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Research Output 2008 2019

2019

Genomic analysis on pygmy hog reveals extensive interbreeding during wild boar expansion

Liu, L., Bosse, M., Megens, H-J., Frantz, L. A. F., Lee, Y. L., Irving-Pease, E. K., Narayan, G., Groenen, M. A. M. & Madsen, O., 1 Dec 2019, In : Nature Communications. 10, 1992.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
genome
admixtures
Genes
expansion
Open Access
gene expression
swine
cells
jejunum
transcriptome
2018
2 Citations (Scopus)

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome

Derks, M. F. L., Lopes, M. S., Bosse, M., Madsen, O., Dibbits, B., Harlizius, B., Groenen, M. A. M. & Megens, H. J., 19 Sep 2018, In : Plos Genetics. 14, 9, 20 p., e1007661.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lethal Genes
lethal genes
allele
Swine
genome
1 Citation (Scopus)
Carnitine Acyltransferases
Choline
Transferases
Protein Isoforms
Carnitine O-Acetyltransferase

Intestinal stem-cell organoids as experimental models to investigate feed efficiency

Ellen, E. D., Taverne, N., Taverne-Thiele, J. J., Madsen, O., Woelders, H., Bergsma, R., Knol, E. F., Kar, S. K., de Haas, Y., Groenen, M. & Wells, J. M., 28 Aug 2018, Book of Abstracts of the 69th Annual Meeting of the European Federation of Animal Science. Wageningen Academic Publishers, p. 478-478 (Book of Abstracts; vol. 24).

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

stem cells
feed conversion
nutrient transport
livestock production
marker-assisted selection
2017

Acomprehensive set of lncRNAs on porcine chromosomeX

Madsen, O. & Groenen, M., 15 Jan 2017.

Research output: Contribution to conferencePosterAcademic

Long Noncoding RNA
Swine
Quantitative Trait Loci
Neurogenesis
Gene Expression Regulation

A Study of Pig Chromosome X lncRNA Expression

Djebali, S., Palasca, O., Anthon, C., Derrien, T., Madsen, O., Thomas, M., Floden, E., Havgaard, J. H., Seemann, S. E., Gonzales, J. M., Junge, A., Pacholewska, A., Billis, K., Alkan, F., Eory, L., Amaral, A., Prieto Barja, P., Stadler, P. F., Notredame, C., Groenen, M. & 2 othersHarrow, J. & Gorodkin, J., Jan 2017.

Research output: Contribution to conferencePosterAcademic

Avian Ecological Epigenetics: the role of DNA methylation in the evolution of animal personality

van Oers, K., Derks, M. F. L., Schachtschneider, K. M., Laine, V. N., Madsen, O. & Verhoeven, K. J. F., 23 Aug 2017.

Research output: Contribution to conferencePosterAcademic

Comprehensive analysis of RNA-editing in pigs suggest evolutionary conservation of RNA-editing in mammals

Madsen, O., Crooijmans, R. P. M. A., Schachtschneider, K. M. & Groenen, M., 23 Aug 2017.

Research output: Contribution to conferencePosterAcademic

Flipped evolution of the mitochondrial enzymes CPT1 and CPT2 of the carnitine- and choline acyltransferase

van der Hoek, M. D., Madsen, O., Keijer, J. & van der Leij, F. R., 21 Aug 2017.

Research output: Contribution to conferencePosterAcademic

2 Citations (Scopus)

Gene networks for total number born in pigs across divergent environments

Verardo, L. L., Lopes, M. S., Mathur, P., Madsen, O., Silva, F. F., Groenen, M. A. M., Knol, E. F., Lopes, P. S. & Guimarães, S. E. F., 2017, In : Mammalian Genome. 28, 9-10, p. 426-435

Research output: Contribution to journalArticleAcademicpeer-review

Gene Regulatory Networks
Swine
Breeding
Genes
Genome-Wide Association Study
10 Citations (Scopus)

Oncopig soft-tissue sarcomas recapitulate key transcriptional features of human sarcomas

Schachtschneider, K. M., Liu, Y., Makelainen, S., Madsen, O., Rund, L. A., Groenen, M. A. M. & Schook, L. B., 2017, In : Scientific Reports. 7, 12 p., 2624.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sarcoma
Cell Line
Leiomyosarcoma
Research
Tumor Cell Line
7 Citations (Scopus)

The importance of endophenotypes to evaluate the relationship between genotype and external phenotype

te Pas, M. F. W., Madsen, O., Calus, M. P. L. & Smits, M. A., 2017, In : International Journal of Molecular Sciences. 18, 2, 472.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Endophenotypes
phenotype
genes
genome
Genes
2016
6 Citations (Scopus)

After genome-wide association studies: Gene networks elucidating candidate genes divergences for number of teats across two pig populations

Verardo, L. L., Lopes, M. S., Wijga, S., Madsen, O., Silva, F. F., Groenen, M. A. M., Knol, E. F., Lopes, P. S. & Guimarães, S. E. F., 2016, In : Journal of Animal Science. 94, 4, p. 1446-1458

Research output: Contribution to journalArticleAcademicpeer-review

Gene Regulatory Networks
Genome-Wide Association Study
teats
Swine
swine
10 Citations (Scopus)

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese

Ottenburghs, J., Megens, H. J., Kraus, R. H. S., Madsen, O., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T., 2016, In : Molecular Phylogenetics and Evolution. 101, p. 303-313

Research output: Contribution to journalArticleAcademicpeer-review

Geese
geese
History
phylogenetics
history
57 Citations (Scopus)

Evolutionary signals of selection on cognition from the great tit genome and methylome

Laine, V. N., Gossmann, T. I., Schachtschneider, K. M., Garroway, C. J., Madsen, O., Verhoeven, K. J. F., De Jager, V., Megens, H. J., Warren, W. C., Minx, P., Crooijmans, R. P. M. A., Corcoran, P., Adriaensen, F., Belda, E., Bushuev, A., Cichon, M., Charmantier, A., Dingemanse, N., Doligez, B., Eeva, T. & 26 othersErikstad, K. E., Fedorov, S., Hau, M., Hille, S., Hinde, C., Kempenaers, B., Kerimov, A., Krist, M., Mand, R., Matthysen, E., Nager, R., Norte, C., Orell, M., Richner, H., Slagsvold, T., Tilgar, V., Tinbergen, J., Torok, J., Tschirren, B., Yuta, T., Sheldon, B. C., Slate, J., Zeng, K., Van Oers, K., Visser, M. E. & Groenen, M. A. M., 2016, In : Nature Communications. 7, 10474.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
cognition
genome
Cognition
learning
methylation
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
14 Citations (Scopus)

Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development

Schachtschneider, K. M., Liu, Y., Rund, L. A., Madsen, O., Johnson, R. W., Groenen, M. A. M. & Schook, L. B., 2016, In : BMC Genomics. 17, 1, 856.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
DNA Methylation
Swine
Iron
Genes
Blood-Brain Barrier
19 Citations (Scopus)

Revealing new candidate genes for reproductive traits in pigs: Combining Bayesian GWAS and functional pathways

Verardo, L. L., Silva, F. F., Lopes, M. S., Madsen, O., Bastiaansen, J. W. M., Knol, E. F., Kelly, M., Varona, L., Lopes, P. S. & Guimarães, S. E. F., 2016, In : Genetics, Selection, Evolution. 48, 1, 189.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Genome-Wide Association Study
reproductive traits
pig
teats
piglets

The Conserved Functional Role of Non-CpG Methylation in Mammalian and Avian Brain

Schachtschneider, K. M., Madsen, O., Laine, V. N., Derks, M. F. L., Schook, L. B., Groenen, M., Verhoeven, K. & van Oers, K., 9 Jan 2016.

Research output: Contribution to conferenceOtherAcademic

6 Citations (Scopus)

The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons)

Nuijten, R. J. M., Bosse, M., Crooijmans, R. P. M. A., Madsen, O., Schaftenaar, W., Ryder, O. A., Groenen, M. A. M. & Megens, H. J., 2016, In : International journal of genomcs. 2016, 5613862.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Endangered Species
Genomics
Conservation
Swine
Islands
2015
33 Citations (Scopus)

Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model

Schachtschneider, K. M., Madsen, O., Park, C., Rund, L. A., Groenen, M. A. M. & Schook, L. B., 2015, In : BMC Genomics. 16, 18 p., 743.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
DNA Methylation
Methylation
Swine
Transcription Initiation Site
Genome
11 Citations (Scopus)

Artificial selection on introduced Asian haplotypes shaped the genetic architecture in european commercial pigs

Bosse, M., Soares Lopes, M., Madsen, O., Megens, H. J., Crooijmans, R. P. M. A., Frantz, L. A. F., Harlizius, B., Bastiaansen, J. W. M. & Groenen, M. A. M., 2015, In : Proceedings of the Royal Society. B: Biological Sciences. 282, 1821, 9 p., 20152019.

