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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner CN, Pirklbauer GJ, Bender A, Steen JAJ, Choudhary JS.

J Vis Exp. 2018 May 22;(135). doi: 10.3791/57633.


Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner CN, Pirklbauer GJ, Bender A, Choudhary JS.

Cell Syst. 2017 Aug 23;5(2):152-156.e4. doi: 10.1016/j.cels.2017.07.007.


PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

Chaudhuri R, Sadrieh A, Hoffman NJ, Parker BL, Humphrey SJ, Stöckli J, Hill AP, James DE, Yang JY.

BMC Genomics. 2015 Aug 19;16:617. doi: 10.1186/s12864-015-1820-x.


Proteogenomics from a bioinformatics angle: A growing field.

Menschaert G, Fenyö D.

Mass Spectrom Rev. 2017 Sep;36(5):584-599. doi: 10.1002/mas.21483. Epub 2015 Dec 15. Review.


Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.

Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C.

BMC Genomics. 2019 Jan 17;20(1):56. doi: 10.1186/s12864-019-5431-9.


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.


Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.

Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM.

J Proteome Res. 2016 Mar 4;15(3):800-8. doi: 10.1021/acs.jproteome.5b00817. Epub 2016 Jan 12.


The proteogenomic mapping tool.

Sanders WS, Wang N, Bridges SM, Malone BM, Dandass YS, McCarthy FM, Nanduri B, Lawrence ML, Burgess SC.

BMC Bioinformatics. 2011 Apr 22;12:115. doi: 10.1186/1471-2105-12-115.


proBAMconvert: A Conversion Tool for proBAM/proBed.

Olexiouk V, Menschaert G.

J Proteome Res. 2017 Jul 7;16(7):2639-2644. doi: 10.1021/acs.jproteome.7b00132. Epub 2017 Jun 9.


ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins.

Krassowski M, Paczkowska M, Cullion K, Huang T, Dzneladze I, Ouellette BFF, Yamada JT, Fradet-Turcotte A, Reimand J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D901-D910. doi: 10.1093/nar/gkx973.


proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data.

Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B.

Mol Cell Proteomics. 2016 Mar;15(3):1164-75. doi: 10.1074/mcp.M115.052860. Epub 2015 Dec 11.


Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes.

Sridhara V, Marchler-Bauer A, Bryant SH, Geer LY.

Database (Oxford). 2011 May 13;2011:bar019. doi: 10.1093/database/bar019. Print 2011.


A large-scale proteogenomics study of apicomplexan pathogens-Toxoplasma gondii and Neospora caninum.

Krishna R, Xia D, Sanderson S, Shanmugasundram A, Vermont S, Bernal A, Daniel-Naguib G, Ghali F, Brunk BP, Roos DS, Wastling JM, Jones AR.

Proteomics. 2015 Aug;15(15):2618-28. doi: 10.1002/pmic.201400553. Epub 2015 May 15.


Proteogenomics and systems biology: quest for the ultimate missing parts.

Armengaud J.

Expert Rev Proteomics. 2010 Feb;7(1):65-77. doi: 10.1586/epr.09.104. Review.


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.


The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data.

Menschaert G, Wang X, Jones AR, Ghali F, Fenyö D, Olexiouk V, Zhang B, Deutsch EW, Ternent T, Vizcaíno JA.

Genome Biol. 2018 Jan 31;19(1):12. doi: 10.1186/s13059-017-1377-x.


Reannotation of Genomes by Means of Proteomics Data.

Armengaud J.

Methods Enzymol. 2017;585:201-216. doi: 10.1016/bs.mie.2016.09.019. Epub 2016 Oct 19.


g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.

Keegan S, Cortens JP, Beavis RC, Fenyö D.

J Proteome Res. 2016 Mar 4;15(3):983-90. doi: 10.1021/acs.jproteome.5b01018. Epub 2016 Feb 18.


Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA.

Genome Res. 2007 Sep;17(9):1362-77. Epub 2007 Aug 9.

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