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Items: 1 to 20 of 139

1.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. doi: 10.1093/nar/gkn425. Epub 2008 Jul 26.

2.

Correction of sequencing errors in a mixed set of reads.

Salmela L.

Bioinformatics. 2010 May 15;26(10):1284-90. doi: 10.1093/bioinformatics/btq151. Epub 2010 Apr 8.

PMID:
20378555
3.

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.

Minoche AE, Dohm JC, Himmelbauer H.

Genome Biol. 2011 Nov 8;12(11):R112. doi: 10.1186/gb-2011-12-11-r112.

4.

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

5.

Probabilistic base calling of Solexa sequencing data.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F.

BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.

6.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

7.

De novo sequencing of plant genomes using second-generation technologies.

Imelfort M, Edwards D.

Brief Bioinform. 2009 Nov;10(6):609-18. doi: 10.1093/bib/bbp039. Review.

PMID:
19933209
8.

De novo assembly of short sequence reads.

Paszkiewicz K, Studholme DJ.

Brief Bioinform. 2010 Sep;11(5):457-72. doi: 10.1093/bib/bbq020. Epub 2010 Aug 19. Review.

PMID:
20724458
9.

The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

Droege M, Hill B.

J Biotechnol. 2008 Aug 31;136(1-2):3-10. doi: 10.1016/j.jbiotec.2008.03.021. Epub 2008 Jun 21. Review.

PMID:
18616967
10.

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.

Genome Res. 2008 May;18(5):802-9. doi: 10.1101/gr.072033.107. Epub 2008 Mar 10.

11.

Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80. doi: 10.1093/bioinformatics/btn300.

PMID:
18689821
12.

Quality scores and SNP detection in sequencing-by-synthesis systems.

Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):763-70. doi: 10.1101/gr.070227.107. Epub 2008 Jan 22.

13.

De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.

Farrer RA, Kemen E, Jones JD, Studholme DJ.

FEMS Microbiol Lett. 2009 Feb;291(1):103-11. doi: 10.1111/j.1574-6968.2008.01441.x. Epub 2008 Dec 9.

14.

Characterizing the mouse ES cell transcriptome with Illumina sequencing.

Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H.

Genomics. 2008 Oct;92(4):187-94. doi: 10.1016/j.ygeno.2008.05.011. Epub 2008 Aug 3.

15.

Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

Dunn JJ, McCorkle SR, Everett L, Anderson CW.

Genet Eng (N Y). 2007;28:159-73. Review.

PMID:
17153938
16.

Profiling model T-cell metagenomes with short reads.

Warren RL, Nelson BH, Holt RA.

Bioinformatics. 2009 Feb 15;25(4):458-64. doi: 10.1093/bioinformatics/btp010. Epub 2009 Jan 9.

PMID:
19136549
17.

Fast mapping of short sequences with mismatches, insertions and deletions using index structures.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J.

PLoS Comput Biol. 2009 Sep;5(9):e1000502. doi: 10.1371/journal.pcbi.1000502. Epub 2009 Sep 11.

18.

Fast and accurate short read alignment with Burrows-Wheeler transform.

Li H, Durbin R.

Bioinformatics. 2009 Jul 15;25(14):1754-60. doi: 10.1093/bioinformatics/btp324. Epub 2009 May 18.

19.

Unlocking short read sequencing for metagenomics.

Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.

PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.

20.

Genome-wide high throughput analysis of DNA methylation in eukaryotes.

Pomraning KR, Smith KM, Freitag M.

Methods. 2009 Mar;47(3):142-50. doi: 10.1016/j.ymeth.2008.09.022. Epub 2008 Oct 23.

PMID:
18950712

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