Seminar Winter 2011/2012
Time and place: Tuesday 16-18, M3-115
Instructor: Robert Giegerich
Pattern matching on trees and tree comparison are classical topics in computer science. It is used, for example, in comparing structured documents, structured physical objects assembled in a tree like fashion, or molecular structures that can be represented as trees. Term rewrite systems require to match rewrite rules to target terms, and compiler code generation involves matching patterns that describe machine instructions to intermediate program code.
In bioinformatics, there is a large demand on tree comparison methods for modeling RNA secondary structure and finding novel RNA genes via structural matching.
In the seminar, we shall focus on the algorithmic aspects of tree pattern matching. We shall review some of the classical algorithms, and study some very recent enhancements.
|22.11.: ||Corinna Sickinger|
|29.11.: ||Juri Ritter|
|06.12.: ||Svea Kokott|
|13.12.: ||Sarah Woltmann|
|20.12.: ||Robert Giegerich |
(1) Classical Articles
(2) Applications in RNA structure comparison
(3) Recent applications to XML document processing
- M. Hoechsmann, B. Voss, and R. Giegerich.
Pure multiple RNA secondary structure alignments: A progressive profile approach.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1:53-62, 2004
- S. Schirmer, R.Giegerich.
Forest alignment with affine gaps and anchors. Submitted to TCS, 2011
- Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, and Helene Touzet.
Alignments of RNA Structures.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 2, April-June, 2010
- Peter L. Thomas, David F. Brailsford.
Enhancing Composite Digital Documents Using XML-based Standoff Markup.
Proceedings Document Engineering, 2005
- Sebastian Roennau, Geraint Philipp, Uwe M. Borghoff.
Efficient Change Control of XML Documents. Proceedings Document Engineering, 2009
- Davi de Castro Reis, Paulo B. Golgher, Altigran S. da Silva, Alberto H. F. Laender.
Automatic Web News Extraction Using Tree Edit Distance.
WWW2004, May 17--22, 2005, New York, New York, USA. ACM158113844X/04/0005