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
9. Hidden Markov Models in Bioinformatics: SNV Inference from Next Generation Sequence
Jiawen Bian and Xiaobo Zhou
10. Computationally Tractable Multivariate HMM in Genome-wide Mapping Studies
Hyungwon Choi, Debashis Ghosh, and Zhaohui Qin
11. Hidden Markov Models in Population Genomics
Julien Y. Dutheil
12. Differential Gene Expression (DEX) and Alternative Splicing Events (ASE) for Temporal Dynamic Processes using HMMs and Hierarchical Bayesian Modeling Approaches
Sunghee Oh and Seongho Song
13. Finding RNA-Protein Interaction Sites using HMM
Tao Wang, Jonghyun Yun, Yang Xie, and Guanghua Xiao
14. Automated Estimation of Mouse Social Behaviours Based on a Hidden Markov Model
Toshiya Arakawa, Akira Tanave, Aki Takahashi, Satoshi Kakihara, Tsuyoshi Koide, and Takashi Tsuchiya
15. Modeling Movement Primitives with Hidden Markov Models for Robotic and Biomedical Applications
Michelle Karg and Dana Kulic