-
1
-
-
25144494777
-
Intragenic tandem repeats generate functional variability
-
Verstrepen KJ, Jansen A, Lewitter F, et al. Intragenic tandem repeats generate functional variability. Nat. Genet. 2005;37(9):986-90.
-
(2005)
Nat. Genet.
, vol.37
, Issue.9
, pp. 986-990
-
-
Verstrepen, K.J.1
Jansen, A.2
Lewitter, F.3
-
2
-
-
25844438495
-
Repeat instability:mechanisms of dynamic mutations
-
Pearson CE, Edamura KN, Cleary JD. Repeat instability:mechanisms of dynamic mutations. Nat. Rev. Genet. 2005;6(10):729-42.
-
(2005)
Nat. Rev. Genet.
, vol.6
, Issue.10
, pp. 729-742
-
-
Pearson, C.E.1
Edamura, K.N.2
Cleary, J.D.3
-
3
-
-
77649144557
-
Repeat instability as the basis for human diseases and as a potential target for therapy
-
Castel AL, Cleary JD, Pearson CE. Repeat instability as the basis for human diseases and as a potential target for therapy. Nat. Rev.Mol. Cell Biol. 2010;11(3):165-70.
-
(2010)
Nat. Rev.Mol. Cell Biol.
, vol.11
, Issue.3
, pp. 165-170
-
-
Castel, A.L.1
Cleary, J.D.2
Pearson, C.E.3
-
4
-
-
0027480960
-
A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes
-
MacDonald ME, Ambrose CM, Duyao MP, et al. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. Cell 1993;72(6):971-83.
-
(1993)
Cell
, vol.72
, Issue.6
, pp. 971-983
-
-
MacDonald, M.E.1
Ambrose, C.M.2
Duyao, M.P.3
-
5
-
-
0025905795
-
Identification of a Gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome
-
Verkerk AJMH, Pieretti M, Sutcliffe JS, et al. Identification of a Gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell 1991;65(5):905-14.
-
(1991)
Cell
, vol.65
, Issue.5
, pp. 905-914
-
-
Verkerk, A.J.M.H.1
Pieretti, M.2
Sutcliffe, J.S.3
-
6
-
-
60749097197
-
A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana
-
Sureshkumar S, Todesco M, Schneeberger K, et al. A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana. Science 2009;323(5917):1060-3.
-
(2009)
Science
, vol.323
, Issue.5917
, pp. 1060-1063
-
-
Sureshkumar, S.1
Todesco, M.2
Schneeberger, K.3
-
7
-
-
78549278120
-
Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes
-
Whan V, Hobbs M, McWilliam S, et al. Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes. BMCGenomics 2010;11:654.
-
(2010)
BMCGenomics
, vol.11
, pp. 654
-
-
Whan, V.1
Hobbs, M.2
McWilliam, S.3
-
8
-
-
66349113764
-
Unstable tandem repeats in promoters confer transcriptional evolvability
-
Vinces MD, Legendre M, Caldara M, et al. Unstable tandem repeats in promoters confer transcriptional evolvability. Science 2009;324(5931):1213-6.
-
(2009)
Science
, vol.324
, Issue.5931
, pp. 1213-1216
-
-
Vinces, M.D.1
Legendre, M.2
Caldara, M.3
-
9
-
-
84869768769
-
Backgrounddependent effects of polyglutamine variation in the arabidopsis thaliana gene ELF3
-
Undurraga SF, Press MO, Legendre M, et al. Backgrounddependent effects of polyglutamine variation in the arabidopsis thaliana gene ELF3. Proc. Natl. Acad. Sci. USA 2012;109(47):19363-7.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, Issue.47
, pp. 19363-19367
-
-
Undurraga, S.F.1
Press, M.O.2
Legendre, M.3
-
10
-
-
0035800434
-
Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9
-
Liquori CL, Ricker K, Moseley ML, et al. Myotonic dystrophy type 2 caused by a CCTG expansion in intron 1 of ZNF9. Science 2001;293(5531):864-7.
-
(2001)
Science
, vol.293
, Issue.5531
, pp. 864-867
-
-
Liquori, C.L.1
Ricker, K.2
Moseley, M.L.3
-
11
-
-
0033771685
-
Large expansion of the ATTCT Pentanucleotide repeat in Spinocerebellar Ataxia Type 10
-
Matsuura T, Yamagata T, Burgess DL, et al. Large expansion of the ATTCT Pentanucleotide repeat in Spinocerebellar Ataxia Type 10. Nat. Genet. 2000;26(2):191-4.
