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Research Output 1988 2019

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

Epigenomics
DNA Methylation
Cognition
Genes
Overlapping Genes
2 Citations (Scopus)

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Frantz, L. A. F., Haile, J., Lin, A. T., Scheu, A., Geörg, C., Benecke, N., Alexander, M., Linderholm, A., Mullin, V. E., Daly, K. G., Battista, V. M., Price, M., Gron, K. J., Alexandri, P., Arbogast, R. M., Arbuckle, B., Bǎlǎşescu, A., Barnett, R., Bartosiewicz, L., Baryshnikov, G. & 80 others, Bonsall, C., Borić, D., Boroneanţ, A., Bulatović, J., Çakirlar, C., Carretero, J. M., Chapman, J., Church, M., Crooijmans, R., De Cupere, B., Detry, C., Dimitrijevic, V., Dumitraşcu, V., Du Plessis, L., Edwards, C. J., Erek, C. M., Erim-Özdoǧan, A., Ervynck, A., Fulgione, D., Gligor, M., Götherström, A., Gourichon, L., Groenen, M. A. M., Helmer, D., Hongo, H., Horwitz, L. K., Irving-Pease, E. K., Lebrasseur, O., Lesur, J., Malone, C., Manaseryan, N., Marciniak, A., Martlew, H., Mashkour, M., Matthews, R., Matuzeviciute, G. M., Maziar, S., Meijaard, E., McGovern, T., Megens, H. J., Miller, R., Mohaseb, A. F., Orschiedt, J., Orton, D., Papathanasiou, A., Pearson, M. P., Pinhasi, R., Radmanović, D., Ricaut, F. X., Richards, M., Sabin, R., Sarti, L., Schier, W., Sheikhi, S., Stephan, E., Stewart, J. R., Stoddart, S., Tagliacozzo, A., Tasić, N., Trantalidou, K., Tresset, A., Valdiosera, C., Van Den Hurk, Y., Van Poucke, S., Vigne, J. D., Yanevich, A., Zeeb-Lanz, A., Triantafyllidis, A., Gilbert, M. T. P., Schibler, J., Rowley-Conwy, P., Zeder, M., Peters, J., Cucchi, T., Bradley, D. G., Dobney, K., Burger, J., Evin, A., Girdland-Flink, L. & Larson, G., 27 Aug 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17231-17238 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Sus scrofa
Swine
Middle East
Mitochondrial DNA
Gene Flow

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

Livestock
MicroRNAs
Genome
Sus scrofa
Technology

Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs

Upadhyay, M., Bortoluzzi, C., Barbato, M., Ajmone-Marsan, P., Colli, L., Ginja, C., Sonstegard, T. S., Bosse, M., Lenstra, J. A., Groenen, M. A. M. & Crooijmans, R. P. M. A., Jun 2019, In : Evolutionary Applications. 12, 5, p. 951-963

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Single Nucleotide Polymorphism
cattle
genome
Genome
ancestry
6 Citations (Scopus)

Deleterious alleles in the context of domestication, inbreeding, and selection

Bosse, M., Megens, H-J., Derks, M. F. L., de Cara, Á. M. R. & Groenen, M. A. M., 2019, In : Evolutionary Applications. 12, 1, p. 6-17

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Inbreeding
domestication
inbreeding
allele
domestic species

Detection of a Frameshift Deletion in the SPTBN4 Gene Leads to Prevention of Severe Myopathy and Postnatal Mortality in Pigs

Derks, M. F. L., Harlizius, B., Lopez, M. S., Greijdanus-van der Putten, S., Dibbits, B. W., Laport, K., Megens, H. J. W. C. & Groenen, M., 26 Nov 2019, In : Frontiers in Genetics Livestock Genomics. 10, 9 p., 1226.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Spectrin
Muscular Diseases
Breeding
Swine
Mortality

Detection of reciprocal translocations in pigs using short read sequencing

Bouwman, A. C., te Pas, M. F. W. (ed.), Derks, M. F. L. (ed.), Groenen, M. (ed.), Veerkamp, R. F. (ed.), Broekhuijse, M. (ed.) & Harlizius, B. (ed.), 28 Aug 2019, Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Wageningen Academic Publishers, p. 255-255 (Book of abstracts EAAP; no. 25).

Research output: Chapter in Book/Report/Conference proceedingAbstract

Detection of reciprocal translocations using short read sequencing

Bouwman, A. C., te Pas, M. F. W., Derks, M. F. L., Groenen, M., Veerkamp, R. F., Broekhuijse, M. L. W. J. & Harlizius, B., 10 Feb 2019.

