CS 177: Introduction to Bioinformatics
Course Homepage: Fall 2004
NOTE: CS 177 will be also be offered in Spring 2005.
Announcements:
- NOTE: For Fall 2004, registration priority will be given to
students in the MS Bioinformatics program. Typically, there are
about 15 students in the program. Following that, we will offer
registration on a first-come-first-served basis to other students.
- There will be an offering of CS 177 in Spring 2005, for which
undergraduates will have the higher registration priority.
- Please get Tompkins 405 accounts by filling out an
application in the TA room on the 4th floor of Tompkins.
Fall 2004 information:
- Instructors:
Drs. Anna Panchenko and Tom Madej, National Center for Biotechnology
Information (NCBI).
Emails: panch@ncbi.nlm.nih.gov, madej@ncbi.nlm.nih.gov
Co-instructor: Prof. Rahul Simha
- Office Hours: TBA
- Class Time/Place:
-
CS 177: Mondays, 3.30 - 6.10 pm, Tompkins 405
CRN: 84847
- Prerequisites:
Permission of instructor. To get permission, please show up
the first day of class.
- Course description:
This course will provide a broad introduction to the area of
bioinformatics.
Topics include: biochemistry overview, databases, the alignment
problem, proteins and protein structure-function,
introductory phylogenetics, and use of public databases.
- Textbook:
David W. Mount (2001). Bioinformatics, sequence
and genome analysis. Cold Spring Lab. Press.
Supplementary (optional) textbooks:
- A. M. Campbell and L.J. Heyer (2002). Discovering
genomics, proteomics and bioinformatics. Pearson Education.
- P.E. Bourne and H. Weissig (2003). Structural
bioinformatics. Wiley & Sons.
- C.Gibas and P.Gambeck. Developing Bioinformatics Computer Skills.
O'Reilly.
- Molecular Biology Made Simple and Fun. D.P.Clark and L.D.Russell.
- Lecture schedule:
- Lecture 1 (Sep 13): Introduction (Tom Madej)
(Powerpoint slides)
- Motivating problem (protein sequence example).
- History: traditional biology vs. new information-based biology.
- Bioinformatics: a new approach to deal with the complexity of biological data.
- Motivating problem (protein structure example).
- Course overview, grading, etc.
- Molecular basis of cellular processes.
- Lecture 2 (Sep 20): General principles of DNA/RNA structure and
stability (Anna Panchenko)
(Powerpoint slides)
(HW2 - Word format)
(Fasta seq for HW2)
- Physico-chemical properties of nucleic acids.
- RNA-folding and structure prediction.
- Gene identification.
- Genome analysis.
- Lecture 3 (Sep 27): General principles of protein structure and
stability (AP)
(Powerpoint slides)
(HW3 - Word format)
- Physico-chemical properties of proteins.
- Prediction of protein secondary structure.
- Protein domains and prediction of domain boundaries.
- Protein structure-function relationships.
- Lecture 4 (Oct 4):
The sequence alignment algorithms (TM).
(Powerpoint slides)
(HW4 - Word format)
- The alignment problem.
- Pairwise sequence alignment algorithms.
- Multiple sequence alignment algorithms.
- Sequence profiles and profile alignment methods
- Alignment statistics.
- Lecture 5 (Oct 11):
(Powerpoint slides)
(HW - Word format)
Computational aspects of protein structure, part I (AP).
- Protein folding problem.
- Problem of protein structure prediction.
- Homology modeling.
- Protein design.
- Prediction of functionally important sites.
- Lecture 6 (Oct 18):
Computational aspects of protein structure, part II (TM).
(Powerpoint slides)
(HW - Word format)
(HW - PDB file)
- Structure-structure alignment algorithms.
- Significance of structure-structure similarity.
- Protein structure classification.
- Lecture 7 (Oct 25): Bioinformatics databases (TM)
(Powerpoint slides)
(HW - Word format)
(HW - EST file)
(EST file for class example)
- Sequence and sequence alignment formats, data exchange.
- Public sequence databases.
- Sequence retrieval and examples.
- Public protein structure databases.
- Lab exercises.
- Lecture 8 (Nov 1): Bioinformatics database search tools (TM).
(Powerpoint slides)
(HW - Word format)
- Sequence database search tools.
- Structure database search tools.
- Assessment of results, ROC analysis.
- Lab exercises.
- Lecture 9 (Nov 8): Phylogenetic analysis, part I (AP)
- Molecular basis of evolution.
- Taxonomy and phylogenetics.
- Phylogenetic trees and phylogenetic inference.
- Software tools for phylogenetic analysis.
- Lecture 10 (Nov 15): Phylogenetic analysis, part II (AP)
(Powerpoint slides)
(HW - Word format)
(Paper - PDF format)
- Accuracies and statistical tests of phylogenetic trees.
- Genome comparisons.
- Protein structure evolution.
- Lecture 11 (Nov 22):
Experimental techniques for macromolecular analysis (TM)
(Powerpoint slides)
- Sequencing, PCR.
- Microarrays.
- Protein crystallography.
- Mass-spectroscopy.
- RNA interference.
- Lecture 12 (Nov 29): Systems biology (AP)
(Powerpoint slides)
(HW - Word format)
- Genomic circuits.
- Modeling complex integrated circuits.
- Protein-protein interaction.
- Metabolic networks.
- Lecture 13 (Dec 6):
(Powerpoint slides)
- Lecture 14 (Dec 8): TBA
(Powerpoint slides)
- Supplemental material: