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Results: 1 to 20 of 41

1.

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.

Shiroguchi K, Jia TZ, Sims PA, Xie XS.

Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1347-52. doi: 10.1073/pnas.1118018109. Epub 2012 Jan 9.

PMID:
22232676
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS.

Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053.

PMID:
22153072
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A bias-reducing strategy in profiling small RNAs using Solexa.

Sun G, Wu X, Wang J, Li H, Li X, Gao H, Rossi J, Yen Y.

RNA. 2011 Dec;17(12):2256-62. doi: 10.1261/rna.028621.111. Epub 2011 Oct 20.

PMID:
22016383
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.

Jayaprakash AD, Jabado O, Brown BD, Sachidanandam R.

Nucleic Acids Res. 2011 Nov;39(21):e141. doi: 10.1093/nar/gkr693. Epub 2011 Sep 2.

PMID:
21890899
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

An unbiased genome-wide analysis of zinc-finger nuclease specificity.

Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P, Kaeppel C, Nowrouzi A, Bartholomae CC, Wang J, Friedman G, Holmes MC, Gregory PD, Glimm H, Schmidt M, Naldini L, von Kalle C.

Nat Biotechnol. 2011 Aug 7;29(9):816-23. doi: 10.1038/nbt.1948.

PMID:
21822255
[PubMed - indexed for MEDLINE]
6.

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.

Hafner M, Renwick N, Brown M, Mihailović A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T.

RNA. 2011 Sep;17(9):1697-712. doi: 10.1261/rna.2799511. Epub 2011 Jul 20.

PMID:
21775473
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase.

Zhelkovsky AM, McReynolds LA.

Nucleic Acids Res. 2011 Sep 1;39(17):e117. doi: 10.1093/nar/gkr544. Epub 2011 Jun 30.

PMID:
21724605
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

T4 RNA ligase 2 truncated active site mutants: improved tools for RNA analysis.

Viollet S, Fuchs RT, Munafo DB, Zhuang F, Robb GB.

BMC Biotechnol. 2011 Jul 1;11:72. doi: 10.1186/1472-6750-11-72.

PMID:
21722378
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.

Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, Li R, Zhang L, Schroth GP, Burge CB.

Nat Biotechnol. 2011 Jun 26;29(7):659-64. doi: 10.1038/nbt.1882.

PMID:
21706015
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

miRBase: integrating microRNA annotation and deep-sequencing data.

Kozomara A, Griffiths-Jones S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7. doi: 10.1093/nar/gkq1027. Epub 2010 Oct 30.

PMID:
21037258
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Rapid construction of empirical RNA fitness landscapes.

Pitt JN, Ferré-D'Amaré AR.

Science. 2010 Oct 15;330(6002):376-9. doi: 10.1126/science.1192001.

PMID:
20947767
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sequencing bias: comparison of different protocols of microRNA library construction.

Tian G, Yin X, Luo H, Xu X, Bolund L, Zhang X, Gan SQ, Li N.

BMC Biotechnol. 2010 Sep 6;10:64. doi: 10.1186/1472-6750-10-64. Erratum in: BMC Biotechnol. 2011;11:48. Gan, Shang-Quang [added]; Li, Ning [added].

PMID:
20815927
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available.

Benes V, Castoldi M.

Methods. 2010 Apr;50(4):244-9. doi: 10.1016/j.ymeth.2010.01.026. Epub 2010 Jan 28. Review.

PMID:
20109550
[PubMed - indexed for MEDLINE]
14.

Quantitative miRNA expression analysis: comparing microarrays with next-generation sequencing.

Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T.

RNA. 2009 Nov;15(11):2028-34. doi: 10.1261/rna.1699809. Epub 2009 Sep 10.

PMID:
19745027
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Limitations and possibilities of small RNA digital gene expression profiling.

Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S, Tewari M, Cuppen E.

Nat Methods. 2009 Jul;6(7):474-6. doi: 10.1038/nmeth0709-474. No abstract available.

PMID:
19564845
[PubMed - indexed for MEDLINE]
16.

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS.

Science. 2009 Apr 10;324(5924):218-23. doi: 10.1126/science.1168978. Epub 2009 Feb 12.

PMID:
19213877
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples.

Kermekchiev MB, Kirilova LI, Vail EE, Barnes WM.

Nucleic Acids Res. 2009 Apr;37(5):e40. doi: 10.1093/nar/gkn1055. Epub 2009 Feb 10.

PMID:
19208643
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

MicroRNAs: target recognition and regulatory functions.

Bartel DP.

Cell. 2009 Jan 23;136(2):215-33. doi: 10.1016/j.cell.2009.01.002. Review.

PMID:
19167326
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A toolkit for analysing large-scale plant small RNA datasets.

Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V.

Bioinformatics. 2008 Oct 1;24(19):2252-3. doi: 10.1093/bioinformatics/btn428. Epub 2008 Aug 19.

PMID:
18713789
[PubMed - indexed for MEDLINE]
Free Article
20.

Profiling microRNA expression with microarrays.

Yin JQ, Zhao RC, Morris KV.

Trends Biotechnol. 2008 Feb;26(2):70-6. doi: 10.1016/j.tibtech.2007.11.007. Epub 2008 Jan 11. Review.

PMID:
18191262
[PubMed - indexed for MEDLINE]

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