List of works by Martien Groenen

2003 Spring meeting of the WPSA French Branch

article

A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwarfism in Chicken.

scientific article published on 7 June 2018

A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the turkey and chicken genomes

scientific article

A chondrogenesis-related lipocalin cluster includes a third new gene, CALgamma

scientific article

A comparative map of chicken chromosome 24 and human chromosome 11.

scientific article

A decade of pig genome sequencing: a window on pig domestication and evolution

scientific article

A genetic linkage map of sole (Solea solea): a tool for evolutionary and comparative analyses of exploited (flat)fishes

scientific article

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

scientific article

A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6.

scientific article

A genome-wide scan for signatures of directional selection in domesticated pigs

scientific article

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

scientific article published on 23 March 2018

A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content.

scientific article

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

scientific article published on 16 December 2008

A high-resolution comparative RH map of porcine Chromosome (SSC) 2

article

A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes

scientific article

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

scientific article

A novel activating chicken IgY FcR is related to leukocyte receptor complex (LRC) genes but is located on a chromosomal region distinct from the LRC and FcR gene clusters

scientific article

A physical map of the chicken genome

scientific article

A radiation hybrid map of chicken Chromosome 4.

scientific article

A survey of functional genomic variation in domesticated chickens.

scientific article published on 16 April 2018

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

scientific article published on 9 November 2017

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

scientific article

ALC (adjacent to LMX1 in chick) is a novel dorsal limb mesenchyme marker

scientific article published on 01 December 2003

Accuracy of Predicted Genomic Breeding Values in Purebred and Crossbred Pigs

scientific article published on 26 May 2015

Accuracy of genomic prediction using deregressed breeding values estimated from purebred and crossbred offspring phenotypes in pigs.

scientific article published on July 2015

Accuracy of genomic prediction using imputed whole-genome sequence data in white layers.

scientific article

Accuracy of imputation using the most common sires as reference population in layer chickens

scientific article published on 18 August 2015

Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae

scientific article published on 20 April 2015

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

scientific article published on 03 December 2020

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

scientific article published on 5 October 2015

Altered Hippocampal Epigenetic Regulation Underlying Reduced Cognitive Development in Response to Early Life Environmental Insults

scientific article published on 04 February 2020

An assessment of European pig diversity using molecular markers: Partitioning of diversity among breeds

Analyses of pig genomes provide insight into porcine demography and evolution

scientific article

Analysis of the ends of bacteriophage Mu using site-directed mutagenesis

scientific article published on 01 June 1986

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

scientific article published on 12 August 2019

Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome.

scientific article published on 12 August 2009

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

article

Asian low-androstenone haplotype on pig chromosome 6 does not unfavorably affect production and reproduction traits

article

Assessing the contribution of breeds to genetic diversity in conservation schemes.

scientific article published in September 2002

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

article

Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

scientific article

Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication

scientific article

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes

scientific article published on 01 February 2020

CNVs are associated with genomic architecture in a songbird.

scientific article published on 13 March 2018

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

scientific article published in December 2012

Characterization of a GlyCAM1-like gene (glycosylation-dependent cell adhesion molecule 1) which is highly and specifically expressed in the lactating bovine mammary gland.

scientific article published on June 1995

Chicken Ig-like receptor B2, a member of a multigene family, is mainly expressed on B lymphocytes, recruits both Src homology 2 domain containing protein tyrosine phosphatase (SHP)-1 and SHP-2, and inhibits proliferation

scientific article

Chromosomal assignment of chicken clone contigs by extending the consensus linkage map

scientific article published on 01 June 2005

Combining two Meishan F2 crosses improves the detection of QTL on pig chromosomes 2, 4 and 6.

scientific article

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

scientific article

Comparative analysis of the natriuretic peptide precursor gene cluster in vertebrates reveals loss of ANF and retention of CNP-3 in chicken.

scientific article published in July 2005

Comparative map between chicken chromosome 15 and human chromosomal region 12q24 and 22q11-q12.

