 Citations (Scopus)

Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium

Viquez-Zamora, M., Caro Rios, C. M., Finkers, H. J., Tikunov, Y. M., Bovy, A. G., Visser, R. G. F., Bai, Y. & van Heusden, A. W., 2014, In : BMC Genomics. 15, 10 p., 1152.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Solanum
Single Nucleotide Polymorphism
Population
Chromosomes, Human, Pair 11
Chromosomes, Human, Pair 3
4 Citations (Scopus)

Possibilities and challenges of the potato genome sequence

Visser, R. G. F., Bachem, C. W. B., Borm, T. J. A., de Boer, J. M., van Eck, H. J., Finkers, H. J., van der Linden, G., Maliepaard, C. A., Uitdewilligen, J. G. A. M. L., Voorrips, R. E., Vos, P. G. & Wolters, A. M. A., 2014, In : Potato Research. 57, 3-4, p. 327-330

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Solanum tuberosum
Haplotypes
haplotypes
potatoes
Genome
2013
200 Citations (Scopus)

Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes

Itkin, M., Heinig, U., Tzfadia, O., Bhide, A. J., Shinde, B., Cardenas, P. D., Bocobza, S. E., Unger, T., Malitsky, S., Finkers, H. J., Tikunov, Y. M., Bovy, A. G., Chikate, Y., Singh, P., Rogachev, I., Beekwilder, J., Giri, A. P. & Aharoni, A., 2013, In : Science. 341, 6142, p. 175-179

Research output: Contribution to journalArticleAcademicpeer-review

glycoalkaloids
alkaloids
biosynthesis
crops
tomatoes

Comparison of Regularized Regression Methods for ~Omics Data

Acharjee, A., Finkers, H. J., Visser, R. G. F. & Maliepaard, C. A., 2013, In : Metabolomics : Open Access. 3, 3, 9 p., 126.

Research output: Contribution to journalArticleAcademicpeer-review

potato
carotenoid
prediction
comparison
method
4 Citations (Scopus)

Crop Ontology: Vocabulary For Crop-related Concepts

Matteis, L., Chibon, P. Y., Espinosa, H., Skofic, M., Finkers, H. J., Bruskiewich, R., Hyman, J. M. & Arnoud, E., 2013.

Research output: Contribution to conferencePaperAcademicpeer-review

Open Access
ontology
vocabulary
functionality
community
programming

De tomatenkaart is klaar, wat nu?

Finkers, H. J. & Visser, R. G. F., 2013, In : Kennis Online. 10, mei, p. 3-5

Research output: Contribution to journalArticleProfessional

Open Access
2 Citations (Scopus)

MQ2: Visualize multi-trait mapped QTL results

Chibon, P. Y. F. R. P., Voorrips, R. E., Visser, R. G. F. & Finkers, H. J., 2013, In : Molecular Breeding. 32, 4, p. 981-985

Research output: Contribution to journalArticleAcademicpeer-review

Quantitative Trait Loci
quantitative trait loci
metabolites
33 Citations (Scopus)

Tomato breeding in the genomics era: insights from a SNP array

Víquez-Zamora, M., Vosman, B., van Geest, H., Bovy, A. G., Visser, R. G. F., Finkers, H. J. & van Heusden, A. W., 2013, In : BMC Genomics. 14, 28 p., 354.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lycopersicon esculentum
Genomics
Breeding
Single Nucleotide Polymorphism
Genetic Linkage
2012
42 Citations (Scopus)

Genetic analysis of metabolites in apple fruits indicates an mQTL hotspot for phenolic compounds on linkage group 16

Khan, S. A., Chibon, P. Y. F. R. P., de Vos, R. C. H., Schipper, B. A., Walraven, A. E. J., Beekwilder, M. J., van Dijk, T., Finkers, H. J., Visser, R. G. F., van de Weg, W. E., Bovy, A. G., Cestaro, A., Velasco, R., Jacobsen, E. & Schouten, H. J., 2012, In : Journal of Experimental Botany. 63, 8, p. 2895-2908

Research output: Contribution to journalArticleAcademicpeer-review

Quantitative Trait Loci
Malus
linkage groups
genetic techniques and protocols
phenolic compounds
6 Citations (Scopus)

Marker2sequence, mine your QTL regions for candidate genes

Chibon, P. Y. F. R. P., Schoof, H., Visser, R. G. F. & Finkers, H. J., 2012, In : Bioinformatics. 28, 14, p. 1921-1922

Research output: Contribution to journalArticleAcademicpeer-review

Quantitative Trait Loci
Genes
Gene
Gene Ontology
Data Integration

Precision breeding in crop plants: future or fiction

Visser, R. G. F. & Finkers, H. J., 2012, Conference Next Generation Plant Breeding, Wageningen, The Netherlands, 11 - 14 November, 2012. van der Linden, C. G. & Visser, R. G. F. (eds.). Wageningen: Wageningen UR, Communication Services, p. 41-41

Research output: Chapter in Book/Report/Conference proceedingConference paper

Using semantic web technology to accelerate plant breeding

Chibon, P. Y., Carreres, B. M., de Weerd, H. H., Visser, R. G. F. & Finkers, H. J., 2012.

Research output: Contribution to conferencePaperAcademicpeer-review

Semantic Web
Genes
Data integration
Metabolites
Proteins
2011
20 Citations (Scopus)

Identification and mapping of quantitative resistance to late blight (Phytophthora infestans) in Solanum habrochaites LA1777

Junming Li, J., Liu, L., Bai, Y., Finkers, H. J., Visser, R. G. F. & van Heusden, A. W., 2011, In : Euphytica. 179, 3, p. 427-438

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Phytophthora infestans
Solanum habrochaites
Solanum
Lycopersicon esculentum
quantitative trait loci
12 Citations (Scopus)

Seedling salt tolerance in tomato

Junming Li, J., Liu, L., Bai, Y., Zhang, P., Finkers, H. J., Du, Y., Visser, R. G. F. & van Heusden, A. W., 2011, In : Euphytica. 178, 3, p. 403-414

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Salt-Tolerance
Chromosomes, Human, Pair 6
Lycopersicon esculentum
Seedlings
salt tolerance
25 Citations (Scopus)

SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species

Vleeshouwers, V. G. A. A., Finkers, H. J., Budding, D. J., Vissers, M., Jacobs, M. M. J., van Berloo, R., Pel, M., Champouret, N., Bakker, E. H., Krenek, P., Rietman, H., Huigen, D. J., Hoekstra, R., Goverse, A., Vosman, B., Jacobsen, E. & Visser, R. G. F., 2011, In : BMC Plant Biology. 11, 24 p., 116.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Solanum
disease resistance
tubers
Phytophthora infestans
potatoes
2010

BreeDB: storage, visualization and integration of data quantitative from greenhouse and field trials

Finkers, H. J., Voorrips, R. E., de Weerd, H. H. & Chibon, P. Y. F. R. P., 2010.

Research output: Contribution to conferencePosterProfessional

De genetica van grauwe schimmelresistentie in tomaat

Finkers, H. J., 2010, In : Gewasbescherming. 41, 5, p. 250-252

Research output: Contribution to journalArticleProfessional

Open Access

From QTLs to potential candidate genes

Chibon, P. Y. F. R. P., de Weerd, H. H., Voorrips, R. E. & Finkers, H. J., 2010.

Research output: Contribution to conferencePosterProfessional

2009

BreedDB: A database supporting quantitative aspects of Plant Breeding

Finkers, H. J., 2009.

Research output: Contribution to conferencePosterProfessional