-
(2000)
Nat. Genet.
, vol.26
, Issue.2
, pp. 191-194
-
-
Matsuura, T.1
Yamagata, T.2
Burgess, D.L.3
-
12
-
-
80054832080
-
Expanded GGGGCC Hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS
-
DeJesus-Hernandez M, Mackenzie IR, Boeve BF, et al. Expanded GGGGCC Hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 2011;72(2):245-56.
-
(2011)
Neuron
, vol.72
, Issue.2
, pp. 245-256
-
-
DeJesus-Hernandez, M.1
Mackenzie, I.R.2
Boeve, B.F.3
-
13
-
-
80054837386
-
A Hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD
-
Renton AE, Majounie E, Waite A, et al. A Hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 2011;72(2):257-68.
-
(2011)
Neuron
, vol.72
, Issue.2
, pp. 257-268
-
-
Renton, A.E.1
Majounie, E.2
Waite, A.3
-
14
-
-
34250878426
-
Expandable DNA Repeats and human disease
-
Mirkin SM. Expandable DNA Repeats and human disease. Nature 2007;447(7147):932-40; doi:10.1038/nature05977.
-
(2007)
Nature
, vol.447
, Issue.7147
, pp. 932-940
-
-
Mirkin, S.M.1
-
15
-
-
78650087192
-
A genome alignment algorithm based on compression
-
Cao MD, Dix TI, Allison L. A genome alignment algorithm based on compression. BMC Bioinformatics 2010;11:599.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 599
-
-
Cao, M.D.1
Dix, T.I.2
Allison, L.3
-
16
-
-
83855165105
-
Repetitive DNA and nextgeneration sequencing: computational challenges and solutions
-
Treangen TJ, Salzberg SL. Repetitive DNA and nextgeneration sequencing: computational challenges and solutions. Nat.Rev. Genet. 2012;13:36-46.
-
(2012)
Nat.Rev. Genet.
, vol.13
, pp. 36-46
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
17
-
-
84896731172
-
Inferring short tandem repeat variations from paired-end short reads
-
Cao MD, Tasker E, Willadsen K, et al. Inferring short tandem repeat variations from paired-end short reads. Nucleic Acids Res. 2013;42(3):e16.
-
(2013)
Nucleic Acids Res.
, vol.42
, Issue.3
, pp. e16
-
-
Cao, M.D.1
Tasker, E.2
Willadsen, K.3
-
18
-
-
84861861291
-
lobSTR: a short tandem repeat profiler for personal genomes
-
Gymrek M, Golan D, Rosset S, et al. lobSTR: a short tandem repeat profiler for personal genomes. Genome Res. 2012;22:1154-62.
-
(2012)
Genome Res.
, vol.22
, pp. 1154-1162
-
-
Gymrek, M.1
Golan, D.2
Rosset, S.3
-
19
-
-
84871774158
-
Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles
-
Highnam G, Franck C, Martin A, et al. Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles. Nucleic Acids Res. 2012;41:e32.
-
(2012)
Nucleic Acids Res.
, vol.41
, pp. e32
-
-
Highnam, G.1
Franck, C.2
Martin, A.3
-
20
-
-
72849144434
-
Sequencing technologies-the next generation
-
Metzker ML. Sequencing technologies-the next generation. Nat. Rev. Genet. 2010;11:31-46.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 31-46
-
-
Metzker, M.L.1
-
21
-
-
84864920004
-
Comparison of next-generation sequencing systems
-
Liu L, Li Y, Li S, et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012;2012:251364.
-
(2012)
J. Biomed. Biotechnol.
, vol.2012
, pp. 251364
-
-
Liu, L.1
Li, Y.2
Li, S.3
-
22
-
-
84860756398
-
Performance comparison of Benchtop high-throughput sequencing platforms
-
Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of Benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012;30(5):434-9.
-
(2012)
Nat. Biotechnol.
, vol.30
, Issue.5
, pp. 434-439
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
-
23
-
-
84865591846
-
A tale of three next generation sequencing platforms: comparison of ion torrent, Pacific biosciences and Illumina MiSeq sequencers
-
Quail MA, Smith M, Coupland P, et al. A tale of three next generation sequencing platforms: comparison of ion torrent, Pacific biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341.
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
Smith, M.2
Coupland, P.3
-
24
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437(7057):376-80.
-
(2005)
Nature
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
-
25
-
-
79960597679
-
An integrated semiconductor device enabling non-optical genome sequencing
-
Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475(7356):348-52.
