BSE633: Bioinformatics and Computational Biology

Semester: 2019-2020 II

TEXTBOOKS

Lectures & Reading Materials

Modeling and Discovery
of Sequence Motifs

Slides

  1. D'haeseleer, Patrik. "What are DNA Sequence Motifs?" Nature Biotechnology 24, no. 4 (2006): 423–25.

  2. D'haeseleer, Patrik. "How does DNA Sequence Motif Discovery Work?" Nature Biotechnology 24, no. 8 (2006): 959–61.

  3. Lawrence, Charles E., Stephen F. Altschul, et al. "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment." Science 262, no. 5131 (1993): 208–14.

  4. Chapter 2 of the book by Phillip Compeau, Pavel Pevzner. “Bioinformatics algorithms: an active learning approach”. [link]

Position Specific Score Matrix (PSSM) & PSI-BLAST

Slides

  1. Chapter 6 of the book "Understanding Bioinformatics", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008.

  2. Henikoff, Steven, and Jorja G. Henikoff. "Position-based sequence weights." Journal of molecular biology 243.4 (1994): 574-578.

  1. Chapter 3 of the book "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin et al., Cambridge University Press.

  2. Eddy, Sean R. "What is a Hidden Markov Model?" Nature Biotechnology 22, no. 10 (2004): 1315–6.

  3. Rabiner, Lawrence. "A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition." Proceedings of the IEEE 77, no. 2 (1989): 257–86.

Modeling Biological Sequences using Hidden Markov Models

Slides

Profile Hidden Markov Models
  1. Chapter 5 and 6 of the book "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin et al., Cambridge University Press.

  2. Chapter 6 of the book "Understanding Bioinformatics", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008.

  3. Krogh, Anders. "An Introduction to Hidden Markov Models for Biological Sequences" In Computational Methods in Molecular Biology, edited by S. L. Salzberg, D. B. Searls and S. Kasif, pages 45-63. Elsevier, 1998.

Slides

Phylogenetics: Recovering Evolutionary History

  1. Chapter 7 of the book "Understanding Bioinformatics", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008.

  2. Paschalia Kapli, Ziheng Yang & Maximilian J. Telford. “Phylogenetic tree building in the genomic age”. Nature Reviews Genetics (2020)  

Slides