@article{Marchand2016,
    author = {Marchand, Virginie and Blanloeil-Oillo, Florence and Helm, Mark and Motorin, Yuri},
    title = "{Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA}",
    journal = {Nucleic Acids Research},
    volume = {44},
    number = {16},
    pages = {e135-e135},
    year = {2016},
    month = {06},
    abstract = "{RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from Bacteria, Archaea and Eukarya. RNAs bearing 2'-O-methylations show increased resistance to degradation and enhanced stability in helices. While the exact role of each 2'-O-Me residue remained elusive, the catalytic protein Fibrillarin (Nop1 in yeast) responsible for 2'-O-methylation in eukaryotes, is associated with human pathologies. Therefore, there is an urgent need to precisely map and quantify hundreds of 2'-O-Me residues in RNA using high-throughput technologies. Here, we develop a reliable protocol using alkaline fragmentation of total RNA coupled to a commonly used ligation approach, and Illumina sequencing. We describe a methodology to detect 2'-O-methylations with high sensitivity and reproducibility even with limited amount of starting material (1 ng of total RNA). The method provides a quantification of the 2'-O-methylation occupancy of a given site, allowing to detect relatively small changes (\\&gt;10\\%) in 2'-O-methylation profiles. Altogether this technique unlocks a technological barrier since it will be applicable for routine parallel treatment of biological and clinical samples to decipher the functions of 2'-O-methylations in pathologies.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkw547},
    url = {https://doi.org/10.1093/nar/gkw547},
    eprint = {https://academic.oup.com/nar/article-pdf/44/16/e135/17437693/gkw547.pdf},
}

@article{Erales2017,
author = {Jenny Erales  and Virginie Marchand  and Baptiste Panthu  and Sandra Gillot  and Stéphane Belin  and Sandra E. Ghayad  and Maxime Garcia  and Florian Laforêts  and Virginie Marcel  and Agnès Baudin-Baillieu  and Pierre Bertin  and Yohann Couté  and Annie Adrait  and Mélanie Meyer  and Gabriel Therizols  and Marat Yusupov  and Olivier Namy  and Théophile Ohlmann  and Yuri Motorin  and Frédéric Catez  and Jean-Jacques Diaz },
title = {Evidence for rRNA 2\&\#x2032;-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes},
journal = {Proceedings of the National Academy of Sciences},
volume = {114},
number = {49},
pages = {12934-12939},
year = {2017},
doi = {10.1073/pnas.1707674114},
URL = {https://www.pnas.org/doi/abs/10.1073/pnas.1707674114},
eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.1707674114}
}

@article{Marcel2021,
    author = {Marcel, Virginie and Kielbassa, Janice and Marchand, Virginie and Natchiar, Kundhavai S and Paraqindes, Hermes and Van Long, Flora Nguyen and Ayadi, Lilia and Bourguignon-Igel, Valérie and Monaco, Piero Lo and Monchiet, Déborah and Scott, Véronique and Tonon, Laurie and Bray, Susan E and Diot, Alexandra and Jordan, Lee B and Thompson, Alastair M and Bourdon, Jean-Christophe and Dubois, Thierry and André, Fabrice and Catez, Frédéric and Puisieux, Alain and Motorin, Yuri and Klaholz, Bruno P and Viari, Alain and Diaz, Jean-Jacques},
    title = "{Ribosomal RNA 2' O-methylation as a novel layer of inter-tumour heterogeneity in breast cancer}",
    journal = {NAR Cancer},
    volume = {3},
    number = {1},
    year = {2021},
    month = {02},
    abstract = "{Following publication of their article (1), the Authors realise that one supplementary file was missing. The published article has been updated to include the file. This correction does not affect the results or the conclusions of the article.}",
    issn = {2632-8674},
    doi = {10.1093/narcan/zcab006},
    url = {https://doi.org/10.1093/narcan/zcab006},
    note = {zcab006},
    eprint = {https://academic.oup.com/narcancer/article-pdf/3/1/zcab006/38376339/zcab006.pdf},
}

@article{birkedal2014,
	title = {Profiling of Ribose Methylations in RNA by High-Throughput Sequencing},
	author = {Birkedal, Ulf and Christensen-Dalsgaard, Mikkel and Krogh, Nicolai and Sabarinathan, Radhakrishnan and Gorodkin, Jan and Nielsen, Henrik},
	year = {2014},
	month = {11},
	date = {2014-11-21},
	journal = {Angewandte Chemie International Edition},
	pages = {n/a--n/a},
	doi = {10.1002/anie.201408362},
	url = {http://dx.doi.org/10.1002/anie.201408362},
	langid = {en}
}

@article{birkedal2014,
	title = {Profiling of Ribose Methylations in RNA by High-Throughput Sequencing},
	author = {Birkedal, Ulf and Christensen-Dalsgaard, Mikkel and Krogh, Nicolai and Sabarinathan, Radhakrishnan and Gorodkin, Jan and Nielsen, Henrik},
	year = {2014},
	month = {11},
	date = {2014-11-21},
	journal = {Angewandte Chemie International Edition},
	pages = {n/a--n/a},
	doi = {10.1002/anie.201408362},
	url = {http://dx.doi.org/10.1002/anie.201408362},
	langid = {en}
}

@article{zhang2020,
	title = {ComBat-seq: batch effect adjustment for RNA-seq count data},
	author = {Zhang, Yuqing and Parmigiani, Giovanni and Johnson, W Evan},
	year = {2020},
	month = {09},
	date = {2020-09-01},
	journal = {NAR Genomics and Bioinformatics},
	volume = {2},
	number = {3},
	doi = {10.1093/nargab/lqaa078},
	url = {http://dx.doi.org/10.1093/nargab/lqaa078},
	langid = {en}
}
