research

Bioinformatics
Network Analysis
Graph Drawing

projects

open student projects

Xanvi

A small framework of plugins and extension points for the analysis and visualization of biological networks.

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PAST

The Polypeptide Angles Suffix Tree (PAST) is data structure that provides fast methods for searching three-dimensional polypeptide (protein) structures and identifying frequent common substructures (structural motifs) in a protein structure database like the PDB. Unlike former approaches in this topic this approach does not consider the sequence of amino acids (i.e. the primary structure). Instead of that it uses a coding of the backbone torsion angles which is invariant to translation and rotation of the molecule in the actual coordinate system.

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teaching

past

Lecture "Fundamental Algorithms" (engl.)" (Script)

Lab Course "Algorithm Design" (Fall 2004) (Fall 2005)
Lab Course "Discrete Optimization" (Spring 2004) (Spring 2005)
Proseminar on Graph Drawing (Spring 2004)
Tutorial for the Lecture "Fundamental Algorithms" (Fall 2003)
Tutorial for the Lecture "Efficient Algorithms II" (Spring 2003)

student works: theses, semester projects & seminars

W. Koska: "A hierarchical graph implementation." (SEP, 10/2006)
C. Mei-Chuan: "2-Dimensional Pattern Matching" (Seminar, 1/2005)
T. Binder: "Centrality-based Analysis of Metabolic Networks" (Dipl. Thesis, 9/2004)
P. Pissang: "Information Content of Genes" (Seminar,12/2003)
S. Strempel: "Sequence Assembly: Shotgun Sequencing" (Seminar, 1/2003)

publications & presentations

J. Griebsch, O. Arafat, W. Koska
xAnVi - An Extensible Visualization and Analysis Framework
July 2006
Information Visualization 2006 , vol., no.pp. 45- 52, 05-07 July 2006
H. Täubig, A. Buchner, J. Griebsch
PAST: Fast Structure-based Searching in the PDB
July 2006
Nucleic Acids Research; 2006 Jul 1; 34:W20-23 (Web Server issue)
M. Baumgart, S. Eckhardt, J. Griebsch, S. Kosub, J. Nowak
All-Pairs Common-Ancestor Problems in Weighted Dags.
April 2006
Technical Report TUM-I0606, Technische Universität München, Institut für Informatik
T. Simpson, S. Clarke, J. Griebsch
Analysis of Support Vector Regression for Approximation of Complex Engineering Analyses
July 2005
ASME, Journal of Mechanical Design, July 2005, MD-03-1319
H. Täubig, A. Buchner, J. Griebsch
A Method for Fast Approximate Searching of Polypeptide Structures in the PDB
Proceedings of the German Conference on Bioinformatics (GCB'04)
(October 4-6 2004, Bielefeld / Germany).
Lecture Notes in Informatics (LNI) Vol. P-53, pp. 65-74.
A. Buchner, H. Täubig, J. Griebsch
A Fast Method for Motif Detection and Searching in a Protein Structure Database
Proceedings of the German Conference on Bioinformatics (GCB'03)
(October 12-14 2003, Munich / Germany).
Vol. II (Poster abstracts), pp. 186-188.
T. Simpson, S. Clarke, J. Griebsch
Analysis of Support Vector Regression for Approximation of complex Engineering Analyses
ASME Design Engineering Technical Conferences - Design Automation Conference, Shimada, K., ed.
(September 2-6, 2003, Chicago, IL
paper no. DETC2003/DAC-48759
J. Griebsch, T. Binder, A. Buchner
A Fast Algorithm for the Iterative Calculation of Betweeness Centrality
Proceedings of the German Conference on Bioinformatics (GCB'04)
(October 04-06 2004, Bielefeld)
Discovery Notes and Poster Abstracts, p. 114-115

miscellaneous

Ferienakademie der deutschen Studienstiftung 2002

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