Cummings CJ, Zoghbi HY: Fourteen and counting: unraveling trinucleotide repeat diseases. Human Molecular Genetics 2000, 9(6):909–916. 10.1093/hmg/9.6.909
Article
CAS
PubMed
Google Scholar
Usdin K: The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases. Genome Research 2008, 18(7):1011–1019. 10.1101/gr.070409.107
Article
PubMed Central
CAS
PubMed
Google Scholar
Mirkin SM: Expandable DNA repeats and human disease. Nature 2007, 447: 932–940. 10.1038/nature05977
Article
CAS
PubMed
Google Scholar
Richard GF, Kerrest A, Dujon B: Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes. Microbiol Mol Biol Rev 2008, 72(4):686–727. 10.1128/MMBR.00011-08
Article
PubMed Central
CAS
PubMed
Google Scholar
Richards RI: Dynamic mutations: a decade of unstable expanded repeats in human genetic disease. Human Molecular Genetics 2001, 10(20):2187–2194. 10.1093/hmg/10.20.2187
Article
CAS
PubMed
Google Scholar
Jasinska A, Michlewski G, de Mezer M, Sobczak K, Kozlowski P, Napierala M, Krzyzosiak WJ: Structures of trinucleotide repeats in human transcripts and their functional implications. Nucleic Acids Research 2003, 31(19):5463–5468. 10.1093/nar/gkg767
Article
PubMed Central
CAS
PubMed
Google Scholar
Wells RD, Dere R, Hebert ML, Napierala M, Son LS: Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Research 2005, 33(12):3785–3798. 10.1093/nar/gki697
Article
PubMed Central
CAS
PubMed
Google Scholar
Nenguke T, Aladjem MI, Gusella JF, Wexler NS, Project TVH, Arnheim N: Candidate DNA replication initiation regions at human trinucleotide repeat disease loci. Human Molecular Genetics 2003, 12(12):1461. 10.1093/hmg/ddg155
Article
CAS
Google Scholar
Cleary J, Nichol K, Wang YH, Pearson C: Evidence of cis-acting factors in replication-mediated trinucleotide repeat instability in primate cells. Nature Genetics 2002, 31: 37–46. 10.1038/ng870
Article
CAS
PubMed
Google Scholar
Brock GJR, Anderson NH, Monckton DG: Cis-Acting Modifiers of Expanded CAG/CTG Triplet Repeat Expandability: Associations with Flanking GC Content and Proximity to CpG Islands. Human Molecular Genetics 1999, 8(6):1061–1067. 10.1093/hmg/8.6.1061
Article
CAS
PubMed
Google Scholar
Libby RT, Hagerman KA, Pineda VV, Lau R, Cho DH, Baccam SL, Axford MM, Cleary JD, Moore JM, Sopher BL, Tapscott SJ, Filippova GN, Pearson CE, La Spada AR: CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination. PLoS Genet 2008, 4(11):e1000257. 10.1371/journal.pgen.1000257
Article
PubMed Central
PubMed
Google Scholar
Warby SC, Montpetit A, Hayden AR, Carroll JB, Butland SL, Visscher H, Collins JA, Semaka A, Hudson TJ, Hayden MR: CAG expansion in the Huntington disease gene is associated with a specific and targetable predisposing haplogroup. Am J Hum Genet 2009, 84(3):351–366. 10.1016/j.ajhg.2009.02.003
Article
PubMed Central
CAS
PubMed
Google Scholar
Boeva V, Regnier M, Papatsenko D, Makeev V: Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 2006, 22(6):676–684. 10.1093/bioinformatics/btk032
Article
CAS
PubMed
Google Scholar
Pellegrini M, Renda ME, Vecchio A: TRStalker: an efficient heuristic for finding fuzzy tandem repeats. Bioinformatics 2010, 26(12):i358–366. 10.1093/bioinformatics/btq209
Article
PubMed Central
CAS
PubMed
Google Scholar
Rolfsmeier ML, Dixon MJ, Pessoa-Brandão L, Pelletier R, Miret JJ, Lahue RS: Cis-Elements Governing Trinucleotide Repeat Instability in Saccharomyces cerevisiae. Genetics 2001, 157(4):1569–1579.
