Additional instructors: Prof. Rahul Simha (Computer Science), Prof. Robert Donaldson (Biology).
- Dr. Wilke: by appointment (send email: mtmtxw@gwumc.edu).
- Prof. Simha: Tue 1.30-3.30pm.
-
CS 177: Mondays, 3.30 - 6.10 pm, Tompkins 405
CRN: TBA
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.
Supplementary (optional) textbooks:
- D.W.Mount. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Lab Press.
- C.Gibas and P.Gambeck. Developing Bioinformatics Computer Skills. O'Reilly.
- Lecture 1 (Jan 6): Introduction
(Slides in PDF format)
- Motivating problem: manufacture of the Polio virus
- Description of problem, and synthesis of virus
- Informal "information perspective" of problem: string searching
- History: Traditional biology vs. new information-based biology
- What is bioinformatics? Narrow (genomics) definition and broad definition.
- Example using GenBank.
- The future: bioinformatics careers.
- Course goals.
- Lecture 2 (Jan 27): Cell Biology Overview
(Powerpoint slides)
- Organisms, organs, tissues, cells.
- Cell components.
- Eukaryotic vs. Prokaryotic cells.
- Overview of disease, immune system.
- Biomolecules
- Proteins
- Lecture 3 (Jan 27): DNA/RNA Overview
(PDF slides)
- DNA and its components.
- DNA replication, transcription, translation, protein synthesis.
- DNA cloning technology: PCR, sequencing.
- Inheritance, mutation, recombination.
- Lecture 4 (Feb 3): Nucleotide and protein databases
(PDF slides)
- Public sequence databases.
- Sequence retrieval and examples.
- Gene identification.
- Genetic and physical map.
- Protein databases.
- Data exchange and management.
- Lecture 5 (Feb 10): Hands-on lab with databases
(PDF slides)
- Motivating problem: a paper from the literature.
- Bio Background for CS students (to understand the paper).
- Dissecting their approach: using GenBank.
- Lab exercises in using GenBank
- Lecture 6 (Feb 24): The Alignment problem
(
Two-sequence alignment - HTML)
(Multiple alignment - PDF slides)
- Pairwise alignment problem.
- Dynamic programming algorithm (from CS151 notes).
- Multiple alignment.
- Editing and formatting alignments.
- Examples of using alignments: a paper from the literature.
- Lecture 7 (Mar 3): The New Biology Lab
- Old technology overview: microscopy, etc
- PCR
- Gels
- Sequencers
- Microarrays
- Crystallography
- Mass-spec
- Lecture 8 (Mar 10): Proteins, part I: Structure-Function Relationships
(Powerpoint slides - first part)
(Powerpoint slides - second part)
- Review of protein structure and function.
- Review of experimental techniques to determine structure
- Mitochondrial DNA and the coalescent.
- RNA structure.
- Protein structure.
- Motifs.
- Lecture 9 (Mar 24) Proteins, part II:
(Powerpoint slides)
- The protein folding problem.
- How folding energy is computed.
- Implications of folding.
- Misfolded proteins.
- Lecture 10 (Mar 31): Phylogenetics I
(Powerpoint slides)
- The study of genetics.
- Evolution: overview
- Taxonomy and phylogenetics.
- Cladistic vs Phenetic analyses.
- Models of sequence evolution.
- Lecture 11 (Apr 7): Phylogenetic II
(Powerpoint slides)
- Phylogenetic trees.
- Phylogenetic networks.
- Cladistic methods.
- Computer software and demos.
- Lecture 12 (Apr 21): field trip
- Additional topics, time-permitting (Apr 28):
- Supplemental material: