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Items: 1 to 20 of 93

1.

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Lin MF, Jungreis I, Kellis M.

Bioinformatics. 2011 Jul 1;27(13):i275-82. doi: 10.1093/bioinformatics/btr209.

2.

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF.

Bioinformatics. 2011 Jul 15;27(14):1894-900. doi: 10.1093/bioinformatics/btr314. Epub 2011 May 26.

3.

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.

Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS.

Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7.

4.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.

RNA. 2011 Apr;17(4):578-94. doi: 10.1261/rna.2536111. Epub 2011 Feb 28.

5.

Enrichment of transcriptional regulatory sites in non-coding genomic region.

Xue W, Wang J, Shen Z, Zhu H.

Bioinformatics. 2004 Mar 1;20(4):569-75. Epub 2004 Jan 22.

6.
7.

Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome.

Zhu Q, Deng Y, Vanka P, Brown SJ, Muthukrishnan S, Kramer KJ.

Bioinformatics. 2004 Jan 22;20(2):161-9.

8.
9.

Towards realistic benchmarks for multiple alignments of non-coding sequences.

Kim J, Sinha S.

BMC Bioinformatics. 2010 Jan 26;11:54. doi: 10.1186/1471-2105-11-54.

10.

Conserved introns reveal novel transcripts in Drosophila melanogaster.

Hiller M, Findeiss S, Lein S, Marz M, Nickel C, Rose D, Schulz C, Backofen R, Prohaska SJ, Reuter G, Stadler PF.

Genome Res. 2009 Jul;19(7):1289-300. doi: 10.1101/gr.090050.108. Epub 2009 May 20.

11.

Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster.

Tupy JL, Bailey AM, Dailey G, Evans-Holm M, Siebel CW, Misra S, Celniker SE, Rubin GM.

Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5495-500. Epub 2005 Apr 4. Erratum in: Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8392.

12.

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.

Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, Roark M, Wiley KL Jr, Kulathinal RJ, Zhang P, Myrick KV, Antone JV, Celniker SE, Gelbart WM, Kellis M.

Genome Res. 2007 Dec;17(12):1823-36. Epub 2007 Nov 7.

13.

Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model.

Hatsuda H.

Bioinformatics. 2012 Sep 15;28(18):i633-i639. doi: 10.1093/bioinformatics/bts371.

14.

Tracing the most parsimonious indel history.

Snir S, Pachter L.

J Comput Biol. 2011 Aug;18(8):967-86. doi: 10.1089/cmb.2010.0325. Epub 2011 Jul 5.

PMID:
21728862
15.

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.

Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M.

Genome Res. 2011 Nov;21(11):1916-28. doi: 10.1101/gr.108753.110. Epub 2011 Oct 12.

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18.

Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements.

Creanza TM, Horner DS, D'Addabbo A, Maglietta R, Mignone F, Ancona N, Pesole G.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S2. doi: 10.1186/1471-2105-10-S6-S2.

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20.

Identification of prokaryotic small proteins using a comparative genomic approach.

Samayoa J, Yildiz FH, Karplus K.

Bioinformatics. 2011 Jul 1;27(13):1765-71. doi: 10.1093/bioinformatics/btr275. Epub 2011 May 5.

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