CSCI 5931 -- Computational Bioinformatics

Updated January 17, 2009

Office and Addresses

Delta 171 Phone 281.283.3805
email: boetticher@cl.uh.edu
Secretary: Ms. Kim Edwards, Delta 161 281.283.3860

Class Hours

Monday 4:00 - 7:00, Delta 237.

Office Hours

Mon. 7 - 8, Tues. 5:30 - 7, Wed. 5:30 - 7, or by appointment. If the suite door is locked, then call my extension (last 4 digits) using the phone in the hallway.

Why Bioinformatics?

Consulting Resources Corporation expects the total worldwide employment numbers to increase to 750,000 by year 2011 (400,000 of those employed in biotech companies). Major worldwide recruiting firms are also certain of this kind of growth, but no one is willing to go on record about the specific areas of technology from which these jobs will be generated.

The biotechnology industry continues to break new ground, creating products and future jobs that will come from bursts of new technology development. To tens of thousands of worldwide biotech employees, it remains a fascinating and yet challenging industry for a career.

Teaching Assistant

TBD, email: TBD
Office Hours: TBD

Course Description

Molecular data analysis Systems biology Analysis of heterogenous information sources Human Computer Interaction in Information Mining Computational proteomics Integrative data analysis Statistical data analysis Data mining Molecular simulation Biological networks / Metabolism Molecular informatics Data pipelining Data visualization Large scale chemical computation Data integration/semantics Grid/web services Computer architectures in life sciences. The traditional graduate student load is 3 courses. Be prepared to commit 15 to 20 hours per week to this course!

Course Goals

The primary goal of this course is to write a paper that is published in a peer-reviewed journal, conference, or workshop. A secondary goal is to provide the student with the necessary knowledge and skills to be very competitive in the Bioinformatics marketplace.

Prerequisites

The prerequisites for this course is the Data Mining Course (CSCI5833). If you do not meet the prerequisites, then you need to drop this course!  

Methodology

Highly interactive.

Appraisal:

Grading:

    93+ = A; 90 = A-; 87+ = B+; 83+ = B; 80+ = B-;

      77+ = C+; 73+ = C; 70 = C-; 67+ = D+; 63+ = D; 60+ = D-; 0+= F

My motto:

Seek the Truth.

Show altruistic love.

Appreciate beauty.

Required Textbook  

NONE

Journals, Conferences, Workshops, and Organizations

• Bioinformatics 2006

• BIOKDD 2005

• European Conference on Computational Bioinformatics

• IEEE Bioinformatics and Bioengineering

• IEEE Symposium on Comp. Intelligence in Bioinformatics and Computational Biology

• IEEE Computational Systems Bioinformatics

• International Society for Computational Biology

• Pacific Symposium on Biocomputing

• Workshop on Algorithms in Bioinformatics (WABI)

Data Bases

• Nucleic Acid Databases

• NCBI (National Center For Biotechnology Information) - GenBank

• EBI (European Bioinformatics Institute) - EMBL

• DISC - DNA Information and Stock Center, Japan

• Protein Databases

• NCBI - GenPept

• ExPASy - SwissProt and TrEMBL

• EBI (European Bioinformatics Institute) SwissProt, TrEMBL, PIR

• DISC - DNA Information and Stock Center, Japan

Computational Bioinformatics Data Resources

• Bioinformatic Resources on the Web

• Duke Center for Bioinformatics & Computational Biology

• 2001 KDD Cup

• Kent Ridge Bio-medical Data Set Repository

• UPITT Cancer Gene Expression Data Set Link Database

• UCSC Genome Browser

Computational Bioinformatics Software

• Microarray Data Analysis Tools

Schedule

Jan 14 – Course Overview, Introduction to Bioinformatics

FOR NEXT WEEK (IF NOT SOONER)

·   Read: Lorentz CP, Wieben ED, Tefferi A, Whiteman DA, Dewald GW. Primer on Medical Genomics, Part I: History of Genetics and Sequencing of the Human Genome. Mayo Clin Proceedings 2002;77:773-782.

