Community links:

• ProteoRE in Galaxy community Hub
• ProteoRE training materials in GTN (Galaxy Training Network)
• ProteoRE in the bio.tools registry (Elixir)
• ProteoRE tools in the Galaxy Toolshed
• ProteoRE github
• Galaxy Proteomics github

Training events:

• ProteoRE training session can be be organized upon request: Contact us!
• ProteoRE training session at IBCP CNRS, Lyon, FR, July 7, 2024
• ProteoRE team at the GCC2021 Training Week, June 28- July 2, 2021: Practical information here.
• ProteoRE team participated to the GTN Smörgåsbord: A Global Galaxy Course, 15-19th February 2021, virtual.
• "Functional analysis and interpretation of proteomics data with ProteoRE", organized by French Institute of Bioinformatics (IFB), 10-11th July 2019, Rennes, FR.
• "Functional analysis and interpretation of proteomics data with ProteoRE", organized by French Institute of Bioinformatics (IFB), 14-15th March 2019, Paris, FR.
• "ProteoRE training session", organized by Proteomics French Infrastructure (ProFI), 7-8th February 2019, Grenoble, FR.

Publications:

• Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics. 2023. 20(11):251-266. PMID:37787106
• Combes F, Loux V, Vandenbrouck Y. A strategy for the annotation and GO enrichment analysis of a list of differentially expressed proteins using ProteoRE. Methods Mol. Biol. 2021. PMID: 34236662
• Vandenbrouck Y, Pineau C, Lane L. The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology. J Proteome Res. 2020. 19(12):4782-4794. PMID:33064489
• Vandenbrouck Y, Christiany D, Combes F, Loux V, Brun V. Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer. Proteomics. 2019. 19 (21-22). PMID:31538697
• Nguyen L, Brun V, Combes F, Loux V, Vandenbrouck Y. Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework. Methods Mol Biol. 2019. 1959:275-289. PMID:30852829
• Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V. Proteomic characterization of human exhaled breath condensate. J Breath Res. 2018. 12(2):021001. PMID:29189203

Oral communications:

• "ProteoRE: A biologist-oriented Galaxy platform for proteomics data interpretation" at the HUPO 2021 Pre-congress Training Courses, 2021
• “ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research”. Combes F., et al. Galaxy Community Conference 2019. July 2019, Freiburg, Germany. Oral presentation & demo. gcc2019
• “ProteoRE, a Galaxy-based platform for the annotation and the interpretation of proteomics data in biomedical research”. Christiany D., et al. JOBIM conference, July 2019. Nantes, France. Oral presentation & demo. Jobim2019
• ” Exploring the dark side of the Human proteome using the ProteoRE platform”. Vandenbrouck Y. et al., 21st "Human Proteome Project" symposium. May, 2019 Saint-Malo, France. Keynote. https://hupo.org/HUPOST/7314404
• “ProteoRE, a Galaxy-based infrastructure for annotating and interpreting proteomics data. Combes F. et al., 35th SFEAP congress, Oct. 2018, Albi, France. Oral presentation. http://sfeap2018.ipbs.fr/program/
• “Using ProteoRE to annotate and explore the human proteome”. Vandenbrouck et al., 12th European Proteomics Association (EuPA), June 2018, Santiago, Spain. Oral presentation. http://www.eupa2018.com/images/program/0112139_PROGRAMA_V5.pdf
• “ProteoRE, a Galaxy-based infrastructure for annotating and interpreting proteomics data”. Combes F. et al., JOBIM July 2018, Marseille, France. Poster presentation. https://jobim2018.sciencesconf.org/data/pages/Book_JOBIM2018_V3.pdf
• ProteoRE, a Galaxy-based infrastructure for interpreting and exploring mass spectrometry-based proteomics data. Nguyen L., et al., 16th Human Proteome Organization World Congress (HUPO) Sept. 2017, Dublin, Ireland. Poster presentation. http://hupo2017.ie/wp-content/uploads/2017/05/HUPO2017_Programme_Posters.pdf
• “ProteoRE, a Galaxy-based infrastructure for interpreting and exploring mass spectrometry-based proteomics data”. Nguyen L., et al. Galaxy Community Conference 2017. June 2017, Montpellier, France. Poster presentation. https://gcc2017.sched.com/event/B8U9/p17-proteore-a-galaxy-based-infrastructure-for-interpreting-and-exploring-mass-spectrometry-based-proteomics-data