BGS Home » Current Students » Academics » Course Information » Fall 2007 Course List » GCB 535 Intro to Bioinformatics

GCB 535 Intro to Bioinformatics

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