Biology (BIOL) 4230/7230, Spring 2018

Bioinformatics and Functional Genomics


Biol4230/Biol7230 - Tues/Thurs 9:30 – 10:45, Ruffner Hall Rm 175; 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 1/18 Course Overview/Molecular Biology Review/Bioinformatics Overview Lecture PDF
Fr 1/19 Unix command line lab Lecture PDF

Tu 1/23 Protein structure, homology, and similarity searching Lecture PDF
Th 1/25 Unix II - shell scripting and Bioinformatics databases Lecture PDF
Fr 1/26 Similarity Searching Lab
Homework - similarity searching

Tu 1/30 Similarity Searching II Lecture PDF
Th 2/1 Programming in Python Lecture PDF
Fr 2/2 Similarity Searching Lab II
Homework - Intro to Python/Python searching

Tu 2/6 From protein domains to PSSMs/HMMs Lecture PDF
Th 2/8 Python II - Using dictionaries Lecture PDF
F 2/9 PSSMs and PSI-BLAST/Scripted Matrix comparison
Homework -- Properties of scoring matrices

Tu 2/13 Alignment Statistics II / HMMs Lecture PDF
Th 2/15 Web scripting, python and XML Lecture PDF
F 2/16 Lab -- searching with HMMs
Homework -- Accession conversion/XML Parsing

Tu 2/20 Multiple Sequence Alignment I Lecture PDF
Th 2/22 Searching/statistics/alignment summary Lecture PDF
F 2/23 Review Session - (Exam due Monday)

Tu 2/27 Introduction to evolutionary tree reconstruction Lecture PDF
Th 3/1 Evolutionary tree reconstruction II Lecture PDF
F 3/2 Building evolutionary trees Lecture PDF
Homework -- PHYLIP trees and consensus

Tu 3/13 Evaluating evolutionary trees Lecture PDF
Th 3/15 Positive and Negative Selection Lecture PDF
F 3/16 Mid-term project -- protein evolutionary tree

Tu 3/20 The Human Genome Project Lecture PDF
Th 3/22 BED Tools Lecture PDF
F 3/23 Lab - Genome Browsers, UCSC and IGV Lecture PDF

Tu 3/27 Differential Gene Expression I Lecture PDF
Th 3/39 Statistics with 'R' Lecture PDF
F 3/30 'R' workshop I

Tu 4/3 Expression Analysis II Lecture PDF
Th 4/5 'R' with Bioconductor Lecture PDF
F 4/6 Bioconductor/edgeR workshop

Tu 4/10 Gene Ontology I Lecture PDF
Th 4/12 Gene Ontology II - ORA and Pathway enrichment Lecture PDF
F 4/13 Lab - BEDTools

Tu 4/17 Regulatory Motifs I Lecture PDF
Th 4/19 Motifs II - high throughput approaches Lecture PDF
F 4/20 Motif finding from BED to MEME

Tu 4/24 Motifs II - high throughput approaches Lecture PDF
Th 4/26 Clustering/Function prediction Lecture PDF
Fr 4/27 Exam review

Tu 5/1 Wrap-up/Final project Lecture PDF

Links to other Computational Biology Courses

wrp@virginia.edu

Last modified: Monday, 19-Feb-2018 11:05:11 EST