Research output: Contribution to conferencePosterAcademic

Open Access
2 Citations (Scopus)

Exploring the unmapped DNA and RNA reads in a songbird genome

Laine, V. N., Gossmann, T. I., van Oers, K., Visser, M. E. & Groenen, M. A. M., 8 Jan 2019, In : BMC Genomics. 20, 1, 19.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Songbirds
Genome
RNA
DNA
Trypanosoma

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

transcriptomics
fetus
fatty acid composition
swine
genotype
1 Citation (Scopus)

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
1 Citation (Scopus)

Genomic relatedness and diversity of Swedish native cattle breeds

Upadhyay, M., Eriksson, S., Mikko, S., Strandberg, E., Stålhammar, H., Groenen, M. A. M., Crooijmans, R. P. M. A., Andersson, G. & Johansson, A. M., 2 Oct 2019, In : Genetics Selection Evolution. 51, 1, 56.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
cattle breeds
relatedness
cattle
genomics
breeds

High resolution copy number variation analysis using two cattle genome assemblies

Lee, Y. L., Bosse, M. (ed.), Veerkamp, R. F. (ed.), Mullaart, E. (ed.), Groenen, M. (ed.) & Bouwman, A. C. (ed.), 26 Aug 2019, Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. Wageningen Academic Publishers, 209 p. (Book of abstracts EAAP; no. 25).

Research output: Chapter in Book/Report/Conference proceedingAbstract

4 Citations (Scopus)

Loss of function mutations in essential genes cause embryonic lethality in pigs

Derks, M. F. L., Gjuvsland, A. B., Bosse, M., Lopes, M. S., van Son, M., Harlizius, B., Tan, B. F., Hamland, H., Grindflek, E., Groenen, M. A. M. & Megens, H. J., 1 Mar 2019, In : Plos Genetics. 15, 3, p. e1008055

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lethal Genes
Essential Genes
lethal genes
pig
mutation
Open Access
placenta
vertebrate
genome
vertebrates
gene

The Genomic Complexity of a Large Inversion in Great Tits

da Silva, V. H., Laine, V. N., Bosse, M., Spurgin, L. G., Derks, M. F. L., van Oers, K., Dibbits, B., Slate, J., Crooijmans, R. P. M. A., Visser, M. E. & Groenen, M. A. M., 1 Jul 2019, In : Genome Biology and Evolution. 11, 7, p. 1870-1881 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Birds
genomics
Haplotypes
birds
haplotypes

The influence of CRISPR-Cas on animal breeding

Groenen, M., 20 Jun 2019

Research output: Non-textual formDigital or Visual ProductsOther research output

Open Access
animal breeding
animal welfare
genes
breeding
animals

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

Suidae
Eurasia
wild boars
history
Sus scrofa
Open Access
domestication
genetic drift
population bottleneck
population size
genome
genomics
homozygosity
inbreeding
population size
genome
2018
Open Access
7 Citations (Scopus)

A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour

Kim, J. M., Santure, A. W., Barton, H. J., Quinn, J. L., Cole, E. F., Visser, M. E., Sheldon, B. C., Groenen, M. A. M., van Oers, K. & Slate, J., Jul 2018, In : Molecular Ecology Resources. 18, 4, p. 877-891

Research output: Contribution to journalArticleAcademicpeer-review

Parus major
genotyping
Single Nucleotide Polymorphism
animal breeding
assays
2 Citations (Scopus)
Open Access
Dwarfism
Chickens
Proteins
Nonsense Codon
Chromosomes, Human, Pair 1

A survey of deleterious variation in highly managed pig populations

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Lopes, M. S., Harlizius, B. & Groenen, M., 24 Feb 2018, Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. 7 p. 11.522

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

Open Access
swine
genome
mutation
lethal genes
inbreeding depression
6 Citations (Scopus)

A survey of functional genomic variation in domesticated chickens

Derks, M. F. L., Megens, H. J., Bosse, M., Visscher, J., Peeters, K., Bink, M. C. A. M., Vereijken, A., Gross, C., De Ridder, D., Reinders, M. J. T. & Groenen, M. A. M., 16 Apr 2018, In : Genetics Selection Evolution. 50, 1, 17.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Chickens
genomics
purebreds
egg
chickens
3 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
3 Citations (Scopus)

CNVs are associated with genomic architecture in a songbird

da Silva, V. H., Laine, V. N., Bosse, M., van Oers, K., Dibbits, B., Visser, M. E., Crooijmans, R. P. M. A. & Groenen, M. A. M., 13 Mar 2018, In : BMC Genomics. 19, Supplement 2, 195.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Songbirds
Birds
History
Overlapping Genes
Genome
5 Citations (Scopus)

Early and late feathering in Turkey and chicken: Same gene but different mutations

Derks, M. F. L., Herrero-Medrano, J. M., Crooijmans, R. P. M. A., Vereijken, A., Long, J. A., Megens, H. J. & Groenen, M. A. M., 22 Mar 2018, In : Genetics Selection Evolution. 50, 1, 7.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Prolactin Receptors
Turkey
Chickens
mutation
Turkey (country)
10 Citations (Scopus)