scientific article published in September 2003

Comparative mapping of human Chromosome 19 with the chicken shows conserved synteny and gives an insight into chromosomal evolution

scientific article published on 01 June 2002

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

scientific article

Comparison of the crystallin mRNA populations from rat, calf and duck lens. Evidence for a longer αA2-mRNA and two distinct αB2-mRNAs in the birds

scientific article published on 01 April 1985

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.

scientific article

Confirmation of quantitative trait loci affecting fatness in chickens.

scientific article published on March 2005

Confirmation that the casein gene cluster resides on cattle Chromosome 6

article

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

scientific article

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

scientific article

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

scientific article published on 22 April 2015

Correction to: Genome-wide SNP data unveils the globalization of domesticated pigs

scientific article published on 04 June 2020

Cytogenetics, conserved synteny and evolution of chicken fucosyltransferase genes compared to human.

scientific article published in January 2003

DNA sequences at the ends of the genome of bacteriophage Mu essential for transposition.

scientific article published on April 1985

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

scientific article published on 08 February 2019

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

scientific article published in January 2019

Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology

scientific article

Detection of QTL for immune response to sheep red blood cells in laying hens

article

Detection of QTL for innate: Non-specific antibody levels binding LPS and LTA in two independent populations of laying hens

article

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

scientific article published on 26 November 2019

Development of a genetic tool for product regulation in the diverse British pig breed market

scientific article

Development of a single nucleotide polymorphism map of porcine chromosome 2.

scientific article published in December 2003

Distinguishing migration events of different timing for wild boar in the Balkans

Distribution and Functionality of Copy Number Variation across European Cattle Populations

scientific article published on 23 August 2017

Domesticated species form a treasure-trove for molecular characterization of Mendelian traits by exploiting the specific genetic structure of these species in across-breed genome wide association studies.

scientific article published on 7 March 2012

ESTIMATION OF THE EXTENT OF LINKAGE DISEQUILIBRIUM IN SEVEN REGIONS OF THE PORCINE GENOME.

scientific article published in January 2005

Early and late feathering in turkey and chicken: same gene but different mutations.

scientific article published on 22 March 2018

East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis.

scientific article published on 10 December 2010

Evidence for adaptation of porcine Toll-like receptors.

scientific article published on 23 December 2015

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

scientific article

Evolution of Tibetan wild boars

scientific article

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

scientific article

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae.

scientific article published on 9 February 2016

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

scientific article published on 25 January 2016

Exploring the unmapped DNA and RNA reads in a songbird genome

scientific article published on 08 January 2019

Extending the chicken-human comparative map by placing 15 genes on the chicken linkage map

article

Extent of linkage disequilibrium in chicken

scientific article published on 01 January 2007

FISH mapping of 57 BAC clones reveals strong conservation of synteny between Galliformes and Anseriformes

scientific article published on 01 June 2007

FISH mapping of the alpha-S2 casein gene on river buffalo and cattle chromosomes identifies a nomenclature discrepancy in the bovine karyotype.

scientific article published in February 1996

FISH on avian lampbrush chromosomes produces higher resolution gene mapping

article

Fine mapping and imprinting analysis for fatness trait QTLs in pigs

article

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

scientific article published on 24 November 2020

Functional and population genetic features of copy number variations in two dairy cattle populations

scientific article published on 28 January 2020

GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

scientific article published on 24 July 2016

Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates

scientific article

Gene networks for total number born in pigs across divergent environments

article

Genetic Diversity Analysis Using Lowly Polymorphic Dominant Markers: The Example of AFLP in Pigs

article

Genetic and phenotypic relationships between blood gas parameters and ascites-related traits in broilers.

scientific article published in March 2009

Genetic consequences of breaking migratory traditions in barnacle geese Branta leucopsis.

scientific article published on 7 November 2013

Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers

scientific article published on 01 June 2006

Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome

scientific article published on 01 December 2005

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

scientific article published on 28 September 2016

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

scientific article published on 11 October 2017

Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)

scientific article

Genetic variances, heritabilities and maternal effects on body weight, breast meat yield, meat quality traits and the shape of the growth curve in turkey birds.

scientific article

Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay.

scientific article

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

scientific article (publication date: 2013)

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

scientific article

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels

scientific article published on 28 October 2020

Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

scholarly article by Robert B Onzima et al published 2018 in Frontiers in Genetics

