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Items: 1 to 20 of 115


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.


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.


SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.


Querying large read collections in main memory: a versatile data structure.

Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E.

BMC Bioinformatics. 2011 Jun 17;12:242. doi: 10.1186/1471-2105-12-242.


NeuroTerrain--a client-server system for browsing 3D biomedical image data sets.

Gustafson C, Bug WJ, Nissanov J.

BMC Bioinformatics. 2007 Feb 5;8:40.


Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

Gautier L, Lund O.

PLoS One. 2013 Dec 31;8(12):e83784. doi: 10.1371/journal.pone.0083784. eCollection 2013.


CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.


A de novo next generation genomic sequence assembler based on string graph and MapReduce cloud computing framework.

Chang YJ, Chen CC, Chen CL, Ho JM.

BMC Genomics. 2012;13 Suppl 7:S28. doi: 10.1186/1471-2164-13-S7-S28. Epub 2012 Dec 13.


BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.

Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y, Liang H.

BMC Genomics. 2012;13 Suppl 8:S9. doi: 10.1186/1471-2164-13-S8-S9. Epub 2012 Dec 17.


BowStrap v1.0: Assigning statistical significance to expressed genes using short-read transcriptome data.

Larsen PE, Collart FR.

BMC Res Notes. 2012 Jun 7;5:275. doi: 10.1186/1756-0500-5-275.


HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads.

Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L.

J Am Med Inform Assoc. 2014 Mar-Apr;21(2):363-73. doi: 10.1136/amiajnl-2013-002147. Epub 2013 Dec 24.


Savant: genome browser for high-throughput sequencing data.

Fiume M, Williams V, Brook A, Brudno M.

Bioinformatics. 2010 Aug 15;26(16):1938-44. doi: 10.1093/bioinformatics/btq332. Epub 2010 Jun 20.


An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads.

Warnke JD, Ali HH.

BMC Bioinformatics. 2013;14 Suppl 11:S7. doi: 10.1186/1471-2105-14-S11-S7. Epub 2013 Nov 4.


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.


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.


Oculus: faster sequence alignment by streaming read compression.

Veeneman BA, Iyer MK, Chinnaiyan AM.

BMC Bioinformatics. 2012 Nov 13;13:297. doi: 10.1186/1471-2105-13-297.


JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.

Liang C, Schmid A, López-Sánchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T.

BMC Bioinformatics. 2009 Nov 29;10:391. doi: 10.1186/1471-2105-10-391.


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

Li H, Durbin R.

Bioinformatics. 2010 Mar 1;26(5):589-95. doi: 10.1093/bioinformatics/btp698. Epub 2010 Jan 15.


Tracembler--software for in-silico chromosome walking in unassembled genomes.

Dong Q, Wilkerson MD, Brendel V.

BMC Bioinformatics. 2007 May 9;8:151.


GPAT: retrieval of genomic annotation from large genomic position datasets.

Krebs A, Frontini M, Tora L.

BMC Bioinformatics. 2008 Dec 15;9:533. doi: 10.1186/1471-2105-9-533.

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