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
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
| 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 | |
Last modified: Thursday, 28-Jun-2018 05:11:15 EDT