Spring 2016

(Fall 2010 offering,Spring 2015 offering)

. | Name | Email address | Office hours |

Instructor | Luay K. Nakhleh | nakhleh@cs.rice.edu | by appointment, DH 3119 |

Teaching Assistant | Leo Elworth | ryan.a.leo.elworth@rice.edu | by appointment, DH 3121 |

Teaching Assistant | Dan Ye | dan.ye@rice.edu | by appointment, DH 3117 |

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**MEETING PLACE AND TIME:**Place HRZ 210, Tuesday and Thursday, 9:25-10:40 AM.**TEXTBOOKS (none required, but highly recommended, especially the first two as they cover most of the material in the course):**- "Genome-scale Algorithm Design", by V. Makinen et al., Cambridge University Press.
- "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids", by Durbin et al., Cambridge University Press.
- "Algorithms on Strings, Trees, and Sequences", by Gusfield. Cambridge University Press.
- "
**Understanding Bioinformatics**", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008. - "
**Population Genetics**", by M.B. Hamilton. Published by Wiley-Blackwell, 2009. - An Introduction to Population Genetics Theory, by Crow and Kimura.
- Inferring Phylogenies, by Felsenstein.
- Fundamentals of Molecular Evolution, by Graur and Li.
- Theoretical Evolutionary Genetics, by Felsenstein (PDF available online).
- Evolutionary Theory: Mathematical and Conceptual Foundations, by Rice.

**SOFTWARE:**here are links to programs (Matlab toolboxes included) that may be useful for homework tasks, and beyond:- For a comprehensive list of phylogeny programs, please see the website maintained by Prof. Joe Felsenstein here.
- The
**Molecular Biology and Evolution**toolbox. Click here for a paper that describes the tool. - The
**Population Genetics and Evolution**toolbox. - The ms tool for generating samples under neutral models.

**INTENDED AUDIENCE:**Anyone interested in learning about algorithms and their use in biological sequence analysis. A solid background in algorithms and good knowledge of probability are essential (without these two, students might struggle in the course). Knowledge of biology is a plus, but is not required. This is__not__a "programming for biologists" course, nor is it a course on how to use bioinformatics tools and databases.**TOPICS TO BE COVERED (tentative, time permitting):**- Pairwise sequence alignment
- Markov chains and HMMs
- Pairwise alignment using HMMS
- Profile HMMs for sequence families
- Multiple sequence alignment
- Phylogenetic tree inference
- Phylogenomics
- Genome-scale index structures (suffix trees, Burrows-Wheeler indexes,..)
- Genome-scale algorithms (read mapping, genome comparison, genome compression,...)
- Genomics, transcriptomics, and metagenomics

**GRADING:**- In-class midterm 1: 20% (February 25, 2016)
- In-class midterm 2: 20% (April 21, 2016)
- A set of homework assignments: 60%

**RICE HONOR CODE:**In this course, all students will be held to the standards of the Rice Honor Code, a code that you pledged to honor when you matriculated at this institution. If you are unfamiliar with the details of this code and how it is administered, you should consult the Honor System Handbook. This handbook outlines the University's expectations for the integrity of your academic work, the procedures for resolving alleged violations of those expectations, and the rights and responsibilities of students and faculty members throughout the process.

Students from other institutions will also be held to the same standards of the Rice Honor Code.**STUDENTS WITH DISABILITY:**If you have a documented disability or other condition that may affect academic performance you should: 1) make sure this documentation is on file with Disability Support Services (Allen Center, Room 111 / adarice@rice.edu / x5841) to determine the accommodations you need; and 2) talk with me to discuss your accommodation needs.

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Slides Set # | Topic | Slides | Materials |

1 | Administrivia and background material | Slides (full), Slides (handout) | syllabus |

2 | Sequence alignment: General overview | Slides (full), Slides (handout) | |

3 | Sequence alignment: Scoring schemes | Slides (full), Slides (handout) | |

4 | Sequence alignment: Dynamic programming algorithms for pairwise alignment | Slides (full), Slides (handout) | homework 1 (due Feb 4) |

5 | Significance of estimated sequence alignments | Slides (full), Slides (handout) | |

6 | Markov chains and hidden Markov models | Slides (full), Slides (handout) | |

7 | Pairwise HMMs and sequence alignment | Slides (full), Slides (handout) | homework 2 (due Feb 18) |

8 | Profiles and multiple sequence alignments | Slides (full), Slides (handout) | |

9 | Phylogenetics: Recovering Evolutionary History | Slides (full), Slides (handout) | |

10 | Phylogenetics: Building Phylogenetic Trees | Slides (full), Slides (handout) | homework 3 (due Mar 29) |

11 | Phylogenetics: Distance-based Methods | Slides (full), Slides (handout) | |

12 | Phylogenetics: Parsimony and Likelihood | Slides (full), Slides (handout) | homework 4 (due Apr 12) |

13 | Phylogenetics: Bayesian Analysis | Slides (full), Slides (handout) | homework 5 (due Apr 22) |

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