PubMed Central
CAS
PubMed
Google Scholar
Bichara M, Wagner J, Lambert IB: Mechanisms of tandem repeat instability in bacteria. Mutat Res 2006, 598(1–2):144–163. 10.1016/j.mrfmmm.2006.01.020
Article
CAS
PubMed
Google Scholar
Sobczak K, de Mezer M, Michlewski G, Krol J, Krzyzosiak WJ: RNA structure of trinucleotide repeats associated with human neurological diseases. Nucleic Acids Research 2003, 31(19):5469–5482. 10.1093/nar/gkg766
Article
PubMed Central
CAS
PubMed
Google Scholar
Heidenfelder BL, Makhof AM, Topal MD: Hairpin formation in Friedreich's Ataxia triplet-repeat expansion. J Biol Chem 2003, 278: 2425–2431. 10.1074/jbc.M210643200
Article
CAS
PubMed
Google Scholar
Marquis Gacy A, Goellner G, Juranic N, Macura S, McMurray CT: Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 1995, 81(4):533–540. 10.1016/0092-8674(95)90074-8
Article
Google Scholar
Reddy K, Tam M, Bowater RP, Barber M, Tomlinson M, Nichol Edamura K, Wang YH, Pearson CE: Determinants of R-loop formation at convergent bidirectionally transcribed trinucleotide repeats. Nucleic Acids Research 2011, 39(5):1749–1762. 10.1093/nar/gkq935
Article
PubMed Central
CAS
PubMed
Google Scholar
Michlewski G, Krzyzosiak WJ: Molecular Architecture of CAG Repeats in Human Disease Related Transcripts. Journal of Molecular Biology 2004, 340(4):665–679. 10.1016/j.jmb.2004.05.021
Article
CAS
PubMed
Google Scholar
Wang X, Vitalis A, Wyczalkowski MA, Pappu RV: Characterizing the conformational ensemble of monomeric polyglutamine. Proteins 2006, 63(2):297–311.
Article
CAS
PubMed
Google Scholar
Faux NG, Bottomley SP, Lesk AM, Irving JA, Morrison JR, de la Banda MG, Whisstock JC: Functional insights from the distribution and role of homopeptide repeat-containing proteins. Genome Research 2005, 15(4):537–551. 10.1101/gr.3096505
Article
PubMed Central
CAS
PubMed
Google Scholar
Kelkar YDD, Tyekucheva S, Chiaromonte F, Makova KDD: The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Research 2008, 18: 30–38.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vogler A, Keys C, Nemoto Y, Colman R, Jay Z, Keim P: Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7. Journal of Bacteriology 2006, 188(12):4253–63. 10.1128/JB.00001-06
Article
PubMed Central
CAS
PubMed
Google Scholar
Wooster R, Cleton-Jansen AM, Collins N, Mangion R, Cornelis J, Cooper C, Gusterson B, Ponder B, von Deimling A, Wiestler O, Cornelisse C, Devilee P, Stratton M: Instability of short tandem repeats (microsatellites) in human cancers. Nature Genetics 1994, 6(2):152–156. 10.1038/ng0294-152
Article
CAS
PubMed
Google Scholar
O'Dushlaine C, Edwards R, Park S, Shields D: Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biology 2005, 6(8):R69. 10.1186/gb-2005-6-8-r69
Article
PubMed Central
PubMed
Google Scholar
Legendre M, Pochet N, Pak T, Verstrepen KJ: Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research 2007, 17(12):1787–1796. 10.1101/gr.6554007
Article
PubMed Central
CAS
PubMed
Google Scholar
Benson G: Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research 1999, 27(2):573–580. 10.1093/nar/27.2.573
Article
PubMed Central
CAS
PubMed
Google Scholar
Grissa I, Vergnaud G, Pourcel C: CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 2007, 35(Web Server issue):W52-W57.
Article
PubMed Central
PubMed
Google Scholar
Kolpakov R, Bana G, Kucherov G: mreps: efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Research 2003, 31(13):3672–3678. 10.1093/nar/gkg617
Article
PubMed Central
CAS
PubMed
Google Scholar
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R: REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research 2001, 29(22):4633–42. 10.1093/nar/29.22.4633
Article
PubMed Central
CAS
PubMed
Google Scholar
Wexler Y, Yakhini Z, Kashi Y, Geiger D: Finding approximate tandem repeats in genomic sequences. Journal of Computational Biology 2005, 12(7):928–942. 10.1089/cmb.2005.12.928
Article
CAS
PubMed
Google Scholar
Sokol D, Benson G, Tojeira J: Tandem repeats over the edit distance. Bioinformatics 2007, 23(2):e30–35. 10.1093/bioinformatics/btl309
Article
CAS
PubMed
Google Scholar
Leclercq S, Rivals E, Jarne P: Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinformatics 2007, 8: 125. 10.1186/1471-2105-8-125
Article
PubMed Central
PubMed
Google Scholar
JasperReports Welcome Page[http://www.jasperforge.org]
ATRhunter Welcome Page[http://bioinfo.cs.technion.ac.il/atrhunter]
mreps Welcome Page[http://bioinfo.lifl.fr/mreps/]
TandemSWAN Welcome Page[http://favorov.imb.ac.ru/swan/home.html]
Tandem Repeats Finder Welcome Page[http://tandem.bu.edu/trf/trf.html]
Butland S, Devon R, Huang Y, Mead CL, Meynert A, Neal S, Lee S, Wilkinson A, Yang G, Yuen M, Hayden M, Holt R, Leavitt B, Ouellette BF: CAG-encoded polyglutamine length polymorphism in the human genome. BMC Genomics 2007, 8: 126. 10.1186/1471-2164-8-126
Article
PubMed Central
PubMed
Google Scholar
Hayes S, Turecki G, Brisebois K, Lopes-Cendes I, Gaspar C, Riess O, Ranum LP, Pulst SM, Rouleau GA: CAG repeat length in RAI1 is associated with age at onset variability in spinocerebellar ataxia type 2 (SCA2). Human Molecular Genetics 2000, 9(12):1753–1758. 10.1093/hmg/9.12.1753
Article
CAS
PubMed
Google Scholar
Ayres JA, Shum L, Akarsu AN, Dashner R, Takahashi K, Ikura T, Slavkin HC, Nuckolls GH: DACH: Genomic Characterization, Evaluation as a Candidate for Postaxial Polydactyly Type A2, and Developmental Expression Pattern of the Mouse Homologue. Genomics 2001, 77(1–2):18–26. 10.1006/geno.2001.6618
Article
CAS
PubMed
Google Scholar
Köttgen A, Pattaro C, Böger CA, Fuchsberger C, Olden M, Glazer NL, Parsa A, Gao X, Yang Q, Smith AV, O'Connell JR, Li M, Schmidt H, Tanaka T, Isaacs A, Ketkar S, Hwang SJ, Johnson AD, Dehghan A, Teumer A, Paré G, Atkinson EJ, Zeller T, Lohman K, Cornelis MC, Probst-Hensch NM, Kronenberg F, Tönjes A, Hayward C, Aspelund T, et al.: New loci associated with kidney function and chronic kidney disease. Nat Genet 2010, 42(5):376–384. 10.1038/ng.568
Article
PubMed Central
PubMed
Google Scholar
Huang H, Winter E, Wang H, Weinstock K, Xing H, Goodstadt L, Stenson P, Cooper D, Smith D, Alba MM, Ponting C, Fechtel K: Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biology 2004, 5(7):R47. 10.1186/gb-2004-5-7-r47
Article
PubMed Central
PubMed
Google Scholar
Ring HZ, Chang H, Guilbot A, Brice A, LeGuern E, Francke U: The human neuregulin-2 (NRG2) gene: cloning, mapping and evaluation as a candidate for the autosomal recessive form of Charcot-Marie-Tooth disease linked to 5q. Human Genetics 1999, 104: 326–332. 10.1007/s004390050961
Article
CAS
PubMed
Google Scholar
Sherry ST, Ward M, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 2001, 29: 308–311. 10.1093/nar/29.1.308
Article
PubMed Central
CAS
PubMed
Google Scholar
dbSNP Welcome Page[http://www.ncbi.nlm.nih.gov/snp]
Boby T, Patch AM, Aves SJ: TRbase: a database relating tandem repeats to disease genes for the human genome. Bioinformatics 2005, 21: 811–816. 10.1093/bioinformatics/bti059
Article
CAS
PubMed
Google Scholar
Payseur BA, Jing P, Haasl RJ: A Genomic Portrait of Human Microsatellite Variation. Molecular Biology and Evolution 2011, 28: 303–312. 10.1093/molbev/msq198
Article
PubMed Central
CAS
PubMed
Google Scholar
Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE: An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Research 2006, 16(9):1182–1190. 10.1101/gr.4565806
Article
PubMed Central
CAS
PubMed
Google Scholar
Reddy PH, Stockburger E, Gillevet P, Tagle DA: Mapping and Characterization of Novel (CAG)n Repeat cDNAs from Adult Human Brain Derived by the Oligo Capture Method. Genomics 1997, 46(2):174–182. 10.1006/geno.1997.5044
Article
CAS
PubMed
Google Scholar