Publications

The General Hidden Markov Model library (GHMM) has been used for published research papers and theses:

Michael Seifert Analyzing Microarray Data Using Homogenous and Inhomogenous Hidden Markov Models. Diplomarbeit im Studiengang Bioinformatik, Martin-Luther-Universität Halle (2006)

A. Schliep, I. G. Costa, C. Steinhoff, A. A. Schönhuth. Analyzing Gene Expression Time-Courses IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Special Issue on Machine Learning for Bioinformatics), 2005, 2(3):179-193.

I. G. Costa, A. Schönhuth, A. Schliep. The Graphical Query Language: a tool for analysis of gene expression time-courses , Bioinformatics, 2005, 21(10):2544-2545.

A. Schliep, B. Georgi, W. Rungsarityotin, I. G. Costa, A. Schönhuth The General Hidden Markov Model Library: Analyzing Systems with Unobservable States , Proceedings of the Heinz-Billing-Price 2004: 121-136,.

Bernhard Knab. Extension of Hidden Markov Models for the analysis of financial time-series data Ph.D. Thesis. ZAIK, University of Cologne, Germany (2000). In German.

Bernd Wichern. Hidden Markov Models for the analysis of data from saving and loan banks Ph.D. Thesis. ZAIK, University of Cologne, Germany (2001). In German.

A. Schliep, A. Schönhuth, C. Steinhoff. Using Hidden Markov Models to Analyze Gene Expression Time Course Data. Proceedings of the ISMB 2003. Bioinformatics. 2003 Jul; 19 Suppl 1: I255-I263

B. Georgi. A Graph-based Apporach to Clustering of Profile Hidden Markov Models Bachelor Thesis, FU Berlin.

A. Weisse. Detecting Circular Permutations in Remote Homologue Proteins. Bachelor Thesis, FU Berlin.

A. Schliep, C. Steinhoff, A. Schönhuth.Robust inference of groups in gene expression time-courses using mixtures of HMM. Proceedings of the ISMB 2004.

Matthias Heinig Development of a Pair HMM based Gene Finder for the Paramecium Genome. Master Thesis, FU Berlin (2005)