Course Materials for Bioinformatics I
What is Bioinformatics I?
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:
Table Browser, and a
tutorial on using sequence conservation
to search for functional noncoding elements.
Notes about PipMaker; more
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
on Gapped Blast and PSI Blast.
probabilistic sequence models
Hidden Markov Models
Some additional readings.
Dr. Richtsmeier's Powerpoint slides
Dr. Azmy's Powerpoint slides
Heather Lawson's Powerpoint slides
SVM: non-coding neutral Sequences Vs regulatory Modules
You might find it amusing to read the
story of how I got involved in bioinformatics.