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Items: 16

1.

Comparative omics-driven genome annotation refinement: application across Yersiniae.

Schrimpe-Rutledge AC, Jones MB, Chauhan S, Purvine SO, Sanford JA, Monroe ME, Brewer HM, Payne SH, Ansong C, Frank BC, Smith RD, Peterson SN, Motin VL, Adkins JN.

PLoS One. 2012;7(3):e33903. doi: 10.1371/journal.pone.0033903. Epub 2012 Mar 27. Erratum in: PLoS One. 2012;7(8). doi: 10.1371/annotation/03110e8b-3e10-4334-9ff7-969c85ad25d8.

2.

The yersiniae--a model genus to study the rapid evolution of bacterial pathogens.

Wren BW.

Nat Rev Microbiol. 2003 Oct;1(1):55-64. Review.

PMID:
15040180
3.

Proteogenomics for environmental microbiology.

Armengaud J, Hartmann EM, Bland C.

Proteomics. 2013 Oct;13(18-19):2731-42. doi: 10.1002/pmic.201200576. Epub 2013 Jun 18. Review.

PMID:
23636904
4.

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes.

Kumar D, Mondal AK, Kutum R, Dash D.

Proteomics. 2016 Jan;16(2):226-40. doi: 10.1002/pmic.201500263. Epub 2015 Nov 23. Review.

PMID:
26773550
5.

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
6.

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.

PMID:
18334489
7.

A perfect genome annotation is within reach with the proteomics and genomics alliance.

Armengaud J.

Curr Opin Microbiol. 2009 Jun;12(3):292-300. doi: 10.1016/j.mib.2009.03.005. Epub 2009 May 4. Review.

PMID:
19410500
8.

[Progress in proteogenomics of prokaryotes].

Zhang C, Xu P, Zhu Y.

Sheng Wu Gong Cheng Xue Bao. 2014 Jul;30(7):1026-35. Review. Chinese.

PMID:
25345005
9.

Using comparative genome analysis to identify problems in annotated microbial genomes.

Poptsova MS, Gogarten JP.

Microbiology. 2010 Jul;156(Pt 7):1909-17. doi: 10.1099/mic.0.033811-0. Epub 2010 Apr 29. Review.

PMID:
20430813
10.

Proteogenomics to discover the full coding content of genomes: a computational perspective.

Castellana N, Bafna V.

J Proteomics. 2010 Oct 10;73(11):2124-35. doi: 10.1016/j.jprot.2010.06.007. Epub 2010 Jul 8. Review.

11.

Omics strategies for revealing Yersinia pestis virulence.

Yang R, Du Z, Han Y, Zhou L, Song Y, Zhou D, Cui Y.

Front Cell Infect Microbiol. 2012 Dec 13;2:157. doi: 10.3389/fcimb.2012.00157. eCollection 2012. Review.

12.

Annotating non-coding regions of the genome.

Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB.

Nat Rev Genet. 2010 Aug;11(8):559-71. doi: 10.1038/nrg2814. Epub 2010 Jul 13. Review.

PMID:
20628352
13.

Genome and proteome annotation: organization, interpretation and integration.

Reeves GA, Talavera D, Thornton JM.

J R Soc Interface. 2009 Feb 6;6(31):129-47. doi: 10.1098/rsif.2008.0341. Review.

14.

The proteogenomic path towards biomarker discovery.

Sigdel TK, Sarwal MM.

Pediatr Transplant. 2008 Nov;12(7):737-47. doi: 10.1111/j.1399-3046.2008.01018.x. Epub 2008 Aug 22. Review.

15.

Microbial virus genome annotation-mustering the troops to fight the sequence onslaught.

Brister JR, Le Mercier P, Hu JC.

Virology. 2012 Dec 20;434(2):175-80. doi: 10.1016/j.virol.2012.09.027. Epub 2012 Oct 18. Review.

16.

The state of play in higher eukaryote gene annotation.

Mudge JM, Harrow J.

Nat Rev Genet. 2016 Dec;17(12):758-772. doi: 10.1038/nrg.2016.119. Epub 2016 Oct 24. Review.

PMID:
27773922

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