GCB/CIS 535: Introduction to Bioinformatics. (Spring 2013). Course Directors:
Stephen Master, MD, PhD. Department of Pathology and Laboratory Medicine.
GCB/CIS 535: Introduction to Bioinformatics (Spring 2013) Course Directors: Stephen Master, MD, PhD Department of Pathology and Laboratory Medicine 613A Stellar-Chance Labs 215-898-8198
[email protected] Benjamin F. Voight, PhD Department of Pharmacology Department of Genetics 10-126 Smilow Center for Translational Research (SCTR) 3400 Civic Center Blvd 215-746-8083
[email protected] TAs: Varun Aggarwala Yih-Chii Hwang
[email protected] [email protected]
Guest Lecturers: Logan Everett Shane Jensen Kim Sharp Li-San Wang Maja Bucan
[email protected] [email protected] [email protected] [email protected] [email protected]
Location/Time: MW 10-11 AM F 10-11 AM
Lecture Lab
Office Hours: Steve Ben Varun Yih-Chii
Wed 11-12p Tue 12-1 PM By appointment Wed 4-5 PM By appointment Mon 3-4 PM By appointment
11-146 SCTR 11-146 SCTR 613A Stellar-Chance Labs 10-146 SCTR 10-146 SCTR 10-120 SCTR 1406 Blockley
Course web site: Available through Blackboard (https://courseweb.library.upenn.edu/)
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. Equipment prerequisite: IMPORTANT To accommodate for an increasing demand for this class, we now require that all students bring a laptop to the lab session on Fridays. TAs will provide help with the material but you should be well versed with your own laptop and should be willing/capable to download and install free software off the internet. Grading: 3 HW (45%); Labs (15%); Project (30%); Class participation (10%) To be fair to all, late submission will be penalized: up to 2 days (10% off), up to 1 week (30% off) after 1 week (80% off). Reference Texts: As this is still a rapidly moving field, there is no textbook required for this course. We will rely on a combination of online material, lecture notes and powerpoint slides. Your best bet for any topic is often to see if there has been a recent tutorial published in a journal like PLOS Computational Biology. A link to these articles can be found at: http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v03. i02
In addition, the following books and online sources can serve as references: 1. Bioinformatics for Biologists, eds. Pavel Pevzner and Ron Shamir, Cambridge University Press, 2011. 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.
Date 9-‐Jan 14-‐Jan 16-‐Jan
Type Lecture Schedule
Lecturer
Lecture Intro/Databases Lecture Stats for Bioinformatics Lecture Sequence Alignment
HW1 Distributed HW1 Due, HW2 Distributed
21-‐Jan
MLK -‐ No Class
23-‐Jan 28-‐Jan 30-‐Jan 4-‐Feb 6-‐Feb 11-‐Feb 13-‐Feb
Lecture Next-‐Gen Sequencing Technologies and Principles of Design Lecture Sequence Alignment for Next-‐Gen Data Lecture Multiple Sequence Alignment Lecture Comparative Genomics Lecture Tree reconstruction Lecture Genomic Variation and its Discovery Lecture Analysis of Genetic Variation
Voight Wang Wang Bucan Wang Voight Voight
18-‐Feb
Lecture Gene Expression Analysis -‐ I
Master
20-‐Feb 25-‐Feb 27-‐Feb
Lecture Gene Expression Analysis -‐ II Lecture Functional Analysis Lecture Proteomics
Master Master Master
-‐
Due Dates
Master Jensen Voight
SPRING BREAK
11-‐Mar
Lecture Protein Domains and families
Master
13-‐Mar
Lecture Protein Structure Visualization
Sharp
18-‐Mar 20-‐Mar 25-‐Mar 27-‐Mar 1-‐Apr 3-‐Apr 8-‐Apr 10-‐Apr 15-‐Apr 17-‐Apr 19-‐Apr 22-‐Apr
Lecture Lecture Lecture Lecture Lecture Lecture Lecture Lecture Lecture Lecture Lab Lecture
Motif Discovery Detecting cis regulatory Modules Transcription Regulation Analysis
Everett Everett Everett
microRNA informatics Systems Biology -‐ I Systems Biology -‐ II Data Management for Informatics Student Presentations Student Presentations Student Presentations Student Presentations Student Presentations
Voight Master Master Master -‐ -‐ -‐ -‐ -‐
Date
Type
Lab Schedule
11-‐Jan 18-‐Jan 25-‐Jan 1-‐Feb 8-‐Feb 15-‐Feb 22-‐Feb
Lab Lab Lab Lab Lab Lab Lab
#1: Seeking biological information online #2: Introduction to R #3: Looking for functional SNPs #4: Alignment, BLAST, Finding homologs/orthologs #5: Building phylogenies from alignments #6: Tools for the analysis of Genetic Variation #7: Interpreting gene expression data, Introduction to Mev
1-‐Mar
Lab
Project Meeting
15-‐Mar
Lab
#8:Deducing protein structures
22-‐Mar
Lab
#9: Discovering novel motifs in promoters
5-‐Apr 12-‐Apr
Lab Lab
#10: microRNAs and their targets #11: Constructing regulatory networks
HW2 Due, HW3 Distributed
HW3 Due #11 Lab HW Due Project Due
Due Dates
-‐ #1 Lab HW Due #2 Lab HW Due #3 Lab HW Due #4 Lab HW Due #5 Lab HW Due #6 Lab HW Due #7 Lab HW Due, Prelim Project Proposal
-‐
#8 Lab HW Due, Project Approval #9 Lab HW Due #10 Lab HW Due
HW1 includes – Alignment, data bases, tree reconstruction HW2 includes – Gene expression, functional analysis, protein structure/proteomics HW3 includes – Motif discovery, microRNAs, networks
