Course Description: The course provides a broad overview of bioinformatics and computational biology as applied to biomedical research. Course material will be geared towards answering specific biological questions ranging from detailed analysis of a single gene through whole-genome analysis, transcriptional profiling, and systems biology. The relevant principles underlying these methods will be addressed at a level appropriate for biologists without a background in computational sciences. This course should enable students to integrate modern bioinformatics tools into their research program.
Should I take the course?
This course will emphasize hands-on experience with application to current biological research problems. However, it is not intended for computer science students who want to learn about biologically motivated algorithmic problems; GCB/CIS/BIO536 would be more appropriate for such individuals. The course will assume a solid knowledge of modern biology. An advanced undergraduate course such as BIO421 or a graduate course in Biology such as BIOL526 (Experimental Principles in Cell and Molecular Biology), BIOL527 (Advanced Molecular Biology and Genetics), BIOL528 (Advanced Molecular Genetics), BIOL540 (Genetic Systems), or equivalent, is a prerequisite.
M,W, F: 2:00 – 3:00 pm
M, W class is held in 212 Moore Bldg
F class is held in 202 Anat-Chem Bldg
Lecturers
Primary
Sridhar Hannenhalli sridharh@pcbi.upenn.edu (215 746 8683)
Steve Master srmaster@mail.med.upenn.edu (215 898 8198)
Guest
Maja Bucan bucan@pobox.upenn.edu
Shane Jensen stjensen@wharton.upenn.edu
Carlo Maley cmaley@wistar.org
Harold Riethman riethamn@wistar.org
Li-San Wang lswang@mail.med.upenn.edu
Grading
4 HW (40%)
2 exams (30%)
Term project (20%)
Class participation (10%)
Reference Texts
There is no text book required for this course. We will rely on a combination of online material, lecture notes and powerpoint slides. The following books will serve as references.
1. Bioinformatics: Sequence and Genome Analysis by David W. Mount
This covers algorithms and methods commonly used in bioinformatics.
2. Bioinformatics and Functional Genomics by Jonathan Pevsner (www.bioinfbook.org/)
This compiles material used for a course at Johns Hopkins.
3. Bioinformatics for Dummies by Jean-Michel Claverie, Cedric Notredame
This is a hands-on reference for bioinformatics analysis without any description of methods.
TAs
Logan Everett loganje@mail.med.upenn.edu
Zhi Wei zhiwei@mail.med.upenn.edu
Schedule:
Lecture Schdule |
||
Date |
Topic |
Lecturer |
10-Sep |
Introduction to the Course |
Master |
12-Sep |
Overview of Biological databases |
Master |
17-Sep |
Pairwise Alignment-I |
Hannenhalli |
19-Sep |
Pairwise Alignment-II (BLAST) |
Hannenhalli |
24-Sep |
Genomic variations, SNPs, HAPMAP |
Riethman |
26-Sep |
Tree reconstruction |
Wang |
1-Oct |
Tree reconstruction |
Wang |
3-Oct |
Case Study #1:Bioinformatics in the study of Barrett's esophagus neoplastic progression |
Maley |
8-Oct |
Multiple Alignment |
Hannenhalli |
10-Oct |
RNA world (microRNA, structure) |
Master |
15-Oct |
Protein world (domains, families) |
Master |
17-Oct |
Transcription regulation analysis |
Hannenhalli |
24-Oct |
MIDTERM |
|
29-Oct |
Motifs Discovery |
Hannenhalli |
31-Oct |
Detecting Cis Regulatory Modules |
Hannenhalli |
5-Nov |
Comparative Genomics VISTA, rVISTA |
Hannenhalli |
7-Nov |
Gene finding |
Hannenhalli |
12-Nov |
Gene Expression Analysis-I |
Master |
14-Nov |
Gene Expression Analysis-II |
Master |
19-Nov |
Statistics for Bioinformatics |
Jensen |
21-Nov |
Proteomics |
Master |
26-Nov |
Functional Analysis |
Master |
28-Nov |
Biological Networks-I |
Master |
3-Dec |
Case Study #2: Computational analysis of pre-synaptic genes |
Bucan |
5-Dec |
Biological Networks-II |
Master |
12-Dec |
FINAL EXAM |
|
LAB Schedule |
||
Topic |
TA |
|
14-Sep |
Seeking biological information online |
Everett |
21-Sep |
Finding candidate homologs/orthologs |
Everett |
28-Sep |
Looking for functional SNPs |
Wei |
5-Oct |
Building phylogenies from alignments |
Everett |
12-Oct |
Guessing RNA secondary structures |
Wei |
19-Oct |
Review |
Everett |
26-Oct |
Project Meeting |
Everett/Wei |
2-Nov |
Discovering novel motifs in promoters |
Everett |
9-Nov |
Finding genes in conserved regions |
Wei |
16-Nov |
Interpreting gene expression data |
Wei |
30-Nov |
Constructing regulatory networks |
Everett |
7-Dec |
Review |
Wei |