·   Read: Tefferi A, Wieben ED, Dewald GW, Whiteman DA, Bernard ME, Spelsberg TC. Primer on Medical Genomics, Part II: Background Principles and Methods in Molecular Genetics. Mayo Clin Proceedings 2002;77:785-808.

·   Read: Online notes from this semester’s CSCI5833 Course

·   Read: Description of the research paper

Jan 28 –  Data Mining Review (What was taught in CSCI5833)

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Tefferi A, Bolander ME, Ansell SM, Wieben ED, Spelsberg TC.  Primer on Medical Genomics, Part III: Microarray Experiments and Data Analysis. Mayo Clin Proceedings 2002;77:927-940.

·  Microarray tutorial links:

http://www.bio.davidson.edu/courses/genomics/chip/chip.html

http://www.affymetrix.com/corporate/outreach/lesson_plan/educator_resources.affx

Feb 04 –  Microarray Data Analysis

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Pardanani A, Wieben ED, Spelsberg TC, Tefferi A. Primer on Medical Genomics, Part IV: Expression Proteomics. Mayo Clin Proceedings 2002;77:1185-1196.

·   Read: W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao, Statistical Methods in Proteomics, Springer Handbook of Enginerring Statistics, 2005, Pp. 1-37.

Feb 11 – Expression Proteomics

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Elkin PL. Primer on Medical Genomics, Part V: Bioinformatics. Mayo Clin Proceedings 2003;78:57-64.

Feb 18 – Bioinformatics

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Ansell SM, Ackerman MJ, Black JL, Roberts LR, Tefferi A. Primer on Medical Genomics, Part VI: Genomics and Molecular Genetics in Clinical Practice. Mayo Clin Proceedings 2003;78:307-317.

Feb 25 – Genomics and Molecular Genetics in Clinical Practice

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Wieben ED.  Primer on Medical Genomics: Part VII: The Evolving Concept of the Gene. Mayo Clin Proceedings 2003;78:580-587.

Mar 03 – The Evolving Concept of the Gene

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Shaughnessy J Jr. Primer on Medical Genomics, Part IX: Scientific and Clinical Applications of DNA Microarrays — Multiple Myeloma as a Disease Model. Mayo Clin Proceedings 2003;78:1098-1109.

Mar 10 –  Scientific & Clinical Applications of DNA Microarrays

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Russell SJ, Peng K-W. Primer on Medical Genomics, Part X: Gene Therapy. Mayo Clin Proceedings 2003;78:1370-1383.

Mar 17 – No class - Spring Break

* Last day to drop a class/withdraw for the semester is Mar 24^th *

Mar 24 –  Gene Therapy

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Goetz MP, Ames MM, Weinshilboum RM. Primer on Medical Genomics, Part XII: Pharmacogenomics — General Principles with Cancer as a Model. Mayo Clin Proceedings 2004;79:376-384.

Mar 31 –  Pharmacogenomics - Gen. Principles with Cancer as a Model

FOR NEXT WEEK (IF NOT SOONER)

·  Read: Morel NM, Holland JM, van der Greef J, et al. Primer on Medical Genomics, Part XIV: Introduction to Systems Biology — A  New Approach to Understanding Disease and Treatment. Mayo Clin Proceedings 2004;79:651-658.

·   Read: Tefferi A, Thomas C., Spelberg TC.  Primer on Medical Genomics: The End of the Beginning, Mayo Clin Proceedings, 2004; 79:659-660.

Apr 07 –  Introduction to Systems Biology, BioGrids  

FOR NEXT WEEK (IF NOT SOONER)

Apr 14 – Paper Presentations

FOR NEXT WEEK (IF NOT SOONER)  

Apr 21 – Review for final

FOR NEXT WEEK (IF NOT SOONER)  

Apr 28 – Final Exam