BILD 94 – Spring 2011 – Building EBU3B - Room 1202 – Gaasterland & Bafna
BILD 94 – Issues in Bioinformatics
Professors:
*
Terry Gaasterland
tgaasterland@ucsd.edu
phone: x2-4600
office: NSB 6117
Vineet Bafna
vbafna@ucsd.edu
phone: x2-4978
office: CSB 4218
Grading:
66% participation; 33% weekly short essay questions.
Schedule:
Ten scheduled class dates: March 30, April 6, 13, 20, 27, May 4, 11, 18, 25. June 1.
Guest Lectures
March 30: *
Terry Gaasterland (UCSD SIO & Biology)
Intro to Personal Genomics
April 6:
Karl Willert (UCSD School of Medicine, CMM)
Stem Cell Protein Systems
Vineet Bafna (UCSD Computer Science)
Genomes & Proteomes
April 20:
Milton Saier (UCSD, Biology)
Microbial Genomics & Phylogeny
April 27:
Andrew McCulloch (UCSD, Bioengineering)
Multiscale Modeling of the Heart
May 4:
Lucila Ohno-Machado (UCSD School of Medicine)
Biomedical Informatics
May 11:
Scott Markel (Accelrys)
Industry
May 18:
James Posakony (UCSD, Biology)
Pattern Formation and Cell Fate
May 25:
Gene Yeo (UCSD School of Medicine, CMM)
Modeling and Predicting Spliceforms
June 1:
Ruben Abagyan (UCSD Skaggs, Pharmaceutical Sci.)
Modeling Proteins in 3D
April 13:
*
Weekly Short Essay Questions
Each week, you will receive a list of questions about next week’s speaker. Use the internet to research
answers to the questions. Write up your answers in short essay form and send as a text, doc, docx, or pdf file
to bild94ucsd@gmail.com by noon on the day of class – with your name and the class date in the file name as
follows: “LASTNAME-FIRSTNAME-DATE.doc”. If you can’t find an answer to one of the questions, say that as
your answer. You are welcome and encouraged to work in teams of two or three if you wish; copy all
contributors on the email and list them at the top of your file.
Short Essay Questions for April 13th ( due at noon to bild94ucsd@gmail.com )
1. What does mass-spectrometry measure?
2. Why is it harder to apply mass-spec to proteins than to small compounds?
3. What are “protein modifications”? Why are they useful to a cell?
4. What kinds of algorithms has Dr. Bafna developed in his career? Give two examples.
5. What is “mass-spec imaging”? What can it tell you about proteins in an organism that massspec used with liquid chromatography (LC-MS) cannot?
6. What is “tandem mass-spec” (MS-MS)? What can it measure that MS alone cannot?