ArticleJournal of proteome research2014
Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed.
- iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.Genome biology · 2026Article
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.Methods in molecular biology (Clifton, N.J.) · 2025Article
- A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.mSphere · 2024Article
- Bioinformatic Workflows for Metaproteomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
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- A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data.Microorganisms · 2022Article
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- Spritz: A Proteogenomic Database Engine.Journal of proteome research · 2021Article
- Identification of Non-Canonical Translation Products inFrontiers in genetics · 2021Article
- Methods for Proteogenomics Data Analysis, Challenges, and Scalability Bottlenecks: A Survey.IEEE access : practical innovations, open solutions · 2021Article
- Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform.Proteomes · 2020Article
- HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics.ACS omega · 2020Article
- Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.GigaScience · 2020Article
- Article
- Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing.Journal of proteome research · 2019Review
- Automated workflow composition in mass spectrometry-based proteomics.Bioinformatics (Oxford, England) · 2019Article
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.BMC genomics · 2019Article
- The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Proteogenomics combines large-scale genomic and transcriptomic data with mass-spectrometry-based proteomic data to discover novel protein sequence variants and improve genome annotation. In contrast with conventional proteomic applications, proteogenomic analysis requires a number of additional data processing steps. Ideally, these required steps would be integrated and automated via a single software platform offering accessibility for wet-bench researchers as well as flexibility for user-specific customization and integration of new software tools as they emerge. Toward this end, we have extended the Galaxy bioinformatics framework to facilitate proteogenomic analysis. Using analysis of whole human saliva as an example, we demonstrate Galaxy's flexibility through the creation of a modular workflow incorporating both established and customized software tools that improve depth and quality of proteogenomic results. Our customized Galaxy-based software includes automated, batch-mode BLASTP searching and a Peptide Sequence Match Evaluator tool, both useful for evaluating the veracity of putative novel peptide identifications. Our complex workflow (approximately 140 steps) can be easily shared using built-in Galaxy functions, enabling their use and customization by others. Our results provide a blueprint for the establishment of the Galaxy framework as an ideal solution for the emerging field of proteogenomics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.