-
(2011)
Nature
, vol.475
, Issue.7356
, pp. 348-352
-
-
Rothberg, J.M.1
Hinz, W.2
Rearick, T.M.3
-
26
-
-
58149234737
-
Real-time DNA sequencing from single polymerase molecules
-
Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science 2009;323(5910):133-8.
-
(2009)
Science
, vol.323
, Issue.5910
, pp. 133-138
-
-
Eid, J.1
Fehr, A.2
Gray, J.3
-
27
-
-
77951107295
-
Real-time tRNA transit on single translating ribosomes at codon resolution
-
Uemura S, Aitken CE, Korlach J, et al. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature 2010;464(7291):1012-7.
-
(2010)
Nature
, vol.464
, Issue.7291
, pp. 1012-1017
-
-
Uemura, S.1
Aitken, C.E.2
Korlach, J.3
-
28
-
-
84870822864
-
Tools for mapping high-throughput sequencing data
-
Fonseca NA, Rung J, Brazma A, et al. Tools for mapping high-throughput sequencing data. Bioinformatics 2012;24:3169-77.
-
(2012)
Bioinformatics
, vol.24
, pp. 3169-3177
-
-
Fonseca, N.A.1
Rung, J.2
Brazma, A.3
-
29
-
-
80053978849
-
Comparative analysis of algorithms for next-generation sequencing read alignment
-
Ruffalo M, LaFramboise T, Koyutürk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27(20):2790-6.
-
(2011)
Bioinformatics
, vol.27
, Issue.20
, pp. 2790-2796
-
-
Ruffalo, M.1
LaFramboise, T.2
Koyutürk, M.3
-
30
-
-
77957272611
-
A survey of sequence alignment algorithms for next-generation sequencing
-
Li H, Homer N. A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform. 2010;11(5):473-83.
-
(2010)
Brief. Bioinform.
, vol.11
, Issue.5
, pp. 473-483
-
-
Li, H.1
Homer, N.2
-
31
-
-
84871593783
-
A comprehensive evaluation of alignment algorithms in the context of RNA-seq
-
Lindner R, Friedel CC. A comprehensive evaluation of alignment algorithms in the context of RNA-seq. PLoS One 2012;7(12):e52403.
-
(2012)
PLoS One
, vol.7
, Issue.12
, pp. e52403
-
-
Lindner, R.1
Friedel, C.C.2
-
32
-
-
79957932376
-
Dindel: accurate indel calls from short-read data
-
Albers CA, Lunter G, MacArthur DG, et al. Dindel: accurate indel calls from short-read data. GenomeRes. 2011;21(6):961-73.
-
(2011)
GenomeRes.
, vol.21
, Issue.6
, pp. 961-973
-
-
Albers, C.A.1
Lunter, G.2
MacArthur, D.G.3
-
33
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009;25(16):2078-9.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
-
34
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011;43(5):491-8.
-
(2011)
Nat. Genet.
, vol.43
, Issue.5
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
-
35
-
-
70449704529
-
Computational methods for discovering structural variation with next-generation sequencing
-
Medvedev P, Stanciu M, Brudno M. Computational methods for discovering structural variation with next-generation sequencing. Nat.Methods 2009;6(11s):S13-20.
-
(2009)
Nat.Methods
, vol.6
, Issue.11 S
, pp. S13-20
-
-
Medvedev, P.1
Stanciu, M.2
Brudno, M.3
-
36
-
-
64849083125
-
CNV-seq, a new method to detect copy number variation using high-throughput sequencing
-
Xie C, Tammi M. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009;10:80.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 80
-
-
Xie, C.1
Tammi, M.2
-
37
-
-
69749122557
-
Sensitive and accurate detection of copy number variants using read depth of coverage
-
Yoon S, Xuan Z, Makarov V, et al. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 2009;19(9):1586-92.
-
(2009)
Genome Res.
, vol.19
, Issue.9
, pp. 1586-1592
-
-
Yoon, S.1
Xuan, Z.2
Makarov, V.3
-
38
-
-
81755172942
-
Copy Number variation detection in whole-genome sequencing data using the Bayesian information criterion
-
Xi R, Hadjipanayis AG, Luquette LJ, et al. Copy Number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc. Natl. Acad. Sci. USA 2011;108(46):E1128-36.
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, Issue.46
, pp. E1128-E1136
-
-
Xi, R.1
Hadjipanayis, A.G.2
Luquette, L.J.3
-
39
-
-
67649580757
-
MoDIL: Detecting small Indels from clone-end sequencing with mixtures of distributions
-
Lee S, Hormozdiari F, Alkan C, et al. MoDIL: Detecting small Indels from clone-end sequencing with mixtures of distributions. Nat.Methods 2009;6(7):473-4.
