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Items: 1 to 20 of 123

1.

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T.

Genome Res. 2011 May;21(5):756-67. doi: 10.1101/gr.114272.110. Epub 2011 Apr 1.

2.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

3.

Proteomics techniques for the detection of translated pseudogenes.

Ucciferri N, Rocchiccioli S.

Methods Mol Biol. 2014;1167:187-95. doi: 10.1007/978-1-4939-0835-6_12. Review.

PMID:
24823778
4.

Whole genome searching with shotgun proteomic data: applications for genome annotation.

Sevinsky JR, Cargile BJ, Bunger MK, Meng F, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2008 Jan;7(1):80-8. Epub 2007 Dec 7.

PMID:
18062665
5.

Improving gene annotation using peptide mass spectrometry.

Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V.

Genome Res. 2007 Feb;17(2):231-9. Epub 2006 Dec 22.

6.

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.

Xing XB, Li QR, Sun H, Fu X, Zhan F, Huang X, Li J, Chen CL, Shyr Y, Zeng R, Li YX, Xie L.

Genomics. 2011 Nov;98(5):343-51. doi: 10.1016/j.ygeno.2011.07.005. Epub 2011 Aug 4.

7.

Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F.

J Proteome Res. 2014 May 2;13(5):2409-19. doi: 10.1021/pr4012206. Epub 2014 Apr 18.

PMID:
24717071
8.
9.

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

Krug K, Carpy A, Behrends G, Matic K, Soares NC, Macek B.

Mol Cell Proteomics. 2013 Nov;12(11):3420-30. doi: 10.1074/mcp.M113.029165. Epub 2013 Aug 1.

10.

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.

11.

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.

12.

LC-MS/MS-based proteome profiling in Daphnia pulex and Daphnia longicephala: the Daphnia pulex genome database as a key for high throughput proteomics in Daphnia.

Fröhlich T, Arnold GJ, Fritsch R, Mayr T, Laforsch C.

BMC Genomics. 2009 Apr 21;10:171. doi: 10.1186/1471-2164-10-171.

13.

Proteogenomics: needs and roles to be filled by proteomics in genome annotation.

Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD.

Brief Funct Genomic Proteomic. 2008 Jan;7(1):50-62. doi: 10.1093/bfgp/eln010. Epub 2008 Mar 10. Review.

14.

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Zhou A, Zhang F, Chen JY.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. doi: 10.1186/1471-2105-11-S6-S7.

15.

The importance of identifying alternative splicing in vertebrate genome annotation.

Frankish A, Mudge JM, Thomas M, Harrow J.

Database (Oxford). 2012 Mar 20;2012:bas014. doi: 10.1093/database/bas014. Print 2012.

16.

A unified gene catalog for the laboratory mouse reference genome.

Zhu Y, Richardson JE, Hale P, Baldarelli RM, Reed DJ, Recla JM, Sinclair R, Reddy TB, Bult CJ.

Mamm Genome. 2015 Aug;26(7-8):295-304. doi: 10.1007/s00335-015-9571-1. Epub 2015 Jun 18.

17.

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.

18.

GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra.

Shadforth I, Xu W, Crowther D, Bessant C.

J Proteome Res. 2006 Oct;5(10):2849-52.

PMID:
17022656
19.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL.

BMC Genomics. 2009 Dec 15;10:606. doi: 10.1186/1471-2164-10-606.

20.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Menschaert G, Van Criekinge W, Notelaers T, Koch A, Crappé J, Gevaert K, Van Damme P.

Mol Cell Proteomics. 2013 Jul;12(7):1780-90. doi: 10.1074/mcp.M113.027540. Epub 2013 Feb 21.

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