Biology (BIOL) 4230/7230, Spring 2017

Bioinformatics and Functional Genomics


Biol4230/Biol7230 - Tues/Thurs 9:30 – 10:45, Ruffner Hall Rm 173; Friday 9:00 – 9:50 Ruffner 173

Course director: William R. Pearson, Pinn (Jordan) Hall Rm 6-057, wrp@virginia.edu
Office hours, 1:00 - 3:00 PM Monday, or by appt.


Course Overview, Policies


Texts:

Bioinformatics and Functional Genomics (2nd ed) (2009) J. Pevzner, Wiley-Blackwell, ISBN:0470085851
Practical Computing for Biologists (2010) S. Haddock and C. Dunn, Sinauer, ISBN: 0878933913

Other texts


Th 1/19 Course Overview/Molecular Biology Review/Bioinformatics Overview Lecture PDF
Fr 1/20 Unix command line lab Lecture PDF

Tu 1/24 Protein structure, homology, and similarity searching Lecture PDF
Th 1/26 Unix II - shell scripting and Bioinformatics databases Lecture PDF
Fr 1/27 Similarity Searching Lab

Tu 1/31 Similarity Searching II Lecture PDF
Th 2/2 Programming in Python Lecture PDF
Fr 2/3 Similarity Searching Lab II

Tu 2/7 From protein domains to PSSMs/HMMs Lecture PDF
Th 2/9 Python II - Using dictionaries Lecture PDF
F 2/10 PSSMs and PSI-BLAST/Scripted Matrix comparison

Tu 2/14 Alignment Statistics II / HMMs Lecture PDF
Th 2/16 Web scripting, python and XML Lecture PDF
F 2/17 Lab -- searching with HMMs

Tu 2/21 Multiple Sequence Alignment I Lecture PDF
Th 2/23 Searching/statistics/alignment summary Lecture PDF
F 2/24 Review Session - (Exam due Monday)

Tu 2/28 Introduction to evolutionary tree reconstruction Lecture PDF
Th 3/2 Evolutionary tree reconstruction II Lecture PDF
F 3/3 Building evolutionary trees Lecture PDF

Tu 3/14 Evaluating evolutionary trees Lecture PDF
Th 3/16 Positive and Negative Selection Lecture PDF
F 3/17 Mid-term project -- protein evolutionary tree

Tu 3/21 The Human Genome Project Lecture PDF
Th 3/23 Differential Gene Expression I Lecture PDF
F 3/24 Lab - Genome Browsers, UCSC and IGV Lecture PDF

Tu 3/28 Expression Analysis II Lecture PDF
Th 3/30 Statistics with 'R' Lecture PDF
F 3/31 'R' workshop I

Tu 4/4 'R' with Bioconductor Lecture PDF
Th 4/6 Bioconductor/edgeR workshop
F 4/7 No class

Tu 4/11 Gene Ontology and Pathway Enrichment Lecture PDF
Th 4/13 BED Tools Lecture PDF
F 4/14 Lab - BEDTools

Tu 4/18 Regulatory Motifs I Lecture PDF
Th 4/20 Motif finding lab
F 4/21 No class

Tu 4/25 Motifs II - high throughput approaches Lecture PDF
Th 4/27 Clustering/Function prediction Lecture PDF
Fr 4/28 Exam review

Tu 5/2 Wrap-up/Final project Lecture PDF

Links to other Computational Biology Courses

wrp@virginia.edu

Last modified: Monday, 07-Nov-2016 11:52:01 EST