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Articles by Mathieu Charles
Abstract Following their domestication, chickens were translocated around the world to novel environments. Through a combination of natural and artificial selection, chickens adapted to these local conditions, creating significant genetic diversity across populations worldwide. Studying this diversity in the context of local environmental conditions may offer insights into mechanisms of adaptation to environmental stressors.
Discovery of a regulatory polymorphism in the bovine PICALM gene associated with milk αS1‐casein concentration
DATA AVAILABILITY STATEMENT No data availability statement is needed as no data were generated, except the luciferase measurements but it is not usually required.
Functional impact of splicing variants in the elaboration of complex traits in cattle - Nature Communications
Abstract GWAS conducted directly on imputed whole genome sequence have led to the identification of numerous genetic variants associated with agronomic traits in cattle. However, such variants are often simply markers in linkage disequilibrium with the actual causal variants, which is a limiting factor for the development of accurate genomic predictions. It is possible to identify causal variants by integrating information on how variants impact gene expression into GWAS output.
Genetic regulation of gene expression across multiple tissues in chickens - Nature Genetics
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Abstract The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking.
By Dailu Guan, Xiaoning Zhu, Conghao Zhong, Yali Hou, Yuelin Yao, Yuzhe Wang, Tianyi Xu, Hongwei Yin, Jinyan Teng, Zhiting Xu, Fabien Degalez, Mingshan Wang, Minsheng Peng, Mathieu Charles, Jacqueline Smith, Albert Johannes Buitenhuis, Goutam Sahana, Wesley C. Warren, Greger Larson, Xin Zhao, Bingjie Li, Ruidong Xiang, Zhe Zhang, Zhang Xuan Zhang, George Liu, Ning Yang, Xiaoxiang Hu, Huaijun Zhou
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Nature
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Nuclear sequences of mitochondrial origin in domestic yak - Scientific Reports
Abstract Mitochondrial DNA sequences are frequently transferred into the nuclear genome, generating nuclear mitochondrial DNA sequences (NUMTs). Here, we analysed, for the first time, NUMTs in the domestic yak genome. We obtained 499 alignment matches covering 340.2 kbp of the yak nuclear genome. After a merging step, we identified 167 NUMT regions with a total length of ~ 503 kbp, representing 0.02% of the nuclear genome.
Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.
Abstract Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs).
Literatuur als versterker van cultureel imperialisme
De meeste uitgeverijen in het Westen zijn witte bastions. Zowel fictie als non-fictie werd lang gedomineerd door mannen. Dat was niet omdat zij beter, interessanter en met meer expertise schreven. Ze hadden op alle cruciale punten in het creatie- en productieproces van een publicatie de touwtjes in handen.
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