COMP 571 BIOINFORMATICS: SEQUENCE ANALYSIS
(More Appropriately:) An Introduction to Population Genetics and Phylogenetics
Fall 2010

Staff

Course Information

• MEETING PLACE AND TIME: Sewall Hall 303 (Sewall is building #65 on the map), Tuesday and Thursday, 2:30-3:50.
• TEXTBOOKS:
  • [UB] "Understanding Bioinformatics", by M. Zvelebil and J.O. Baum. Published by Garland Science, 2008.
  • [PG] "Population Genetics", by M.B. Hamilton. Published by Wiley-Blackwell, 2009.
• HIGHLY RECOMMENDED BOOKS:
  • 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 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:
  1. The Molecular Biology and Evolution toolbox. Click here for a paper that describes the tool.
  2. The Population Genetics and Evolution toolbox.
  3. The ms tool for generating samples under neutral models.
  4. For a comprehensive list of phylogeny programs, please see the website maintained by Prof. Joe Felsenstein here.
• INTENDED AUDIENCE: anyone who's interested in learing about exciting developments at the intersection of evolutionary biology and computing. Knowledge of biology, math, and computer science is a plus; yet, the course will be taught in a way that is equally accessible to students from any background as long as the student is interested in the material.
• TOPICS TO BE COVERED:
  1. [Chapters 1 and 3 in [UB]] Background basics.
  2. [Chapter 2 in [PG]] Genotype frequencies.
  • Mendel's model of particulate genetics, Hardy-Weinberg expected genotype frequencies, the fixation index and heterozygosity, mating among relatives, and gametic (aka linkage) disequilibrium.
  3. [Chapter 3 in [PG]] Genetic drift and effective population size.
  • The effects of sampling, models of genetic drift, effective population size, parallelism between drift and inbreeding, the coalescent model, and effective population size in the coalescent model.
  4. [Chapter 4 in [PG]] Population structure and gene flow.
  • Genetic populations, measure of gene flow, fixation indices, population subdivision and the Wahlund effect, models of population structure, and the coalescent with population structure.
  5. [Chapter 5 in [PG]] Mutation.
  • The source of all genetic variation, the fate of a new mutation, mutation models, the influence of mutation on allele frequency and autozygosity, and the coalescent with mutation.
  6. [Chapters 6 and 7 in [PG]] Natural selection.
  • Natural selection, natural selection on a diallelic locus, natural selection and fitness, viability selection with three alleles or two loci, alternative models of natural selection, combining natural selection with other processes, and the coalescent with natural selection.
  7. [Chapter 8 in [PG]] Molecular evolution.
  • The neutral theory, measures of divergence and polymorphism, DNA sequence divergence and the molecular clock, testing the molecular clock hypothesis, testing the neutral theory null model of DNA sequence evolution, and molecular evolution of loci that are not independent.
  8. [Chapters 4-6 in [UB]] Sequence alignment.
  • Scoring schemes and substitution matrices, dynamic programming algorithms for pairwise sequence alignment, Markov chains and hidden Markov models (HMMs), HMM-based alignment, profile HMMs for sequence families, and multiple sequence alignment.
  9. [Chapters 7-8 in [UB]] Phylogenetic trees.
  • The structure and interpretation of phylogenetic trees, molecular evolution and its consequences, models of evolution, phylogenetic tree reconstruction methods (UPGMA, neighbor joining, maximum parsimony, maximum likelihood, and Bayesian inference), and assessing the quality of inferred trees (bootstrap).
  10. [Additional reading material] Phylogenomics and population genomics.
  • The gene tree / species tree problem, incomplete lineage sorting, gene duplication and loss, horizontal gene transfer and reticulate evolution.
• GRADING:
  • The grades will be based on class participation (20%) and a set of 6-8 homework assignments (80%).
• STUDENTS WITH DISABILITY: Any student with a documented disability needing academic adjustments or accommodations is requested to speak with me during the first two weeks of class. All discussions will remain confidential. Students with disabilities will need to also contact Disability Support Services in the Ley Student Center.

Course Material