Proteomics Data Analysis

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As advertised at the website.

   IMPORTANT DATES for this Course
   Deadline for applications: April 5th 2016 (New)
   Course date: April 11th - April 15th 2016

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


Lennart Martens Lennart Martens is professor of systems biology at Ghent University, and group leader of the Computational Omics and Systems Biology (CompOmics) group at VIB, both in Ghent, Belgium. He has been working in proteomics bioinformatics since his Master's degree, which focused on the computational interpretation of peptide mass spectra. He then worked as a software developer and framework architect for a software company for a few years, before returning to Ghent University to pursue a Ph.D. focused on proteomics and proteomics informatics. During this time, he worked on the development of high-throughput peptide centric proteomics techniques and on bioinformatics tools to support these new approaches. In 2003 he started the PRIDE proteomics database at the EBI as a Marie Curie fellow of the European Commission. After obtaining his Ph.D., he rejoined the PRIDE group at EBI, which he coordinated for several years before moving back to Ghent University to take up his current position. Prof. Martens served as the chair of the ABRF iPRG in 2011, sits on the Board of DELSA (http://www.delsaglobal.org), the Royal Flemish Society for Chemistry - Proteomics, and the Belgian Proteomics Association. He serves as Academic Editor for PLoS ONE and Open Proteomics and holds Editorial Board positions at PROTEOMICS, BBA Proteins and Proteomics and Molecular BioSystems. An author on more than 135 peer-reviewed papers and has co-written two popular Wiley textbooks: Computational Methods for Mass Spectrometry Proteomics (ISBN: 978-0-470-51297-5), and Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (ISBN: 978-1-119-96400-1).

Affiliation: Ghent University and VIB, Ghent, BE

Harald Barsnes is a group leader at the Department of Biomedicine and at the Department of Informatics, both at the University of Bergen in Norway. He has a PhD from the same university in 2010, with a focus on bioinformatics and proteomics. Since then he has worked first as a senior engineer and then a postdoc at the Proteomics Unit at the Department of Biomedicine, and later as a researcher at the Department of Clinical Medicine, both in Bergen. The main focus throughout his career has been the development of user-friendly open source bioinformatics tools that enable and empower researchers to analyze their own proteomics data. This has resulted in numerous publications and a long list of freely available software, including PRIDE Converter, SearchGUI and PeptideShaker. Barsnes has also been a guest editor in PROTEOMICS and has co-authored a Wiley text book called Computational and Statistical Methods for Protein Quantification by Mass Spectrometry (ISBN: 978-1-1199-6400-1). In 2015 he received the prestigious Meltzer Award for Excellent Young Researchers at the University of Bergen.

Affiliation: Department of Biomedicine and Department of Informatics, University of Bergen, NO

Marc Vaudel currently works as a postdoc at the Department of Biomedicine at the University of Bergen, Norway. Marc obtained an engineer degree in France at the École Centrale de Lyon, followed by a PhD at the biomedical department of the Ghent University, Belgium, in cooperation with the Leibniz - Institut für Analytische Wissenschaften - ISAS - e.V. in Dortmund, Germany, under the joint supervision by Prof. Dr. Lennart Martens (Gent, Belgium) and Prof. Dr. Albert Sickmann (Dortmund, Germany). His main focus is the investigation of biomedical samples using proteomics. Marc is also an associated member of the Computational Omics and Systems Biology (CompOmics) group at VIB in Ghent, headed by Prof. Dr. Lennart Martens, of the Bergen stem cell consortium headed by Prof. Dr. Helge Ræder, and member of the educational committee of the European Proteomics Association (EuPA).

Affiliation: Department of Biomedicine, University of Bergen, NO

Course description

Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The course will rely exclusively on free and user friendly software, all of which can be directly applied in your lab upon your return from the course.

An introduction to the available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses.
In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories.

The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics.

Course Pre-requisites

The participants should have a basic knowledge about mass spectrometry based proteomics. Experience in analyzing proteomics data is an advantage, but not mandatory. The course does not require advanced computer skills.


Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  Feb 29th 2016