Course Materials for Bioinformatics I
Fall 2005


  • What is Bioinformatics I?
  • Basic Definitions
  • Website associated with the textbook
  • Introduction to elements of biology -- cells, molecules, genes, functional genomics, microarrays
  • 2004 NAR Database Issue
  • 2004 NAR Web Server Issue
  • 2005 NAR Database Issue
  • 2005 NAR Web Server Issue
  • chimp genome paper
  • study guide for the exam
  • the "non-tree" part of the Fall 2005 exam

    Examples of class projects from 2004:

  • Protein modularity and evolution
  • Analysis of large deletions in human-chimp genomic alignments
  • Profile hidden Markov models
  • Comparison of drosophila genomes

    Class notes and readings:

  • The UCSC Browser.
  • Papers about the UCSC website: Genome Browser, Gene Sorter, Proteome Browser, Table Browser, and a tutorial on using sequence conservation to search for functional noncoding elements.
  • Papers on GenBank, NCBI and blast. NCBI Website
  • Notes about PipMaker; more notes about PipMaker; PipMaker publication; MultiPipMaker publication.
  • Amit Vaish's Powerpoint slides on BDNF and CREB
  • Start of a bioinformatic anaylsis of BDNF regulation
  • Notes for lecture on Ch. 2 (Jones/Pevzner)
  • Some concepts from chapters 4 and 5
  • Notes about the dynamic-programming algorithm for aligning two sequences.
  • Notes about alignments scores and Psi Blast.
  • Blast outline and paper on Gapped Blast and PSI Blast.
  • probabilistic sequence models
  • Hidden Markov Models
  • Genscan paper


  • assignment #1


  • Some additional readings.
  • Dr. Richtsmeier's Powerpoint slides
  • Dr. Azmy's Powerpoint slides
  • Heather Lawson's Powerpoint slides

    Class projects:

  • SVM: non-coding neutral Sequences Vs regulatory Modules

    You might find it amusing to read the story of how I got involved in bioinformatics.