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Results: 1 to 20 of 23

1.

Identification and correction of systematic error in high-throughput sequence data.

Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L.

BMC Bioinformatics. 2011 Nov 21;12:451. doi: 10.1186/1471-2105-12-451.

PMID:
22099972
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Very few RNA and DNA sequence differences in the human transcriptome.

Schrider DR, Gout JF, Hahn MW.

PLoS One. 2011;6(10):e25842. doi: 10.1371/journal.pone.0025842. Epub 2011 Oct 12.

PMID:
22022455
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Synthetic spike-in standards for RNA-seq experiments.

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.

Genome Res. 2011 Sep;21(9):1543-51. doi: 10.1101/gr.121095.111. Epub 2011 Aug 4.

PMID:
21816910
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

A mosaic activating mutation in AKT1 associated with the Proteus syndrome.

Lindhurst MJ, Sapp JC, Teer JK, Johnston JJ, Finn EM, Peters K, Turner J, Cannons JL, Bick D, Blakemore L, Blumhorst C, Brockmann K, Calder P, Cherman N, Deardorff MA, Everman DB, Golas G, Greenstein RM, Kato BM, Keppler-Noreuil KM, Kuznetsov SA, Miyamoto RT, Newman K, Ng D, O'Brien K, Rothenberg S, Schwartzentruber DJ, Singhal V, Tirabosco R, Upton J, Wientroub S, Zackai EH, Hoag K, Whitewood-Neal T, Robey PG, Schwartzberg PL, Darling TN, Tosi LL, Mullikin JC, Biesecker LG.

N Engl J Med. 2011 Aug 18;365(7):611-9. doi: 10.1056/NEJMoa1104017. Epub 2011 Jul 27.

PMID:
21793738
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.

Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T.

RNA. 2011 Sep;17(9):1697-712. doi: 10.1261/rna.2799511. Epub 2011 Jul 20.

PMID:
21775473
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing.

Chen EZ, Chiu RW, Sun H, Akolekar R, Chan KC, Leung TY, Jiang P, Zheng YW, Lun FM, Chan LY, Jin Y, Go AT, Lau ET, To WW, Leung WC, Tang RY, Au-Yeung SK, Lam H, Kung YY, Zhang X, van Vugt JM, Minekawa R, Tang MH, Wang J, Oudejans CB, Lau TK, Nicolaides KH, Lo YM.

PLoS One. 2011;6(7):e21791. doi: 10.1371/journal.pone.0021791. Epub 2011 Jul 6.

PMID:
21755002
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Widespread RNA and DNA sequence differences in the human transcriptome.

Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG.

Science. 2011 Jul 1;333(6038):53-8. doi: 10.1126/science.1207018. Epub 2011 May 19.

PMID:
21596952
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Detection and quantification of rare mutations with massively parallel sequencing.

Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9530-5. doi: 10.1073/pnas.1105422108. Epub 2011 May 17.

PMID:
21586637
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories.

Pine PS, Rosenzweig BA, Thompson KL.

BMC Biotechnol. 2011 Apr 12;11:38. doi: 10.1186/1472-6750-11-38.

PMID:
21486464
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

PMID:
21478889
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Improving RNA-Seq expression estimates by correcting for fragment bias.

Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L.

Genome Biol. 2011;12(3):R22. doi: 10.1186/gb-2011-12-3-r22. Epub 2011 Mar 16.

PMID:
21410973
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

High-throughput discovery of rare insertions and deletions in large cohorts.

Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD.

Genome Res. 2010 Dec;20(12):1711-8. doi: 10.1101/gr.109157.110. Epub 2010 Nov 1.

PMID:
21041413
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A map of human genome variation from population-scale sequencing.

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.

Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Deborah A].

PMID:
20981092
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA.

Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.

PMID:
20644199
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Hansen KD, Brenner SE, Dudoit S.

Nucleic Acids Res. 2010 Jul;38(12):e131. doi: 10.1093/nar/gkq224. Epub 2010 Apr 14.

PMID:
20395217
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Stephens PJ, McBride DJ, Lin ML, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, Greenman CD, Jia M, Latimer C, Teague JW, Lau KW, Burton J, Quail MA, Swerdlow H, Churcher C, Natrajan R, Sieuwerts AM, Martens JW, Silver DP, Langerød A, Russnes HE, Foekens JA, Reis-Filho JS, van 't Veer L, Richardson AL, Børresen-Dale AL, Campbell PJ, Futreal PA, Stratton MR.

Nature. 2009 Dec 24;462(7276):1005-10. doi: 10.1038/nature08645.

PMID:
20033038
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordoñez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ.

Nature. 2010 Jan 14;463(7278):184-90. doi: 10.1038/nature08629. Epub 2009 Dec 16.

PMID:
20016488
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A comprehensive catalogue of somatic mutations from a human cancer genome.

Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR.

Nature. 2010 Jan 14;463(7278):191-6. doi: 10.1038/nature08658. Epub 2009 Dec 16.

PMID:
20016485
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Improved base calling for the Illumina Genome Analyzer using machine learning strategies.

Kircher M, Stenzel U, Kelso J.

Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.

PMID:
19682367
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Identifying sequence variants in the human mitochondrial genome using high-resolution melt (HRM) profiling.

Dobrowolski SF, Hendrickx AT, van den Bosch BJ, Smeets HJ, Gray J, Miller T, Sears M.

Hum Mutat. 2009 Jun;30(6):891-8. doi: 10.1002/humu.21003. Erratum in: Hum Mutat. 2009 Dec;30(12):1713. Hendrickx, Alexandra T M [added]; van den Bosch, Bianca J C [added]; Smeets, Hubert J M [added].

PMID:
19370763
[PubMed - indexed for MEDLINE]

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