|. ||Name ||Email address ||Office
||Luay K. Nakhleh
||by appointment, DH 3119 |
||by appointment, TBD|
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- MEETING PLACE AND TIME: Place TBD, 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):
Algorithm Design", by V. Makinen et al., Cambridge University
Sequence Analysis: Probabilistic Models of Proteins and Nucleic
Acids", by Durbin et al., Cambridge University Press.
on Strings, Trees, and Sequences", by Gusfield. Cambridge University
Bioinformatics", by M. Zvelebil and J.O. Baum. Published
by Garland Science, 2008.
Genetics", by M.B.
Published by Wiley-Blackwell, 2009.
Introduction to Population Genetics Theory, by Crow and Kimura.
Phylogenies, by Felsenstein.
of Molecular Evolution, by Graur and Li.
Evolutionary Genetics, by Felsenstein (PDF available online).
Theorey: 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
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
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
- Genome-scale index structures (suffix trees, Burrows-Wheeler
- Genome-scale algorithms (read mapping, genome comparison, genome
- Genomics, transcriptomics, and metagenomics
- GRADING: TBA
- 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
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 / email@example.com / x5841) to determine the
accommodations you need; and 2) talk with me to discuss your accommodation
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Course material (homework assignments, schedule of topics, slides, etc.)
will be posted in this section.
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