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Giuffra, E., Tuggle, C. K. & Groenen, M., 31 Oct 2018, In : Annual Review of Animal Biosciences. 7, p. 13.1-13.24

Research output: Contribution to journalArticleAcademicpeer-review

Genome
genome
animals
genomics
Domestic Animals
10 Citations (Scopus)

Genome-wide characterization of selection signatures and runs of homozygosity in Ugandan goat breeds

Onzima, R. B., Upadhyay, M. R., Doekes, H. P., Brito, L. F., Bosse, M., Kanis, E., Groenen, M. A. M. & Crooijmans, R. P. M. A., 14 Aug 2018, In : Frontiers in Genetics. 9, 318.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Goats
Inbreeding
Genome
Genetic Selection
Body Size
6 Citations (Scopus)

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds

Onzima, R. B., Upadhyay, M. R., Mukiibi, R., Kanis, E., Groenen, M. A. M. & Crooijmans, R. P. M. A., 1 Feb 2018, In : Animal Genetics. 49, 1, p. 59-70

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
goat breeds
Boer (goat breed)
Goats
population structure
Genome

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

stem cells
feed conversion
nutrient transport
livestock production
marker-assisted selection
5 Citations (Scopus)
Inbreeding
Breeding
Chickens
Demography
Gene Flow
6 Citations (Scopus)
Open Access
Livestock
selection response
livestock
marker-assisted selection
Multifactorial Inheritance
Open Access
selection response
marker-assisted selection
livestock
genome
alleles
Open Access
homozygosity
demography
poultry
genome
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 genomic perspective about wild boar demography and evolution

Amills, M., Megens, H. J. W. C., Manunza, A., Ramos-Onsins, S. E. & Groenen, M., 2017, Ecology, Conservation and Management of Wild Pigs and Peccaries. Melletti, M. & Meijaard, E. (eds.). Cambridge University Press, p. 376-387

Research output: Chapter in Book/Report/Conference proceedingChapter

wild boars
demography
genomics
Suidae
Sus
7 Citations (Scopus)

A history of hybrids? Genomic patterns of introgression in the True Geese

Ottenburghs, J., Megens, H. J., Kraus, R. H. S., van Hooft, P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. T., 2017, In : BMC Evolutionary Biology. 17, 1, 201.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
introgression
geese
genomics
hybridization
history

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

A survey of deleterious variants in highly managed commercial layer lines

Derks, M. F. L., Megens, H. J. W. C., Bosse, M., Gross, C., Reijnders, M., de Ridder, D. & Groenen, M., 2017.

Research output: Contribution to conferencePosterAcademic

Open Access
12 Citations (Scopus)

A systematic survey to identify lethal recessive variation in highly managed pig populations

Derks, M. F. L., Megens, H. J., Bosse, M., Lopes, M. S., Harlizius, B. & Groenen, M. A. M., 9 Nov 2017, In : BMC Genomics. 18, 1, 858.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Swine
Haplotypes
Population
Mummies
Genome Size

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

10 Citations (Scopus)

Distribution and functionality of copy number variation across European cattle populations

Upadhyay, M., Da Silva, V. H., Megens, H. J., Visker, M. H. P. W., Ajmone-Marsan, P., Bâlteanu, V. A., Dunner, S., Garcia, J. F., Ginja, C., Kantanen, J., Groenen, M. A. M. & Crooijmans, R. P. M. A., 2017, In : Frontiers in Genetics. 8, 12 p., 108.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Population
Odorant Receptors
Overlapping Genes
Balkan Peninsula
Genes

Evolutionary History, Selective Sweeps and Deleterious Variation in the Pig

Groenen, M., Jan 2017.

Research output: Contribution to conferenceOtherAcademic

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
30 Citations (Scopus)

Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

Upadhyay, M. R., Chen, W., Lenstra, J. A., Goderie, C. R. J., MacHugh, D. E., Park, S. D. E., Magee, D. A., Matassino, D., Ciani, F., Megens, H. J., van Arendonk, J. A. M. & Groenen, M. A. M., 2017, In : Heredity. 118, p. 169-176

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Gene Flow
Population
Ancient History
Human Migration
Demography
25 Citations (Scopus)

Genome-wide SNP data unveils the globalization of domesticated pigs

Yang, B., Cui, L., Pérez-Enciso, M., Traspov, A., Crooijmans, R. P. M. A., Zinovieva, N., Schook, L. B., Archibald, A., Gatphayak, K., Knorr, C., Triantafyllidis, A., Alexandri, P., Semiadi, G., Hanotte, O., Dias, D., Dovč, P., Uimari, P., Iacolina, L., Scandura, M., Groenen, M. A. M. & 2 others, Huang, L. & Megens, H. J., 2017, In : Genetics, Selection, Evolution. 49, 15 p., 71.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Internationality
globalization
pig
single nucleotide polymorphism
Single Nucleotide Polymorphism

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

milk consumption
transcriptomics
finishing
lambs
liver
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