Genome-wide SNP data unveils the globalization of domesticated pigs. ⬇️

scientific article published on 21 September 2017

Genome-wide SNP detection in the great tit Parus major using high throughput sequencing.

scientific article

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds.

scientific article

Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus)

scientific article published on 09 June 2021

Genome-wide candidate regions for selective sweeps revealed through massive parallel sequencing of DNA across ten turkey populations

scientific article

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.

scientific article

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

scientific article published on 17 January 2018

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

article

Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

scientific article

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

scientific article published on 30 April 2019

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

scientific article

Genomic diversity and differentiation of a managed island wild boar population

scientific article

Genomic relatedness and diversity of Swedish native cattle breeds

scientific article published on 02 October 2019

Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses

scientific article published on 19 January 2021

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

scientific article

Identification of QTLs involved in open-field behavior in young and adult laying hens.

scientific article published in May 2004

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

scientific article

Identification of high utility SNPs for population assignment and traceability purposes in the pig using high-throughput sequencing

scientific article published on 25 April 2011

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

scientific article published on 23 January 2014

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

scientific article published on 28 January 2020

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

scientific article

Improving the comparative map of SSC2p-q13 by sample sequencing of BAC clones.

scientific article

In SilicoIdentification and Mapping of Microsatellite Markers onSus ScrofaChromosome 4

scientific article published on 01 January 2007

Integration of chicken genomic resources to enable whole-genome sequencing.

scientific article published in January 2003

Interactions of the transposase with the ends of Mu: formation of specific nucleoprotein structures and non-cooperative binding of the transposase to its binding sites.

scientific article

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

scientific article

Large scale variation in DNA copy number in chicken breeds

scientific article

Linkage disequilibrium decay and haplotype block structure in the pig.

scientific article published on May 2008

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

article

Mapping of 16 ESTs expressed in the bovine mammary gland during lactation.

scientific article

Mapping of a site for packaging of bacteriophage Mu DNA

scientific article published on 01 July 1985

Metabolism of benzidine-based dyes and the appearance of mutagenic metabolites in urine of rats after oral or intraperitoneal administration.

scientific article published in June 1984

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

scientific article (2009)

Microarray data mining using Bioconductor packages.

scientific article

Mining for single nucleotide polymorphisms in pig genome sequence data

scientific article

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

scientific article published on 09 March 2020

Molecular cytogenetic definition of the chicken genome: the first complete avian karyotype.

scientific article

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Multicolour fluorescent detection and mapping of AFLP markers in chicken (Gallus domesticus)

scientific article published on 01 August 1999

Nucleotide sequence of the chicken HMGI-C cDNA and expression of the HMGI-C and IGF1 genes in autosomal dwarf chicken embryos.

scientific article published in July 1998

Number and mode of inheritance of QTL influencing backfat thickness on SSC2p in Sino-European pig pedigrees.

scientific article

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

scientific article published on 16 July 2009

On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis.

scientific article published on 09 January 2014

Oncopig Soft-Tissue Sarcomas Recapitulate Key Transcriptional Features of Human Sarcomas

scientific article

Overproduction of bovine beta-casein in Escherichia coli and engineering of its main chymosin cleavage site.

scientific article published on September 1993

POSA: perl objects for DNA sequencing data analysis

scientific article

Parallel genetic origin of foot feathering in birds

scientific article published on 28 April 2020

Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.

scientific article

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

scientific article

Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics

scientific article (publication date: April 2013)

Pig genome sequence--analysis and publication strategy

scientific article published on 19 July 2010

Population-level consequences of complementary sex determination in a solitary parasitoid.

scientific article published on 30 May 2015

Porcine colonization of the Americas: a 60k SNP story.

scientific article published on 19 December 2012

Precise centromere positioning on chicken chromosome 3.

scientific article published on 3 July 2010

Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region

scientific article

Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD

scientific article published on 23 September 2020

Quantitative genetics of wing morphology in the parasitoid wasp Nasonia vitripennis: hosts increase sibling similarity

scientific article published on 19 May 2020

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development

scientific article published on 28 August 2020

Recent natural selection causes adaptive evolution of an avian polygenic trait.

