, Mobile Interspersed Repeats Are Major Structural Variants in the Human Genome, Cell, vol.141, issue.7, pp.1171-1182, 2010.
DOI : 10.1016/j.cell.2010.05.026
, TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates, Nucleic Acids Research, vol.12, issue.suppl_1, pp.47-52, 2008.
DOI : 10.1101/gr.229102
, Retrotransposons as epigenetic mediators of phenotypic variation in mammals, Nature Genetics, vol.25, issue.4, pp.361-365, 2001.
DOI : 10.1038/75546
, Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene, Nature Genetics, vol.11, issue.3, pp.261-262, 2003.
DOI : 10.1101/gr.172701
URL : https://hal.archives-ouvertes.fr/hal-00022443
, Mammalian microRNAs derived from genomic repeats, Trends in Genetics, vol.21, issue.6, pp.322-326, 2005.
DOI : 10.1016/j.tig.2005.04.008
, Regulatory BC1 RNA and the Fragile X Mental Retardation Protein: Convergent Functionality in Brain, PLoS ONE, vol.313, issue.11, p.15509, 2010.
DOI : 10.1371/journal.pone.0015509.s002
URL : https://doi.org/10.1371/journal.pone.0015509
, Specific expression of long noncoding RNAs in the mouse brain, Proceedings of the National Academy of Sciences, vol.8, issue.11, pp.716-721, 2008.
DOI : 10.1038/nn1576
, NONCODING RNAS IN THE MAMMALIAN CENTRAL NERVOUS SYSTEM, Annual Review of Neuroscience, vol.29, issue.1, pp.77-103, 2006.
DOI : 10.1146/annurev.neuro.29.051605.112839
, Noncoding RNAs in the Brain, Journal of Neuroscience, vol.27, issue.44, pp.11856-11859, 2007.
DOI : 10.1523/JNEUROSCI.3624-07.2007
, The impact of multiple splice sites in human L1 elements, Gene, vol.411, issue.1-2, pp.38-45, 2008.
DOI : 10.1016/j.gene.2007.12.022
, Non-coding RNAs: hope or hype?, Trends in Genetics, vol.21, issue.5, pp.289-297, 2005.
DOI : 10.1016/j.tig.2005.03.007
, Non-coding RNAs: regulators of disease, The Journal of Pathology, vol.444, issue.2, pp.126-139, 2010.
DOI : 10.1093/nass/2.1.251
, Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence, Nature Genetics, vol.589, issue.3, pp.359-364, 2009.
DOI : 10.1038/sj.onc.1208421
URL : https://hal.archives-ouvertes.fr/hal-00406268
, Germline deletion of the miR-17???92 cluster causes skeletal and growth defects in humans, Nature Genetics, vol.117, issue.10, pp.1026-1030, 2011.
DOI : 10.1111/j.1399-0004.2010.01374.x
, L'anorexie s??v??re du nourrisson r??unionnais : une nouvelle affection autosomique r??cessive ?, Archives de P??diatrie, vol.6, issue.7, pp.725-734, 1999.
DOI : 10.1016/S0929-693X(99)80354-6
, Regulating Gene Expression through RNA Nuclear Retention, Cell, vol.123, issue.2, pp.249-263, 2005.
DOI : 10.1016/j.cell.2005.08.033
URL : https://doi.org/10.1016/j.cell.2005.08.033
, Alu-SINE Exonization: En Route to Protein-Coding Function, Molecular Biology and Evolution, vol.22, issue.8, pp.1702-1711, 2005.
DOI : 10.1038/353864a0
URL : https://academic.oup.com/mbe/article-pdf/22/8/1702/13432748/msi164.pdf
, The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons, Science, vol.300, issue.5623, pp.1288-1291, 2003.
DOI : 10.1126/science.1082588
, Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature, Human Genomics, vol.5, issue.2, pp.90-98, 2011.
DOI : 10.1038/nrm2738
URL : https://humgenomics.biomedcentral.com/track/pdf/10.1186/1479-7364-5-2-90?site=humgenomics.biomedcentral.com
, Transposable elements in disease-associated cryptic exons, Human Genetics, vol.71, issue.2, pp.135-154, 2010.
DOI : 10.1128/MCB.14.2.951
, In Drosophila melanogaster the COM Locus Directs the Somatic Silencing of Two Retrotransposons through both Piwi-Dependent and -Independent Pathways, PLoS ONE, vol.16, issue.2, p.1526, 2008.