Research output: Contribution to journalArticleAcademicpeer-review

artificial selection
pig
Haplotypes
haplotypes
Swine
27 Citations (Scopus)

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors

Paudel, Y., Madsen, O., Megens, H. J. W. C., Frantz, L. A. F., Bosse, M., Crooijmans, R. P. M. A. & Groenen, M. A. M., 2015, In : BMC Genomics. 16, 14 p., 330.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Odorant Receptors
Swine
Gene Flow
Mya
Overlapping Genes
79 Citations (Scopus)

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

Frantz, L. A. F., Schraiber, J. G., Madsen, O., Megens, H. J. W. C., Cagan, A., Bosse, M., Paudel, Y., Crooijmans, R. P. M. A., Larson, G. & Groenen, M. A. M., 2015, In : Nature Genetics. 47, 10, p. 1141-1148

Research output: Contribution to journalArticleAcademicpeer-review

Sus scrofa
Gene Flow
Genome
Reproductive Isolation
Swine
7 Citations (Scopus)

Evolution of Tibetan wild boars

Frantz, L. A. F., Madsen, O., Megens, H. J., Schraiber, J. G., Paudel, Y., Bosse, M., Crooijmans, R. P. M. A., Larson, G. & Groenen, M. A. M., 2015, In : Nature Genetics. 47, 3, p. 188-189

Research output: Contribution to journalComment/Letter to the editorAcademic

Finding the genes which make great tits innovators

Laine, V., Gossmann, T. I., Schachtschneider, K. M., Madsen, O., Megens, H. J. W. C., Crooijmans, R. P. M. A., van Oers, K., Visser, M. E. & Groenen, M., 2015.

Research output: Contribution to conferencePosterAcademic

Genome Wide Analysis of Porcine miRNA Editing

Arya, A., Crooijmans, R. P. M. A., Giuffra, E., Groenen, M. & Madsen, O., Jan 2015.

Research output: Contribution to conferencePosterAcademic

Open Access
10 Citations (Scopus)

Hybrid origin of European commercial pigs examined by an in-depth haplotype analysis on chromosome 1

Bosse, M., Madsen, O., Megens, H. J. W. C., Frantz, L. A. F., Paudel, Y., Crooijmans, R. P. M. A. & Groenen, M., 2015, In : Frontiers in Genetics. 5, 442.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chromosomes, Human, Pair 1
Haplotypes
Swine
Sus scrofa
Genome

Speciation and domestication in Suiformes: a genomic perspective

Frantz, L. A. F., 2015, Wageningen: Wageningen University. 227 p.

Research output: Thesisinternal PhD, WUAcademic

Open Access
history
biodiversity
source of information
fluctuation
social isolation

Structural variations in pig genomes

Paudel, Y., 2015, Wageningen: Wageningen University. 204 p.

Research output: Thesisinternal PhD, WUAcademic

Open Access
swine
genome
olfactory receptors
single nucleotide polymorphism
genes

The Functional Annotation of Animal Genomes (FAANG) Initiative

Giuffra, E., Foissac, S., Madsen, O., Groenen, M., Crooijmans, R. P. M. A., Ross, P. J., Korf, I. & Zhou, H., Jan 2015.

Research output: Contribution to conferenceAbstractAcademic

Open Access
Sus scrofa
haplotypes
swine
genome

The impact of gene flow, standing genetic variations and strong artificial selection during pig domestication

Frantz, L. A. F., Schraiber, J. G., Megens, H. J. W. C., Madsen, O., Battista, V., Larson, I. & Groenen, M., 2015.

Research output: Contribution to conferenceAbstractAcademic

31 Citations (Scopus)

Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations

Bosse, M., Megens, H. J. W. C., Madsen, O., Crooijmans, R. P. M. A., Ryder, O. A., Austerlitz, F., Groenen, M. A. M. & de Cara, M. A. R., 2015, In : Genome Research. 25, 7, p. 970-981

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Inbreeding
Breeding
Swine
Demography
2014

Analyses of Eurasian wild and domestic pig genomes reveals long-term gene-flow during domestication

Frantz, L. A. F., Schraiber, J. G., Madsen, O., Megens, H. J. W. C., Cagan, A., Bosse, M., Paudel, Y., Crooijmans, R. P. M. A., Larson, G. & Groenen, M. A. M., 31 Oct 2014, BioRxiv, 23 p.

