Dr. Sebastian Will

I am post-doc researcher at Rolf Backofen's Bioinformatics group at the University of Freiburg. I studied biology and computer science at the Ludwig-Maximillians-University of Munich (LMU). In Apr, 2000, I recieved my degree in Computer Science. Holding a scholarship of GKLI (Graduiertenkolleg "Logic in Computer Science") of the LMU until 2002, I moved to the University of Jena, where I finished my PhD in April, 2005 (Dr.rer.nat., "Exact, Constraint-Based Structure Prediction in Simple Protein Models"). In October, 2005, I moved to the University of Freiburg, where I hold a post-doc researcher position.

Contact

Email
Address	Dr. Sebastian Will Bioinformatics @ Institute of Computer Science Albert-Ludwigs-University Freiburg Georges-Koehler-Allee, Geb. 106 D-79110 Freiburg, Germany
Phone Fax	+49 (761) 203-8246 +49 (761) 203-7462
Room	02 011

Scientific Publications

Please see Sebastian's publications for a full list of my publications with abstracts and preprints available.

Research Interests

sequence-structure alignment of RNA
locality in the alignment of RNA
constrained-based alignment
protein structure prediction
theoretical protein models
protein evolution and energy landscapes
constraints in bioinformatics
constraint search and symmetry

Research Activities

(selected talks, presentations, organizing and group visits)

Visit and talk at CSAIL, MIT at the group of Bonnie Berger in April 08
Visit of Ivo Hofacker at TBI, Vienna in December 07
Co-organizer of the Workshop on Constraints for Bioinformatics 2007 (WCB07) at ICLP07 in Porto, Portugal, together with Rolf Backofen and Alessandro Dal Palu
Guest-editor of the Constraints Journal Special Issue on Bioinformatics, 2007 together with Agostino Dovier and Alessandro Dal Palu.
Co-organizer of the Workshop on Constraints for Bioinformatics 2006 (WCB06) at CP06 in Nantes, France, together with Agostino Dovier and Alessandro Dal Palu.
Visit at the TBI in Vienna, Austria, 2005
Talk at WCB 2005 in Sitges, Spain
Program commitee member of the Workshop on Constraints for Bioinformatics 2005 (WCB05) at ICLP05 in Sitges, Spain.
Short talks at REWERSE/A2 meetings in Munich, Dresden, Edingburgh, and Lisbon in 2004/05
Visit of Bornberg-Bauers group in Münster, Germany, 2004
Presentation at PSB 2002 in Kauwai, USA
Talk at CPM 2001 in Jerusalem, Israel
Talk at PACLP 2000 in Manchester, UK
Talk at GCB 1999 in Köln, Germany
Visit at Eugen I. Shakhnovich's group at Harvard University, Boston in 1998

Research Projects & Cooperations

With Mathias Möhl I am discussing solutions to particularly complex alignment problems.
With Jérôme Waldispühl in the group of Bonnie Berger at CSAIL, MIT, Cambridge, MA, I am investigating special cases of protein alignment.
With Ivo Hofacker, Peter Stadler, and Kristin Missal we investigate the structural clustering of ncRNAs and their multiple alignment.
Member of the EU project Emergent Organisation in Complex Biomolecular Systems (EMBIO).
Together with Alessandro Dal Palu and Agostino Dovier we are organizing the workshop on constraints in bioinfomratics series (WCB). Also, I pursued a cooperation regarding constraint-based protein structure prediction using secondary structural information.
I was member of the EU "Network of Excellence" REWERSE, Reasoning on the Web with Rules and Semantics, where I am involved in the group A2, Bioinformatics in the Semantic Web.
Together with Erich Bornberg-Bauer we have investigated protein evolutionary questions using the 3D-cubic HP and HPNX model for proteins.
Furthermore there was a cooperation with Ivo Hofacker, Peter Stadler, and Michael Wolfinger on the topic of energy landscapes.
With Guido Tack we were investigating a new search method for counting the solutions of constraint satisfaction problems.

