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COMP 571 BIOINFORMATICS: SEQUENCE ANALYSIS
Fall 2008

[Staff] [Information] [Materials]

Staff

. Name Email address Office hours
Instructor Luay K. Nakhleh nakhleh@cs.rice.edu by appointment, DH 3119
Teaching Assistant Cuong Than druths@cs.rice.edu by appointment, DH 3117

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Course Information


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Course Material

Course material (homework assignments, schedule of topics, slides, etc.) will be posted in this section.

Slides Set # Topic Slides Homework assignments
1 Administrivia and background material PDF
2 General overview of sequence alignment PDF
3 Sequence alignment: scoring schemes PDF
4 Pairwise sequence alignment: dynamic programming algorithms PDF
5 Markov chains and hidden Markov models PDF
6 Sequence alignment using pair HMMs and statistical significance of alignment scores PDF hw1 (due: Oct 14), hw2 (due: Oct 28)
7 Algorithmic approximations and database search PDF
8 Profile HMMs PDF
9 Multiple sequence alignment PDF
10 Phylogenetics I: Recovering evolutionary history PDF
11 Phylogenetics II: Building phylogenetic trees PDF hw3 (due: Nov 13)
12 Phylogenetics III: Theory behind building phylogenetic trees PDF List of paper assignments for student presentations, hw4 (due: Dec 4)


STUDENT PRESENTATIONS
Student Paper title Journal/Proceedings Slides
Ben Bachman Discovery of regulatory elements by a computational method for phylogenetic footprinting Genome Research, 12:739-748, 2002. PDF
Raj Barik Combining statistical alignment and phylogenetic footprinting to detect regulatory elements Bioinformatics, 24(10):1236-1242, 2008. PDF
Drew Bryant Evolutionary predictions of binding surfaces and interactions Curr. Opin. Struct. Biol., 12(1):21-27, 2002. PDF
Joanna Crompton T-Coffee: A novel method for fast and accurate multiple sequence alignment J. Mol. Biol., 302(1):205-217, 2000. PDF
Jun Inoue MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Research, 30:3059-3066, 2002. PDF
Chase Jenkins MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Boinformatics, 5:113, 2004. PDF
Jeff Kilpartick Genome-wide strategies for detecting multiple loci that influence complex diseases Nature Genetics, 37:413-417, 2005. PDF
Biao Li Multilocus association mapping using variable-length Markov chains Am. J. Hum. Gen., 78(6):903-913, 2006. PDF
Shuwei Li Efficient whole-genome association mapping using local phylogenies for unphased genotype data Bioinformatics, 2008 (advance access). PDF
Xiaoyun Liao Orthologs, paralogs, and evolutionary genomics Annu. Rev. Genet., 39(1):309-338, 2005. PDF
Dajiang Liu Stochastic models for horizontal gene transfer: taking a random walk through tree space Genetics, 170:419-431, 2005. PDF
Connor Magill Reconciliation problems for duplication, loss and horizontal gene transfer RECOMB proceedings, 316-325, 2004. PDF
Jatin Narula The probability of topological concordance of gene trees and species trees Theoretical Population Biology, 61(2):225-247, 2002. PDF
Justin Park Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model PLoS Genetics, 3(2): e7, 2007. PDF
Masoud Rostami High-resolution species tree without concatenation PNAS, 104(14):5936-5945, 2007. (with supporting information) PDF
Troy Ruths Combining phylogenetic and hidden Markov models in biosequence analysis J. Comput. Biol., 11:413-428, 2004. PDF
Ching-Hua Shih Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J. Mol. Biol., 296(5): 1205-1214, 2000. PDF
Xuebei Yang LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA Genome Research, 13(4): 721-731, 2003. PDF
Sagnak Tasirlar PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny PLoS Computational Biology, 1(7): e67, 2005. PDF
Abhinav Tiwari Genome rearrangements in Mammalian evolution: Lessons from human and mouse genomes Genome Research, 13(1): 37-45, 2003. PDF
Natalie Yudin Mauve: multiple alignment of conserved genomic sequences with arrangements Genome Research, 14(7):1394-1403, 2004. PDF

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