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Results: 1 to 20 of 33

1.

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis.

Shang J, Zhu F, Vongsangnak W, Tang Y, Zhang W, Shen B.

Biomed Res Int. 2014;2014:309650. doi: 10.1155/2014/309650. Epub 2014 Mar 23.

PMID:
24779008
[PubMed - in process]
Free PMC Article
2.

A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype.

Vitulo N, Forcato C, Carpinelli EC, Telatin A, Campagna D, D'Angelo M, Zimbello R, Corso M, Vannozzi A, Bonghi C, Lucchin M, Valle G.

BMC Plant Biol. 2014 Apr 17;14:99. doi: 10.1186/1471-2229-14-99.

PMID:
24739459
[PubMed - in process]
Free PMC Article
3.

Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.

Ghosh D, Qin ZS.

Genes (Basel). 2010 Sep 27;1(2):317-34. doi: 10.3390/genes1020317.

PMID:
24710049
[PubMed]
Free PMC Article
4.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.

PMID:
24708189
[PubMed - in process]
Free PMC Article
5.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.

PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.

PMID:
24599324
[PubMed - in process]
Free PMC Article
6.

Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection.

Jubin C, Serero A, Loeillet S, Barillot E, Nicolas A.

G3 (Bethesda). 2014 Apr 16;4(4):707-15. doi: 10.1534/g3.113.009464.

PMID:
24558267
[PubMed - in process]
Free PMC Article
7.

RNA sequencing of the exercise transcriptome in equine athletes.

Capomaccio S, Vitulo N, Verini-Supplizi A, Barcaccia G, Albiero A, D'Angelo M, Campagna D, Valle G, Felicetti M, Silvestrelli M, Cappelli K.

PLoS One. 2013 Dec 31;8(12):e83504. doi: 10.1371/journal.pone.0083504. eCollection 2013.

PMID:
24391776
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Discovering epistasis in large scale genetic association studies by exploiting graphics cards.

Chen GK, Guo Y.

Front Genet. 2013 Dec 3;4:266. doi: 10.3389/fgene.2013.00266. Review.

PMID:
24348518
[PubMed]
Free PMC Article
9.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

PMID:
24185836
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Benchmarking short sequence mapping tools.

Hatem A, Bozdağ D, Toland AE, Çatalyürek ÜV.

BMC Bioinformatics. 2013 Jun 7;14:184. doi: 10.1186/1471-2105-14-184.

PMID:
23758764
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

In vivo NCL targeting affects breast cancer aggressiveness through miRNA regulation.

Pichiorri F, Palmieri D, De Luca L, Consiglio J, You J, Rocci A, Talabere T, Piovan C, Lagana A, Cascione L, Guan J, Gasparini P, Balatti V, Nuovo G, Coppola V, Hofmeister CC, Marcucci G, Byrd JC, Volinia S, Shapiro CL, Freitas MA, Croce CM.

J Exp Med. 2013 May 6;210(5):951-68. doi: 10.1084/jem.20120950. Epub 2013 Apr 22.

PMID:
23610125
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

CGAP-align: a high performance DNA short read alignment tool.

Chen Y, Hong J, Cui W, Zaneveld J, Wang W, Gibbs R, Xiao Y, Chen R.

PLoS One. 2013 Apr 11;8(4):e61033. doi: 10.1371/journal.pone.0061033. Print 2013.

PMID:
23593381
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Contradiction between plastid gene transcription and function due to complex posttranscriptional splicing: an exemplary study of ycf15 function and evolution in angiosperms.

Shi C, Liu Y, Huang H, Xia EH, Zhang HB, Gao LZ.

PLoS One. 2013;8(3):e59620. doi: 10.1371/journal.pone.0059620. Epub 2013 Mar 18.

PMID:
23527231
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

High Performance Multiple Sequence Alignment System for Pyrosequencing Reads from Multiple Reference Genomes.

Saeed F, Perez-Rathke A, Gwarnicki J, Berger-Wolf T, Khokhar A.

J Parallel Distrib Comput. 2012 Jan;72(1):83-93. Epub 2011 Sep 16.

PMID:
23125479
[PubMed]
Free PMC Article
15.

The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain.

Campanaro S, Pascale FD, Telatin A, Schiavon R, Bartlett DH, Valle G.

BMC Genomics. 2012 Oct 29;13:567. doi: 10.1186/1471-2164-13-567.

PMID:
23107454
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

Zomer A, Burghout P, Bootsma HJ, Hermans PW, van Hijum SA.

PLoS One. 2012;7(8):e43012. doi: 10.1371/journal.pone.0043012. Epub 2012 Aug 10.

PMID:
22900082
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Recent advances in molecular technologies and their application in pathogen detection in foods with particular reference to yersinia.

Gui J, Patel IR.

J Pathog. 2011;2011:310135. doi: 10.4061/2011/310135. Epub 2011 Oct 29.

PMID:
22567329
[PubMed]
Free PMC Article
18.

Alignment-free design of highly discriminatory diagnostic primer sets for Escherichia coli O104:H4 outbreak strains.

Pritchard L, Holden NJ, Bielaszewska M, Karch H, Toth IK.

PLoS One. 2012;7(4):e34498. doi: 10.1371/journal.pone.0034498. Epub 2012 Apr 5.

PMID:
22496820
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.

Rogers MF, Thomas J, Reddy AS, Ben-Hur A.

Genome Biol. 2012 Jan 31;13(1):R4. doi: 10.1186/gb-2012-13-1-r4.

PMID:
22293517
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.

Nucleic Acids Res. 2012 Mar;40(6):e42. doi: 10.1093/nar/gkr1248. Epub 2011 Dec 22.

PMID:
22199257
[PubMed - indexed for MEDLINE]
Free PMC Article

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