scientific article

Regional differences in recombination hotspots between two chicken populations

scientific article

Regional regulation of transcription in the bovine genome.

scientific article published on 3 June 2011

Regional regulation of transcription in the chicken genome

scientific article

Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape

scientific article

Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations

scientific article published on 10 December 2015

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates.

scientific article published on 23 October 2013

Response to Perrier and Charmantier: On the importance of time scales when studying adaptive evolution.

scientific article published on 4 April 2019

SNP marker detection and genotyping in tilapia

scientific article published on 24 April 2012

Second report on chicken genes and chromosomes 2005

article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Signatures of diversifying selection in European pig breeds.

scientific article

Signatures of selection in the genomes of commercial and non-commercial chicken breeds

scientific article (publication date: 2012)

Strong signatures of selection in the domestic pig genome

scientific article

Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.

scientific article

Systematic differences in the response of genetic variation to pedigree and genome-based selection methods.

scientific article published on 30 July 2014

TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data

scientific article

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations

scientific article

The Evolution of Suidae.

scientific article

The Genome of Winter Moth (Operophtera brumata) Provides a Genomic Perspective on Sexual Dimorphism and Phenology.

scientific article

The Genomes of the Livebearing Fish Species Poeciliopsis retropinna and Poeciliopsis turrubarensis Reflect Their Different Reproductive Strategies

scientific article published on 21 January 2020

The Genomic Complexity of a Large Inversion in Great Tits

scientific article published on 01 July 2019

The IGF2-intron3-G3072A substitution explains a major imprinted QTL effect on backfat thickness in a Meishan×European white pig intercross

scientific article published on 01 October 2004

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

scientific article published on 16 March 2016

The Visayan Warty Pig (<i>Sus cebifrons</i>) Genome Provides Insight Into Chromosome Evolution and Sensory Adaptation in Pigs

scientific article published in 2022

The X Chromosome harbors quantitative trait loci for backfat thickness and intramuscular fat content in pigs

The chicken leukocyte receptor complex: a highly diverse multigene family encoding at least six structurally distinct receptor types

scientific article published on July 2005

The complete sequence of the gene encoding bovine alpha s2-casein.

scientific article published on January 1993

The design and cross-population application of a genome-wide SNP chip for the great tit Parus major.

scientific article published on 5 April 2012

The development and characterization of a 60K SNP chip for chicken.

scientific article

The development of a genome wide SNP set for the Barnacle goose Branta leucopsis.

scientific article published on 10 July 2012

The distal end of porcine chromosome 6p is involved in the regulation of skatole levels in boars ⬇️

scientific article

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

scientific article

The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity

scientific article published on 28 March 2018

The genome of the live-bearing fish Heterandria formosa implicates a role of conserved vertebrate genes in the evolution of placental fish

scientific article published on 26 July 2019

The impact of genome editing on the introduction of monogenic traits in livestock.

scientific article published on 16 April 2018

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

scientific article

The nucleotide sequence of bovine MHC class IIDQB andDRB genes

article

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations

scientific article published on 30 September 2019

The use of blood gas parameters to predict ascites susceptibility in juvenile broilers.

scientific article published on August 2010

Third Report on Chicken Genes and Chromosomes 2015.

scientific article published on 14 July 2015

Time Course Transcriptomic Study Reveals the Gene Regulation During Liver Development and the Correlation With Abdominal Fat Weight in Chicken

scientific article published on 10 September 2021

Two genes involved in penicillin biosynthesis are linked in a 5.1 kb SalI fragment in the genome of Penicillium chrysogenum

article

Typing single-nucleotide polymorphisms using a gel-based sequencer: a new data analysis tool and suggestions for improved efficiency.

scientific article

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

scientific article

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

scientific article published on 10 June 2015

Variance component analysis of quantitative trait loci for pork carcass composition and meat quality on SSC4 and SSC111

article

Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey.

scientific article

Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo).

scientific article

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

scientific article

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

scientific article

Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

scientific article

pCADD: SNV prioritisation in Sus scrofa

scientific article published on 07 February 2020

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