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Items: 1 to 20 of 60

1.

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation.

Naeem R, Rashid M, Pain A.

Bioinformatics. 2013 Feb 1;29(3):391-2. doi: 10.1093/bioinformatics/bts684. Epub 2012 Nov 28.

2.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

3.

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma.

Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, Holt RA.

Genome Res. 2012 Feb;22(2):299-306. doi: 10.1101/gr.126516.111. Epub 2011 Oct 18.

4.

Rapid identification of non-human sequences in high-throughput sequencing datasets.

Bhaduri A, Qu K, Lee CS, Ungewickell A, Khavari PA.

Bioinformatics. 2012 Apr 15;28(8):1174-5. doi: 10.1093/bioinformatics/bts100. Epub 2012 Feb 28.

5.

Enrich: software for analysis of protein function by enrichment and depletion of variants.

Fowler DM, Araya CL, Gerard W, Fields S.

Bioinformatics. 2011 Dec 15;27(24):3430-1. doi: 10.1093/bioinformatics/btr577. Epub 2011 Oct 17.

6.

OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing.

Das S, Vikalo H.

Bioinformatics. 2012 Jul 1;28(13):1677-83. doi: 10.1093/bioinformatics/bts256. Epub 2012 May 7.

7.

Identifying viral integration sites using SeqMap 2.0.

Hawkins TB, Dantzer J, Peters B, Dinauer M, Mockaitis K, Mooney S, Cornetta K.

Bioinformatics. 2011 Mar 1;27(5):720-2. doi: 10.1093/bioinformatics/btq722. Epub 2011 Jan 17.

8.

Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.

Kong Y.

Genomics. 2011 Aug;98(2):152-3. doi: 10.1016/j.ygeno.2011.05.009. Epub 2011 May 30.

9.

Informed and automated k-mer size selection for genome assembly.

Chikhi R, Medvedev P.

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.

PMID:
23732276
10.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
11.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

12.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

13.

PathSeq: software to identify or discover microbes by deep sequencing of human tissue.

Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M.

Nat Biotechnol. 2011 May;29(5):393-6. doi: 10.1038/nbt.1868. No abstract available.

14.

ReadDB provides efficient storage for mapped short reads.

Rolfe PA, Gifford DK.

BMC Bioinformatics. 2011 Jul 7;12:278. doi: 10.1186/1471-2105-12-278.

15.

Dissect: detection and characterization of novel structural alterations in transcribed sequences.

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC.

Bioinformatics. 2012 Jun 15;28(12):i179-87. doi: 10.1093/bioinformatics/bts214.

16.

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.

Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF.

Bioinformatics. 2013 Mar 1;29(5):649-51. doi: 10.1093/bioinformatics/btt011. Epub 2013 Jan 12.

17.

Mauve assembly metrics.

Darling AE, Tritt A, Eisen JA, Facciotti MT.

Bioinformatics. 2011 Oct 1;27(19):2756-7. doi: 10.1093/bioinformatics/btr451. Epub 2011 Aug 2.

18.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

19.

Efficient alignment of pyrosequencing reads for re-sequencing applications.

Fernandes F, da Fonseca PG, Russo LM, Oliveira AL, Freitas AT.

BMC Bioinformatics. 2011 May 16;12:163. doi: 10.1186/1471-2105-12-163.

20.

ReRep: computational detection of repetitive sequences in genome survey sequences (GSS).

Otto TD, Gomes LH, Alves-Ferreira M, de Miranda AB, Degrave WM.

BMC Bioinformatics. 2008 Sep 9;9:366. doi: 10.1186/1471-2105-9-366.

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