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Research Output 2008 2019

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Article
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
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
2017
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
9 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
6 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
55 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
15 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
12 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
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
31 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
76 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
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
28 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
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
49 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
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
5 Citations (Scopus)
Open Access
Chromosomes, Human, Pair 6
Haplotypes
Testis
Alleles
Quantitative Trait Loci
18 Citations (Scopus)
Sus
Islands
genome
divergence
Genome
31 Citations (Scopus)
Sus scrofa
pig
Haplotypes
haplotypes
Swine
2013
68 Citations (Scopus)

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

Paudel, Y., Madsen, O., Megens, H. J. W. C., Frantz, L. A. F., Bosse, M., Bastiaansen, J. W. M., Crooijmans, R. P. M. A. & Groenen, M., 2013, In : BMC Genomics. 14, 449.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Swine
Genome
Genes
Demography
69 Citations (Scopus)

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Frantz, L. A. F., Madsen, O., Megens, H. J. W. C., Paudel, Y., Bosse, M., Crooijmans, R. P. M. A., Groenen, M. & Schraiber, J. G., 2013, In : Genome Biology. 14, 9, 12 p., R107.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus
Southeastern Asia
Gene Flow
genome
History
2012
670 Citations (Scopus)

Analyses of pig genomes provide insight to porcine demography and evolution

Groenen, M. A. M., Megens, H. J. W. C., Frantz, L. A. F., Bosse, M., Crooijmans, R. P. M. A., Dibbits, B. W., Madsen, O. & Paudel, Y., 2012, In : Nature. 491, p. 393-398

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
demography
swine
genome
smell
olfactory receptors
12 Citations (Scopus)

Prediction of Altered 3'- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region

Endale, M. L., Fritz, E. R., Estelle, J., Hu, Z. L., Madsen, O. & Groenen, M. A. M., 2012, In : PLoS ONE. 7, 11, e48607.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
3' Untranslated Regions
3' untranslated regions
MicroRNAs
microRNA
binding sites
100 Citations (Scopus)

Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape

Bosse, M., Megens, H. J. W. C., Madsen, O., Paudel, Y., Frantz, L. A. F., Schook, L. B., Crooijmans, R. P. M. A. & Groenen, M. A. M., 2012, In : Plos Genetics. 8, 11, e1003100.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
homozygosity
demography
Genetic Recombination
recombination
Swine
18 Citations (Scopus)

The imprinted gene DIO3 is a candidate gene for litter size in pigs

Coster, N. B., Madsen, O., Heuven, H. C. M., Dibbits, B. W., Groenen, M. A. M., van Arendonk, J. A. M. & Bovenhuis, H., 2012, In : PLoS ONE. 7, 2, e31825.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Litter Size
genomic imprinting
litter size
Single Nucleotide Polymorphism
Swine
86 Citations (Scopus)

Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in Madagascar

Crottinia, A., Madsen, O., Poux, C., Straussa, A., Vieites, D. R. & Vences, M., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 14, p. 5358-5363

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
vertebrate
ancestry
rainforest
vicariance
biota
2010

Loss of Octarepeats in Two Processed Prion Pseudogenes in the Red Squirrel, Sciurus vulgaris

Madsen, O., Kortum, T. T., Hupkes, H., Kohlen, W., Rheede, T. & de Jong, W. W., 2010, In : Journal of Molecular Evolution. 71, 5-6, p. 356-363

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sciuridae
Pseudogenes
pseudogenes
Prions
prions
2009
8 Citations (Scopus)

Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates

Chiari, Y., van der Meijden, A., Madsen, O., Vences, M. & Meyer, A., 2009, In : Frontiers in Zoology. 6, 15 p., 32.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
recombination
vertebrate
vertebrates
phylogenetics
gene
8 Citations (Scopus)

Phylogenetic analyses of the leaf beetle genus Galerucella: evidence for host switching at speciation?

Borghuis, A., Madsen, O., Ouborg, N. J. & van Groenendael, J., 2009, In : Molecular Phylogenetics and Evolution. 53, 2, p. 361-367

Research output: Contribution to journalArticleAcademicpeer-review

Galerucella
Beetles
Chrysomelidae
Herbivory
beetle
2008
9 Citations (Scopus)

Evolution of closely linked gene pairs in vertebrate genomes

Franck, E., Hulsen, T., Huynen, M. A., de Jong, W. W., Lunsen, N. H. & Madsen, O., 2008, In : Molecular Biology and Evolution. 25, 9, p. 1909-1921

Research output: Contribution to journalArticleAcademicpeer-review

Vertebrates
vertebrate
genome
vertebrates
Genome
54 Citations (Scopus)

Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses

Poux, C., Madsen, O., Glos, J., de Jong, W. W. & Vences, M., 2008, In : BMC Evolutionary Biology. 8, 16 p., 102.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
phylogeny
partitioning
divergence
sampling
colonization