-
(2009)
Nat.Methods
, vol.6
, Issue.7
, pp. 473-474
-
-
Lee, S.1
Hormozdiari, F.2
Alkan, C.3
-
40
-
-
69549116107
-
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
-
Chen K, Wallis JW, McLellan MD, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat.Methods 2009;6(9):677-81.
-
(2009)
Nat.Methods
, vol.6
, Issue.9
, pp. 677-681
-
-
Chen, K.1
Wallis, J.W.2
McLellan, M.D.3
-
41
-
-
80053132716
-
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
-
Gan X, Stegle O, Behr J, et al. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 2011;477(7365):419-23.
-
(2011)
Nature
, vol.477
, Issue.7365
, pp. 419-423
-
-
Gan, X.1
Stegle, O.2
Behr, J.3
-
42
-
-
0033555906
-
Tandem repeats finder: a program to analyze DNA sequences
-
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573-80.
-
(1999)
Nucleic Acids Res.
, vol.27
, Issue.2
, pp. 573-580
-
-
Benson, G.1
-
43
-
-
84873048644
-
Repeat-encoded poly-Q tracts show statistical commonalities across species
-
Willadsen K, Cao MD, Wiles J, et al. Repeat-encoded poly-Q tracts show statistical commonalities across species. BMC Genomics 2013;14:76.
-
(2013)
BMC Genomics
, vol.14
, pp. 76
-
-
Willadsen, K.1
Cao, M.D.2
Wiles, J.3
-
44
-
-
38849170546
-
Sequence-based estimation of minisatellite and microsatellite repeat variability
-
Legendre M, Pochet N, Pak T, et al. Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. 2007;17(12):1787-96.
-
(2007)
Genome Res.
, vol.17
, Issue.12
, pp. 1787-1796
-
-
Legendre, M.1
Pochet, N.2
Pak, T.3
-
45
-
-
84857145150
-
ART: a Next-generation sequencing read simulator
-
Huang W, Li L, Myers JR, et al. ART: a Next-generation sequencing read simulator. Bioinformatics 2012;28(4):593-4.
-
(2012)
Bioinformatics
, vol.28
, Issue.4
, pp. 593-594
-
-
Huang, W.1
Li, L.2
Myers, J.R.3
-
46
-
-
84871779381
-
PBSIM: PacBio reads simulator- toward accurate genome assembly
-
Ono Y, Asai K, Hamada M. PBSIM: PacBio reads simulator- toward accurate genome assembly. Bioinformatics 2012;29:119-21.
-
(2012)
Bioinformatics
, vol.29
, pp. 119-121
-
-
Ono, Y.1
Asai, K.2
Hamada, M.3
-
47
-
-
67649884743
-
Fast and Accurate short read alignment with burrows-wheeler transform
-
Li H, Durbin R. Fast and Accurate short read alignment with burrows-wheeler transform. Bioinformatics 2009;25(14):1754-60.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
48
-
-
77949587649
-
Fast and Accurate long-read alignment with burrows-wheeler transform
-
Li H, Durbin R. Fast and Accurate long-read alignment with burrows-wheeler transform. Bioinformatics 2010;26(5):589-95.
-
(2010)
Bioinformatics
, vol.26
, Issue.5
, pp. 589-595
-
-
Li, H.1
Durbin, R.2
-
49
-
-
84859210032
-
Fast Gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. Fast Gapped-read alignment with Bowtie 2. Nat.Methods 2012;9(4):357-9.
-
(2012)
Nat.Methods
, vol.9
, Issue.4
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
50
-
-
79956307251
-
Stampy: a statistical algorithm for sensitive and fast mapping of illumina sequence reads
-
Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of illumina sequence reads. Genome Res. 2011;21(6):936-9.
-
(2011)
Genome Res.
, vol.21
, Issue.6
, pp. 936-939
-
-
Lunter, G.1
Goodson, M.2
-
51
-
-
0034764307
-
SSAHA: a fast search method for large DNA databases
-
Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res. 2001;11(10):1725-9.
-
(2001)
Genome Res.
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
52
-
-
84866447703
-
long read alignment based on maximal exact match seeds
-
Liu Y, Schmidt B. long read alignment based on maximal exact match seeds. Bioinformatics 2012;28(18):i318-24.
-
(2012)
Bioinformatics
, vol.28
, Issue.18
, pp. i318-i324
-
-
Liu, Y.1
Schmidt, B.2
|