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PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.
Bioinformatics. 2014 May 15;30(10):1469-70. doi: 10.1093/bioinformatics/btu051. Epub 2014 Jan 27.
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A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.
BMC Bioinformatics. 2016 Jun 30;17(1):260. doi: 10.1186/s12859-016-1142-2.
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Proteogenomic Methods to Improve Genome Annotation.
Methods Mol Biol. 2016;1410:77-89. doi: 10.1007/978-1-4939-3524-6_5.
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A computational genomics pipeline for prokaryotic sequencing projects.
Bioinformatics. 2010 Aug 1;26(15):1819-26. doi: 10.1093/bioinformatics/btq284. Epub 2010 Jun 2.
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Omics Pipe: a community-based framework for reproducible multi-omics data analysis.
Bioinformatics. 2015 Jun 1;31(11):1724-8. doi: 10.1093/bioinformatics/btv061. Epub 2015 Jan 30.
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DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.
Bioinformatics. 2018 Mar 15;34(6):1037-1039. doi: 10.1093/bioinformatics/btx713.
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COSMOS: Python library for massively parallel workflows.
Bioinformatics. 2014 Oct 15;30(20):2956-8. doi: 10.1093/bioinformatics/btu385. Epub 2014 Jun 30.
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Proteogenomics from a bioinformatics angle: A growing field.
Mass Spectrom Rev. 2017 Sep;36(5):584-599. doi: 10.1002/mas.21483. Epub 2015 Dec 15.
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Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.
J Proteome Res. 2016 Dec 2;15(12):4686-4695. doi: 10.1021/acs.jproteome.6b00765. Epub 2016 Nov 10.
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µProteInS-a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs.
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A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.
J Bacteriol. 2022 Jan 18;204(1):e0035321. doi: 10.1128/JB.00353-21. Epub 2021 Nov 8.
2
Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.
PLoS Genet. 2021 Jun 1;17(6):e1009585. doi: 10.1371/journal.pgen.1009585. eCollection 2021 Jun.
3
Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.
IEEE Access. 2021;9:5497-5516. doi: 10.1109/ACCESS.2020.3047588. Epub 2020 Dec 25.
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An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.
Genome Res. 2017 Dec;27(12):2083-2095. doi: 10.1101/gr.218255.116. Epub 2017 Nov 15.
5
Proteomics progresses in microbial physiology and clinical antimicrobial therapy.
Eur J Clin Microbiol Infect Dis. 2017 Mar;36(3):403-413. doi: 10.1007/s10096-016-2816-4. Epub 2016 Nov 4.
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GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.
Mol Cell Proteomics. 2016 Nov;15(11):3529-3539. doi: 10.1074/mcp.M116.060046. Epub 2016 Sep 14.
7
Proteogenomics from a bioinformatics angle: A growing field.
Mass Spectrom Rev. 2017 Sep;36(5):584-599. doi: 10.1002/mas.21483. Epub 2015 Dec 15.
8
A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.
PLoS One. 2015 Nov 5;10(11):e0142162. doi: 10.1371/journal.pone.0142162. eCollection 2015.
9
The bacterial proteogenomic pipeline.
BMC Genomics. 2014;15 Suppl 9(Suppl 9):S19. doi: 10.1186/1471-2164-15-S9-S19. Epub 2014 Dec 8.
10
Proteogenomics: concepts, applications and computational strategies.
Nat Methods. 2014 Nov;11(11):1114-25. doi: 10.1038/nmeth.3144.

本文引用的文献

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Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.
Mol Cell Proteomics. 2013 Nov;12(11):3388-97. doi: 10.1074/mcp.M112.027169. Epub 2013 Jul 23.
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The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W557-61. doi: 10.1093/nar/gkt328. Epub 2013 May 2.
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Plant proteogenomics: from protein extraction to improved gene predictions.
Methods Mol Biol. 2013;1002:267-94. doi: 10.1007/978-1-62703-360-2_21.
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Peppy: proteogenomic search software.
J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w. Epub 2013 May 6.
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Proteogenomic analysis of bacteria and archaea: a 46 organism case study.
PLoS One. 2011;6(11):e27587. doi: 10.1371/journal.pone.0027587. Epub 2011 Nov 17.
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The proteogenomic mapping tool.
BMC Bioinformatics. 2011 Apr 22;12:115. doi: 10.1186/1471-2105-12-115.
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The RAST Server: rapid annotations using subsystems technology.
BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.
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The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.
Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. doi: 10.1093/nar/gkm846. Epub 2007 Oct 12.
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Galaxy: a platform for interactive large-scale genome analysis.
Genome Res. 2005 Oct;15(10):1451-5. doi: 10.1101/gr.4086505. Epub 2005 Sep 16.

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