1. Introduction to Hidden Markov Models and its Applications in Biology
M S Vijayabaskar
2. HMMs in Protein Fold Classification
Christos Lampros, Costas Papaloukas, Themis Exarchos, and Dimitrios I. Fotiadis
3. Application of Hidden Markov Models in Biomolecular Simulations
Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam, and Diwakar Shukla
4. Predicting Beta Barrel Transmembrane Proteins using HMMs
Georgios N. Tsaousis, Stavros J. Hamodrakas , and Pantelis G. Bagos
5. Predicting Alpha Helical Transmembrane Proteins using HMMs
Georgios N. Tsaousis, Margarita C. Theodoropoulou, Stavros J. Hamodrakas, and Pantelis G. Bagos
6. Self-Organizing Hidden Markov Model Map (SOHMMM): Biological Sequence Clustering and Cluster Visualization
Christos Ferles, William-Scott Beaufort, and Vanessa Ferle
7. Analyzing Single Molecule FRET Trajectories using HMM
Kenji Okamoto
8. Modelling ChIP-seq Data using HMMs
Veronica Vinciotti