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Items: 1 to 20 of 127

1.

Proteogenomic analysis of bacteria and archaea: a 46 organism case study.

Venter E, Smith RD, Payne SH.

PLoS One. 2011;6(11):e27587. doi: 10.1371/journal.pone.0027587. Epub 2011 Nov 17.

2.

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
3.

A proteogenomic update to Yersinia: enhancing genome annotation.

Payne SH, Huang ST, Pieper R.

BMC Genomics. 2010 Aug 5;11:460. doi: 10.1186/1471-2164-11-460.

4.

A metaproteomic approach gives functional insights into anaerobic digestion.

Abram F, Enright AM, O'Reilly J, Botting CH, Collins G, O'Flaherty V.

J Appl Microbiol. 2011 Jun;110(6):1550-60. doi: 10.1111/j.1365-2672.2011.05011.x. Epub 2011 Apr 27.

5.

Bioinformatics analysis of disordered proteins in prokaryotes.

Pavlović-Lažetić GM, Mitić NS, Kovačević JJ, Obradović Z, Malkov SN, Beljanski MV.

BMC Bioinformatics. 2011 Mar 2;12:66. doi: 10.1186/1471-2105-12-66.

6.

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
7.

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

Kolmogorov M, Liu X, Pevzner PA.

J Proteome Res. 2016 Jan 4;15(1):144-51. doi: 10.1021/acs.jproteome.5b00610. Epub 2015 Dec 17.

PMID:
26629978
8.

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
9.

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.

10.

Sensing of environmental signals: classification of chemoreceptors according to the size of their ligand binding regions.

Lacal J, García-Fontana C, Muñoz-Martínez F, Ramos JL, Krell T.

Environ Microbiol. 2010 Nov;12(11):2873-84. doi: 10.1111/j.1462-2920.2010.02325.x. Epub 2010 Aug 25. Review.

PMID:
20738376
11.
12.

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.

Zivanovic Y, Armengaud J, Lagorce A, Leplat C, Guérin P, Dutertre M, Anthouard V, Forterre P, Wincker P, Confalonieri F.

Genome Biol. 2009;10(6):R70. doi: 10.1186/gb-2009-10-6-r70. Epub 2009 Jun 26.

13.

Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.

Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A.

Mol Cell Proteomics. 2011 Dec;10(12):M111.011627. doi: 10.1074/mcp.M111.011445. Epub 2011 Oct 3.

14.

Proteogenomic Methods to Improve Genome Annotation.

Datta KK, Madugundu AK, Gowda H.

Methods Mol Biol. 2016;1410:77-89. doi: 10.1007/978-1-4939-3524-6_5.

PMID:
26867739
15.

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.

Zhu H, Hu GQ, Yang YF, Wang J, She ZS.

BMC Bioinformatics. 2007 Mar 16;8:97.

16.

The origins of modern proteomes.

Kurland CG, Canbäck B, Berg OG.

Biochimie. 2007 Dec;89(12):1454-63. Epub 2007 Sep 15.

PMID:
17949885
17.

Towards multidimensional genome annotation.

Reed JL, Famili I, Thiele I, Palsson BO.

Nat Rev Genet. 2006 Feb;7(2):130-41. Review.

PMID:
16418748
18.

Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes.

Gaasterland T, Ragan MA.

Microb Comp Genomics. 1998;3(4):199-217.

PMID:
10027190
19.

Genome-wide survey of transcription factors in prokaryotes reveals many bacteria-specific families not found in archaea.

Minezaki Y, Homma K, Nishikawa K.

DNA Res. 2005;12(5):269-80. Epub 2006 Jan 10.

PMID:
16769689
20.

The application of terminomics for the identification of protein start sites and proteoforms in bacteria.

Berry IJ, Steele JR, Padula MP, Djordjevic SP.

Proteomics. 2016 Jan;16(2):257-72. doi: 10.1002/pmic.201500319. Epub 2015 Nov 23. Review.

PMID:
26442651

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