Biostatistics & Medical Informatics 776
Computer Sciences 776
Advanced Bioinformatics (Spring 2017)

General Course Information
Course Overview
Announcements
Syllabus, Readings, Lecture Notes
Schedule
Homework and Project
Past Semesters
DNA

Syllabus, Readings and Lecture Notes

Course Overview
  • lecture notes
    • Course Overview (PDF, PPTX) (1/17)

Motif and cis-Regulatory Module (CRM) Modeling
Genotype Analysis
  • topics: haplotype inference, genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, multiple hypothesis testing
  • required reading
  • optional reading
  • lecture notes
    • Linking Genetic Variation to Important Phenotypes (PDF, PPTX) (2/9, 2/14)
    • GWAS and multiple testing correction (PDF, PPTX) (2/14, 2/16, 2/21)

Epigenomics
RNA-Seq and Mass Spectrometry
Biological Network Analysis
Gene Finding
Large-Scale and Whole-Genome Sequence Alignment
RNA Structure Analysis
  • topics: predicting RNA secondary structure, Nussinov/energy-minimization algorithms, stochastic context free grammars
  • required reading
    • Chapter 9 in Durbin et al.
    • Sections 10.1, 10.2 in Durbin et al.
  • optional reading
  • lecture notes
    • RNA Secondary Structure Prediction (PDF, PPTX) (4/25, 4/27)
    • Stochastic Context Free Grammars for RNA Structure Modeling (PDF, PPTX) (4/27, 5/2)

Protein Structure Prediction
Lecture Notes

Thank you to Professors Mark Craven and Colin Dewey for providing lecture material. These slides, excluding third-party material, are licensed under CC BY-NC 4.0 by Mark Craven, Colin Dewey, and Anthony Gitter.