Research output: Working paperAcademic

domestication
gene flow
swine
genome
reproductive isolation

Domestication with gene-flow in pigs

Frantz, L. A. F., Bosse, M., Megens, H. J. W. C., Madsen, O., Paudel, Y., Crooijmans, R. P. M. A. & Groenen, M., 2014.

Research output: Contribution to conferenceAbstractAcademic

Effects of peripheral viral infection on hippocampal dna methylation and gene expression patterns in a pig model of cognitive development

Schachtschneider, K. M., Rund, L. A., Madsen, O., Johnson, R. & Groenen, M., 2014.

Research output: Contribution to conferenceAbstractAcademic

FAANG Pilot projects: Comprehensive analysis of RNA-editing in pigs

Madsen, O., Crooijmans, R. P. M. A., Paudel, Y., Frantz, L. A. F., Bosse, M., Megens, H. J. W. C. & Groenen, M., 2014.

Research output: Contribution to conferenceAbstractAcademic

3 Citations (Scopus)

Genetic connections between dressage and show-jumping horses in Dutch Warmblood horses

Rovere, G. A., Madsen, O., Norberg, E., van Arendonk, J. A. M. & Ducro, B. J., 2014, In : Acta Agriculturae Scandinavica Section A-Animal Science. 64, 1, p. 57-66

Research output: Contribution to journalArticleAcademicpeer-review

jumping
Horses
horses
Breeding
ancestry
51 Citations (Scopus)

Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression

Bosse, M., Megens, H. J. W. C., Frantz, L. A. F., Madsen, O., Paudel, Y., Duijvestein, N., Crooijmans, R. P. M. A. & Groenen, M., 2014, In : Nature Communications. 5, 8 p., 4392.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
swine
genes
Haplotypes
Sus scrofa
Swine

Great tit de novo genome assembly and annotation

Laine, V., van Oers, K., Madsen, O., Megens, H. J. W. C., Verhulst, E. C., Verhoeven, M. T. W., Visser, M. E. & Groenen, M., 2014.

Research output: Contribution to conferenceAbstractAcademic

14 Citations (Scopus)

Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis

Perez-montarelo, D., Madsen, O., Alves, E. R., Rodriguez, C., Floch, J. M. & Groenen, M., 2014, In : Physiological genomics. 46, 6, p. 195-206

Research output: Contribution to journalArticleAcademicpeer-review

Gene Expression Profiling
Swine
Growth
Genes
Hypothalamus
16 Citations (Scopus)

Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq

Du, Z., Eisley, C. J., Onteru, S. K., Madsen, O., Groenen, M., Ross, J. W. & Rothschild, M. F., 2014, In : Animal Genetics. 45, 2, p. 198-204

Research output: Contribution to journalArticleAcademicpeer-review

Swine
RNA
swine
Reproduction
genomics

Influence Of Specialisation On Connectedness And Genetic Parameters In The Dutch Warmblood Horse Population

Rovere, G. A., Madsen, O., Norberg, E., van Arendonk, J. A. M. & Ducro, B. J., 2014.

Research output: Contribution to conferencePaperAcademic

Open Access
5 Citations (Scopus)
Open Access
Chromosomes, Human, Pair 6
Haplotypes
Testis
Alleles
Quantitative Trait Loci

Pig variomics: understanding the when, where, and why of variation in the genome of Sus scrofa

Megens, H. J. W. C., Bosse, M., Madsen, O., Frantz, L. A. F., Paudel, Y., Herrero-Medrano, J., Crooijmans, R. P. M. A. & Groenen, M., 2014.

Research output: Contribution to conferenceAbstractAcademic

18 Citations (Scopus)
Sus
Islands
genome
divergence
Genome

The International Swine Methylome Consortium (ISMC): Supporting Epigenomics and Biomedical research

Schachtschneider, K. M., Rund, L. A., Madsen, O., Johnson, R., Archibald, A. L., Groenen, M. & Schook, L. B., 2014, book of abstracts the 34th International Society for Animal Genetics Conference. p. 189-189

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Open Access