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Items: 1 to 20 of 445

1.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

2.

Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.

Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, Cawley S.

Bioinformatics. 2005 May 1;21(9):1958-63. Epub 2005 Jan 18.

PMID:
15657097
3.

dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data.

Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C.

Bioinformatics. 2004 May 22;20(8):1233-40. Epub 2004 Feb 10.

PMID:
14871870
4.

ESTprep: preprocessing cDNA sequence reads.

Scheetz TE, Trivedi N, Roberts CA, Kucaba T, Berger B, Robinson NL, Birkett CL, Gavin AJ, O'Leary B, Braun TA, Bonaldo MF, Robinson JP, Sheffield VC, Soares MB, Casavant TL.

Bioinformatics. 2003 Jul 22;19(11):1318-24.

PMID:
12874042
5.

SNVHMM: predicting single nucleotide variants from next generation sequencing.

Bian J, Liu C, Wang H, Xing J, Kachroo P, Zhou X.

BMC Bioinformatics. 2013 Jul 15;14:225. doi: 10.1186/1471-2105-14-225.

6.

Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.

Crisan A, Goya R, Ha G, Ding J, Prentice LM, Oloumi A, Senz J, Zeng T, Tse K, Delaney A, Marra MA, Huntsman DG, Hirst M, Aparicio S, Shah S.

PLoS One. 2012;7(8):e41551. doi: 10.1371/journal.pone.0041551. Epub 2012 Aug 16.

7.

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.

Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP.

Bioinformatics. 2012 Apr 1;28(7):907-13. doi: 10.1093/bioinformatics/bts053. Epub 2012 Jan 27.

8.

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
9.

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.

10.

Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.

Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP.

Bioinformatics. 2012 Jan 15;28(2):167-75. doi: 10.1093/bioinformatics/btr629. Epub 2011 Nov 13.

11.

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Genome Res. 2009 Jul;19(7):1270-8. doi: 10.1101/gr.088633.108. Epub 2009 May 15.

12.

BING: biomedical informatics pipeline for Next Generation Sequencing.

Kriseman J, Busick C, Szelinger S, Dinu V.

J Biomed Inform. 2010 Jun;43(3):428-34. doi: 10.1016/j.jbi.2009.11.003. Epub 2009 Nov 28.

13.

TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

Menges F, Narzisi G, Mishra B.

Bioinformatics. 2011 Sep 1;27(17):2330-7. doi: 10.1093/bioinformatics/btr393. Epub 2011 Jun 30.

PMID:
21724593
14.

SpliceMachine: predicting splice sites from high-dimensional local context representations.

Degroeve S, Saeys Y, De Baets B, Rouzé P, Van de Peer Y.

Bioinformatics. 2005 Apr 15;21(8):1332-8. Epub 2004 Nov 25.

PMID:
15564294
15.

Whole genome sequencing.

Ng PC, Kirkness EF.

Methods Mol Biol. 2010;628:215-26. doi: 10.1007/978-1-60327-367-1_12. Review.

PMID:
20238084
16.

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.

17.

Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays.

Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP.

Bioinformatics. 2004 Nov 1;20(16):2534-44. Epub 2004 Apr 29.

PMID:
15117752
18.

Probabilistic nucleotide assembling method for sequencing by hybridization.

Endo TA.

Bioinformatics. 2004 Sep 22;20(14):2181-8. Epub 2004 Apr 8.

PMID:
15073000
19.

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ.

BMC Genomics. 2006 Sep 29;7:246.

20.

Characterizing and interpreting genetic variation from personal genome sequencing.

Johansson AC, Feuk L.

Methods Mol Biol. 2012;838:343-67. doi: 10.1007/978-1-61779-507-7_17.

PMID:
22228021

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