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Results: 1 to 20 of 351

1.

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.

PMID:
23044541
[PubMed - indexed for MEDLINE]
Free Article
2.

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.

Li A, Zhang J, Zhou Z.

BMC Bioinformatics. 2014 Sep 19;15:311. doi: 10.1186/1471-2105-15-311.

PMID:
25239089
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

PMID:
22955987
[PubMed - indexed for MEDLINE]
Free PMC Article
4.
5.

Characterization of 954 bovine full-CDS cDNA sequences.

Harhay GP, Sonstegard TS, Keele JW, Heaton MP, Clawson ML, Snelling WM, Wiedmann RT, Van Tassell CP, Smith TP.

BMC Genomics. 2005 Nov 23;6:166.

PMID:
16305752
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

PMID:
22480257
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.

J Proteomics. 2013 Jun 28;86:27-42. doi: 10.1016/j.jprot.2013.04.036. Epub 2013 May 9.

PMID:
23665149
[PubMed - indexed for MEDLINE]
8.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.

PMID:
22955982
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21622663
[PubMed - indexed for MEDLINE]
Free Article
10.

Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ.

Genome Biol. 2006;7(4):R35. Epub 2006 Apr 28.

PMID:
16646984
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genome-wide computational identification and manual annotation of human long noncoding RNA genes.

Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L.

RNA. 2010 Aug;16(8):1478-87. doi: 10.1261/rna.1951310. Epub 2010 Jun 29.

PMID:
20587619
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs.

Risueño A, Fontanillo C, Dinger ME, De Las Rivas J.

BMC Bioinformatics. 2010 Apr 29;11:221. doi: 10.1186/1471-2105-11-221.

PMID:
20429936
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

High-throughput protein analysis integrating bioinformatics and experimental assays.

del Val C, Mehrle A, Falkenhahn M, Seiler M, Glatting KH, Poustka A, Suhai S, Wiemann S.

Nucleic Acids Res. 2004 Feb 3;32(2):742-8. Print 2004.

PMID:
14762202
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.

Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB.

BMC Bioinformatics. 2006 Jan 23;7:33.

PMID:
16426464
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF.

Zhao L, Liu L, Leng W, Wei C, Jin Q.

BMC Genomics. 2011 Oct 28;12:528. doi: 10.1186/1471-2164-12-528.

PMID:
22032405
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

PMID:
16925838
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database.

Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping P, Pounds J, Adkins J, Qian X, Wang R, Wasinger V, Wu CY, Zhao X, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM.

Proteomics. 2005 Aug;5(13):3226-45.

PMID:
16104056
[PubMed - indexed for MEDLINE]
18.

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

Bininda-Emonds OR.

BMC Bioinformatics. 2005 Jun 22;6:156.

PMID:
15969769
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

Kalume DE, Peri S, Reddy R, Zhong J, Okulate M, Kumar N, Pandey A.

BMC Genomics. 2005 Sep 19;6:128.

PMID:
16171517
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

PMID:
15723693
[PubMed - indexed for MEDLINE]
Free PMC Article
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