Dagstuhl Seminar 08101
Computational Proteomics
( Mar 02 – Mar 07, 2008 )
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https://www.dagstuhl.de/08101
Organizers
- Christian Huber (Universität Salzburg, AT)
- Oliver Kohlbacher (Universität Tübingen, DE)
- Michal Linial (The Hebrew University of Jerusalem, IL)
- Katrin Marcus (Ruhr-Universität Bochum, DE)
- Knut Reinert (FU Berlin, DE)
Contact
Impacts
- In silico fragmentation for computer assisted identification of metabolite mass spectra : article - Wolf, Sebastian; Schmidt, Stephan; Müller-Hannemann, Matthias; Neumann, Steffen - Berlin : Springer, 2010. - 12 pp. - (BMC Bioinformatics ; 11. 2010, article 148).
- MetFrag relaunched : incorporating strategies beyond in silico fragmentation : article - Ruttkies, Christoph; Schymanski, Emma; Wolf, Sebastian; Hollender, Juliane; Neumann, Steffen - Berlin : Springer, 2016. - 16 pp. - (Journal of Cheminformatics ; 8. 2016, Article 3).
- MetFusion : integration of compound identification strategies : article - Gerlich, Michael; Neumann, Steffen - Chichester : Wiley, 2013. - pp. 291-298 - (Journal of Mass Spectrometry ; 48. 2013, 3).
The field of Computational Proteomics has grown rapidly and gained a lot of momentum over the last years. Computational Proteomics was previously a field with a small and specialized community. Over the last few years, however, it has been recognized by experimental groups, that the analysis of the increasingly complex proteomics studies has become intractable without efficient algorithms implemented in easy-to-use tools. Conversely, the computer science and bioinformatics communities started to realize the wealth of interesting problems in this area. Both sides are thus eager to come together and work on these problems. To initiate this close collaboration of researchers from different fields (biology, medical sciences, biochemistry, analytical chemistry, bioinformatics, and computer science), we need opportunities to bring both communities together in an inspiring and relaxed atmosphere. Past experience from our 2005 seminar has shown that Dagstuhl is an ideal place for this.
Currently, computational proteomics faces a number of challenges. The increasing speed and accuracy of the new instrument generation yields datasets that are up to an order of magnitude larger than datasets seen a few years ago. This implies new algorithmic techniques and data analysis capabilities. The computer science problems to be tackled range from data management, over optimization problems, to machine learning. On the experimental side, the development of high mass accuracy and better separation techniques pose new challenges.
The seminar brought together a mixed audience from proteomics and bioinformatics: At the beginning we took a pool showing that there were 10 people who declared themselves as “wet lab” and 26 as “computer science”. Moreover, there were 21 people “holding a PhD degree” and 15 “working on it”. We are happy to see that the communities really grow together.
The talks and discussions were arranged on a daily basis featuring related topics:
- Systems Biology and novel experimental techniques.
- Quantitative analysis.
- Identification.
- Pathway analysis and biomarkers.
In conclusion, the workshop was very successful. It sparked interesting discussions, research collaborations, several joint grant proposals (e.g. for the BMBF program QuantPro), and joint publications. Other publications sparked by the seminar will certainly follow in the near future. The seminar also initiated the implementation of a webpage for interchanging proteomics data (www.computationalproteomics.net). The success of the seminar and the positive feedback of the participants encourage us to organize a follow-up for this style of meeting.
- Manor Askenazi (The Hebrew University of Jerusalem, IL) [dblp]
- Nuno Bandeira (University of California - San Diego, US) [dblp]
- Andreas Bertsch (Universität Tübingen, DE)
- Chris Bielow (FU Berlin, DE)
- Rainer Bischoff (University Medical Center Groningen, NL)
- Sebastian Böcker (Universität Jena, DE) [dblp]
- John Cottrell (Matrix Science Ltd. - London, GB)
- Jens Decker (Bruker Daltonik GmbH - Bremen, DE)
- Johan Gobom (University of Göteborg/Sahlgrenska - Mölndal, SE)
- Clemens Gröpl (FU Berlin, DE)
- Thomas Aarup Hansen (University of Southern Denmark - Odense, DK)
- Henning Hermjakob (European Bioinformatics Institute - Cambridge, GB) [dblp]
- Christian Huber (Universität Salzburg, AT)
- Hans-Michael Kaltenbach (Institut Curie - Paris, FR)
- Oliver Kohlbacher (Universität Tübingen, DE) [dblp]
- Sebastian Kühner (EMBL Heidelberg, DE)
- Bernhard Küster (TU München, DE) [dblp]
- Eva Lange (The Beatson Inst. f. Cancer Research - Glasgow, GB)
- Michael Lappe (MPI für Molekulare Genetik, DE) [dblp]
- Wolf D. Lehmann (DKFZ - Heidelberg, DE) [dblp]
- Michal Linial (The Hebrew University of Jerusalem, IL) [dblp]
- Katrin Marcus (Ruhr-Universität Bochum, DE) [dblp]
- Katja Melchior (Universität des Saarlandes, DE)
- Markus Müller (Swiss Institute of Bioinformatics, CH)
- Sven Nahnsen (Universität Tübingen, DE) [dblp]
- Anton Pervukhin (Universität Jena, DE)
- Nico Pfeifer (Universität Tübingen, DE) [dblp]
- Katharina Podwojski (TU Dortmund, DE)
- Jörg Rahnenführer (TU Dortmund, DE)
- Florian Rasche (Universität Jena, DE)
- Knut Reinert (FU Berlin, DE) [dblp]
- Hartmut Schlüter (Charité - Berlin, DE)
- Ole Schulz-Trieglaff (FU Berlin, DE)
- Benno Schwikowski (Inst. Pasteur et LIX (Paris) & MPI (Berlin), FR) [dblp]
- Albert Sickmann (Universität Würzburg, DE) [dblp]
- Christian Stephan (Ruhr-Universität Bochum, DE)
- Jens Stoye (Universität Bielefeld, DE) [dblp]
- Marc Sturm (Universität Tübingen, DE)
- Joel Vandekerckhove (Ghent University, BE)
- Mathias Vandenbogaert (Institut Curie - Paris, FR)
- René Zahedi (Universität Würzburg, DE)
- Alexandra Zerck (MPI für Molekulare Genetik - Berlin, DE)
- Roman Zubarev (University of Uppsala, SE) [dblp]
Related Seminars
- Dagstuhl Seminar 05471: Computational Proteomics (2005-11-20 - 2005-11-25) (Details)
- Dagstuhl Seminar 13491: Computational Mass Spectrometry (2013-12-01 - 2013-12-06) (Details)
- Dagstuhl Seminar 15351: Computational Mass Spectrometry (2015-08-23 - 2015-08-28) (Details)
- Dagstuhl Seminar 17421: Computational Proteomics (2017-10-15 - 2017-10-20) (Details)
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- Dagstuhl Seminar 23301: Computational Proteomics (2023-07-23 - 2023-07-28) (Details)
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Classification
- interdisciplinary with non-informatics-topic bioinformatics
Keywords
- bioinformatics
- biomedicine
- proteomics
- analytical chemistry