Teaching Experience

Lectures

After gathering first teaching experience in Munich, I held exercises to the lecture "Höhere Programmierung" (high-level programming) in summer 2002 in Jena.
In winter 2002/03, I offered a practical course Data-Mining und Sequenzanalyse (data mining & sequence analysis), wich I offered again in winter 2003/04 and 2004/05. In summer 2003, I organized a seminar on constraint-satisfaction-problems in bioinformatics together with Rolf Backofen, which I offered again in summer 2004.
In summer 2005, I held the lecture "Vereinfachte Proteinmodelle" (Simplified Protein Models). A lecture "Strukturvorhersage in Vereinfachten Proteinmodellen" (structure prediciton in simplified protein models) took place in summer 2006 at the University of Freiburg.
At the Summer School "Biology, Computation and Information" (BCI 06) in Dobbiaco, Italy, I gave a course on computational protein structure prediction with constraints.
In winter 2006/2007, I gave a course about Constraint Programming.
In the summer term 2007, I offered a course "Introduction to Bioinformatics"/"Bioinformatics I" and in Winter 2007/2008 the follow up lecture "Bioinformatics II". In summer 2008, I offer the lecture "Protein Folding and Energy Landscapes".
In the winter term 2008/2009, I offered our regular course "RNA Bioinformatics".

Supervised Students

I supervise(d) several students in Jena and Freiburg, coaching their work as student researcher and/or advising them during the work on their master thesis, among them

Wolfgang Otto (finished master thesis about multiple local alignment of RNA)
Martin Mann (student researcher, finished master thesis about constraint-based structure enumeration using an advanced meta-search-strategy)
Andreas Richter (student researcher, finished master thesis)
Oliver Liegmann (student researcher, finished project)
Sebastian Barth (finished master thesis about constrained alignment)
Mounir Stino (finished Bachelor's thesis on extensions to LocARNA)
Hannes Kochniss (finished Master Thesis on Energy Landscapes)
Dennis Wehrle (Benchmarking Multiple RNA Alignment)
Mohamad Rabbath (Prediction in side chain models, finished Master's Thesis)
Fernando Meyer (Affix Arrays, Master, ongoing)
Farah Majad (Variants of the Sankoff Algorithm, Bachelor, ongoing)
Abdallah El Guindy (Search Algorithms, Bachelor, ongoing)

Software

I am author of LocARNA, a tool for very efficient Sankoff-style Multiple Local and Global Alignment of RNA. LocARNA is free for non-commercial use and available as source code.
The algorithm and an interesting application of the tool is described in the paper Inferring Non-Coding RNA Families and Classes by Means of Structure-Based Clustering with Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen.
I wrote software for structure prediction in FCC and cubic HP and HPNX models.

CPSP-Tools are a partial re-implementation and extension of my work for structure prediction in simple protein models.
CTE-Alignment. Alignment in a constraint-formulation that allows the integration of various constraints of different nature into alignment at a time.
I contributed (mostly conceptually) to the Energy Landscape Library and related projects.

Sebastian on Tour

You could have met me at ...

...
ICLP/CP 05 and at WCB 05 workshop
EMBIO meeting in Cambridge
TBI Winterseminar, Bled 06
REWERSE annual meeting 06
EMBIO meeting and EBSV06 in Vienna, Austria
ISMB 06 in Forteleza, Brazil
Summer School "Biology, Computation and Information" (BCI 06) in Dobbiaco, Italy
CP 06/WCB 06 in Nantes, France
Short visit in Saarbrücken of Gerd Smolka's group
Visit of Peter Schuster's group in Vienna
Winterseminar of our group, Schauinsland'07
TBI Winterseminar, Bled 07
REWERSE annual meeting 07
EMBIO meeting 07
Short visit of Fabrice Jossinet in Eric Westhof's group, Strasbourg
ISMB 07 in Vienna
ICLP 07 in Porto
IMA workshop on RNA, Oct 07
Visit of Ivo Hofacker in Vienna
IMA workshop on Proteins, Jan, 08
TBI Winterseminar, Bled 08
MIT in Cambridge, MA (April, 13-19)
Seminar Bioinformatics Group Freiburg, April, 8-10, 08
EMBIO meeting 08 in Venice
CPAIOR 08 and WCB 08 in Paris
CPM 08 in Pisa
GCB 08 in Dresden
Bled TBI Winterseminar 2009
Short visit in Udine (March, 3-5)

You still have the chance to meet me at ...

Stringology Workshop 2009, Tel Aviv, Israel
Winterseminar of our group, Simonswald 09
RECOMB 2009, Tucson, Arizona, USA
...

See you there ...

Created by Sebastian Will. Last updated in March, 2009