DOI : 10.1371/journal.pone.0001526.g007
, germline development, The Journal of Cell Biology, vol.1, issue.5, pp.905-913, 2010.
DOI : 10.1016/j.cell.2008.06.053
, Altered Expression of PIWI RNA in the Rat Brain After Transient Focal Ischemia, Stroke, vol.42, issue.4, pp.1105-1109, 2011.
DOI : 10.1161/STROKEAHA.110.598391
, Identification of piRNAs in the central nervous system, RNA, vol.17, issue.6, pp.1090-1099, 2011.
DOI : 10.1261/rna.2565011
, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003.
DOI : 10.1093/nar/gkg595
URL : https://academic.oup.com/nar/article-pdf/31/13/3406/9487491/gkg595.pdf
, S-domain assembly of the signal recognition particle, Current Opinion in Structural Biology, vol.13, issue.1, pp.64-70, 2003.
DOI : 10.1016/S0959-440X(02)00010-6
, Crystal Structure of the Ribonucleoprotein Core of the Signal Recognition Particle, Science, vol.287, issue.5456, pp.1232-1239, 2000.
DOI : 10.1126/science.287.5456.1232
, Prediction of signal recognition particle RNA genes, Nucleic Acids Research, vol.30, issue.15, pp.3368-3377, 2002.
DOI : 10.1093/nar/gkf468
URL : https://academic.oup.com/nar/article-pdf/30/15/3368/6375059/gkf468.pdf
, Self Containment, a Property of Modular RNA Structures, Distinguishes microRNAs, PLoS Computational Biology, vol.31, issue.8, p.1000150, 2008.
DOI : 10.1371/journal.pcbi.1000150.s006
URL : https://doi.org/10.1371/journal.pcbi.1000150
, Molecular Evolution of piRNA and Transposon Control Pathways in Drosophila, Cold Spring Harbor Symposia on Quantitative Biology, vol.74, issue.0, pp.225-234, 2009.
DOI : 10.1101/sqb.2009.74.052
URL : http://europepmc.org/articles/pmc3181074?pdf=render
, Identification of Mammalian microRNA Host Genes and Transcription Units, Genome Research, vol.14, issue.10a, pp.1902-1910, 2004.
DOI : 10.1101/gr.2722704
URL : http://genome.cshlp.org/content/14/10a/1902.full.pdf
, Failure of neuronal homeostasis results in common neuropsychiatric phenotypes, Nature, vol.313, issue.7215, pp.912-918, 2008.
DOI : 10.1038/nature07457
, Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease, Physiological Reviews, vol.87, issue.3, pp.799-823, 2007.
DOI : 10.1126/science.1111444
URL : http://physrev.physiology.org/content/physrev/87/3/799.full.pdf
, Translational Regulation of the Human Achaete-scute Homologue-1 by Fragile X Mental Retardation Protein, Journal of Biological Chemistry, vol.126, issue.7, pp.4255-4266, 2009.
DOI : 10.1126/science.1155998
, Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor, BMC Bioinformatics, vol.7, issue.1, p.474, 2006.
DOI : 10.1186/1471-2105-7-474
, Human genetic variation recognizes functional elements in noncoding sequence, Genome Research, vol.20, issue.3, pp.311-319, 2010.
DOI : 10.1101/gr.094151.109
URL : http://genome.cshlp.org/content/20/3/311.full.pdf
, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389
URL : https://academic.oup.com/nar/article-pdf/25/17/3389/3639509/25-17-3389.pdf
, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.235, issue.4, pp.955-964, 1997.
DOI : 10.1006/jmbi.1994.1074
, fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences, Nucleic Acids Research, vol.35, issue.Database, pp.145-148, 2007.
DOI : 10.1093/nar/gkl837
URL : https://academic.oup.com/nar/article-pdf/35/suppl_1/D145/3839909/gkl837.pdf
, Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data, Bioinformatics, vol.22, issue.14, pp.197-202, 2006.
DOI : 10.1093/bioinformatics/btl257
URL : https://academic.oup.com/bioinformatics/article-pdf/22/14/e197/617128/btl257.pdf
, microPred: effective classification of pre-miRNAs for human miRNA gene prediction, Bioinformatics, vol.31, issue.Database Issue, pp.989-995, 2009.
DOI : 10.1093/nar/gkg595
URL : https://academic.oup.com/bioinformatics/article-pdf/25/8/989/16892646/btp107.pdf
, , p.4985, 2012.