20032020

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Article
2020

Altered hippocampal epigenetic regulation underlying reduced cognitive development in response to early life environmental insults

Schachtschneider, K. M., Welge, M. E., Auvil, L. S., Chaki, S., Rund, L. A., Madsen, O., Elmore, M. R. P., Johnson, R. W., Groenen, M. A. M. & Schook, L. B., 4 Feb 2020, In : Genes. 11, 2, 162.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Impact of genotype, body weight and sex on the prenatal muscle transcriptome of Iberian pigs

García-Contreras, C., Madsen, O., Groenen, M. A. M., López-García, A., Vázquez-Gómez, M., Astiz, S., Núñez, Y., Benítez, R., Fernández, A., Isabel, B., Rey, A. I., González-Bulnes, A. & Óvilo, C., 28 Jan 2020, In : PLoS ONE. 15, 1, e0227861.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
1 Citation (Scopus)
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
3 Citations (Scopus)
2018

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
3 Citations (Scopus)

Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants

van der Hoek, M. D., Madsen, O., Keijer, J. & van der Leij, F. R., 1 Aug 2018, In : Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. 1863, p. 909-918

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)
2017

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

2 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
11 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
10 Citations (Scopus)
2016

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

6 Citations (Scopus)
13 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 others, Erikstad, 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
65 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
17 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
18 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
21 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
7 Citations (Scopus)
2015

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
36 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

13 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
29 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

97 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
11 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
36 Citations (Scopus)
2014

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

4 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
61 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

15 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

17 Citations (Scopus)
Open Access
5 Citations (Scopus)
19 Citations (Scopus)
35 Citations (Scopus)
2013

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
75 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
76 Citations (Scopus)
2012

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
726 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
12 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
123 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
19 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
92 Citations (Scopus)
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
2009

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
9 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

9 Citations (Scopus)
2008

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

10 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
57 Citations (Scopus)