20032020

Research output per year

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Research Output

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
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)

The chromosome-scale genome assembly of Visayan warty pig provides insight into porcine evolutionary history

Liu, L., Megens, H. J. W. C., Crooijmans, R. P. M. A., Groenen, M. & Madsen, O., 14 Feb 2020, WIAS Annual Conference 2020: Frontiers in Animal Sciences. WIAS, p. 25-25

Research output: Chapter in Book/Report/Conference proceedingAbstract

Open Access
2019

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. & Schook, L. B., 7 Jul 2019, ISAG 2019 Abstract Book: 37th International Society for Animal Genetics Conference, July 7-12, 2019 - Lleida, Spain. p. 158-158

Research output: Chapter in Book/Report/Conference proceedingAbstract

Broadening the miRNA catalogue in livestock species: A contribution to the functional annotation of animal genomes.

Amaral, A. J., Anthon, C., Corsi, G., Vasconcelos, A., Marthey, S., Hoffmann, A., Lagnel, J., Haack, F., Pokharel, K., Palasca, O., Seemann, S. E., Gama, L., Groenen, M., Kantanen, J., Crooijmans, R. P. M. A., Rijnkels, M., Kalbfleisch, T., Giuffra, E., Stadler, P. F., Madsen, O. & 1 others, Gorodkin, J., 9 Jul 2019, ISAG 2019 Abstracts Book: 37th International Society for Animal Genetics Conference, July 7-12, 2019 - Lleida, Spain. p. 51-52

Research output: Chapter in Book/Report/Conference proceedingAbstract

Fetal genotype effects on morphomics, fatty acids composition and transcriptomics in swine

Garcia Contreras, C., Vazquez-Gomez, M., Madsen, O., Groenen, M., Astiz, S., Nunez, Y., Benitez, R., Heras-Molina, A., Fernandez, A., Isabel, B., Rey, A. I., Gonzalez-Bulnes, A. & Ovilo, C., 7 Jul 2019, ISAG 2019 Abstract Book: 37th International Society for Animal Genetics Conference, July 7-12, 2019 - Lleida, Spain. p. 148-149

Research output: Chapter in Book/Report/Conference proceedingAbstract

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)
Open Access

The little Pygmy hog (Porcula salvania), a big piece in resolving the fascinating history of the complex speciation of the Suidae

Liu, L., Bosse, M., Megens, H. J. W. C., Frantz, L. A. F., Lee, Y. L., Irving-Pease, E. K., Narayan, G., Groenen, M. & Madsen, O., 9 Jul 2019, ISAG 2019 Abstracts Book: 37th International Society for Animal Genetics Conference, July 7-12, 2019 - Lleida, Spain. p. 24-25

Research output: Chapter in Book/Report/Conference proceedingAbstract

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)

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 proceedingAbstract

2017

A comprehensive set of lncRNAs on porcine chromosomeX

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

Research output: Contribution to conferencePosterAcademic

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 others, Harrow, 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

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)

Modifications in liver transcriptomic profile of fattening lambs by early suckled milk intake level

Santos, A., Giraldez, F. J., Groenen, M., Madsen, O., Frutos, J., Valdes, C. & Andres, S., 28 Aug 2017, p. 388.

Research output: Contribution to conferenceAbstractAcademic

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
12 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
13 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)
14 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
70 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
18 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
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
25 Citations (Scopus)

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

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

14 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
31 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

101 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

8 Citations (Scopus)

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

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)

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

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

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
40 Citations (Scopus)
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 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

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
64 Citations (Scopus)

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

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

16 Citations (Scopus)