Bioinformatics II. Advanced Genome Informatics.
BCB/GDCB/STAT/COM S 568 Spring 2010
Time & Location: Tu, Th 9:30a - 10:50a (Units: 3); 1424 MBB
Instructors: Volker Brendel (2112 MBB; Tel.: 294-9884) Karin Dorman (534 Science Hall II; Tel.: 294-6078) Xun Gu (536 Science Hall II; Tel.: 294-8075)
Teaching Assistant: Xiaoyong Sun (BCB and Dept. Statistics)
Teaching Philosophy:
emphasizes integration of research and textbook learning
and interdisciplinary study.
Email: VB, vbrendel@iastate.edu;
KD, kdorman@iastate.edu;
XG, xgu@iastate.edu;
XS, sunx1@iastate.edu
WWW:
http://brendelgroup.org/
Office Hours:
Tu, Th 11-11:30, MBB 2nd floor interaction area (XS, VB) and by appointment.
Grades: will be determined as described below.
Schedule:
http://brendelgroup.org/teaching/bcb568Spring2010.php
Computing Resources:
You may need access to UNIX or LINUX based computers for your project assignments.
Synopsis
Precipitated by an enormous increase in molecular sequence data (both DNA and protein), computational tools have become essential to molecular biology and genome research. Expertise in computational biology/bioinformatics is in great demand, and some level of proficiency in the subject is expected of anyone engaged in biological research at the molecular level. This course seeks to provide a general introduction to the subject as well as a discussion of several current research topics, with emphasis on statistical concepts and approaches. In this respect, this course is complementary to other courses offered at ISU that emphasize algorithmic issues and solutions, in particular the prerequisite BCB 567 course. Lectures will cover the biological motivation of various problems and the theoretical foundations of modeling solutions. Homework assignments will include exercises and programming tasks for practical applications. Topics to be covered include: statistical sequence models, Markov models, Hidden Markov models, score-based sequence analysis, gene structure prediction and other tasks of genome annotation, basic methods in molecular phylogeny, computational approaches to comparative and functional genomics, introduction to gene expression analysis.
The goal of the class is to prepare students to critically read and contribute to the relevant research literature.
Prerequisites
This interdisciplinary course is primarily directed at graduate and advanced undergraduate students in biology, computer science, statistics, or related disciplines who aspire to a professional career in this field. Familiarity with basic concepts and knowledge in molecular biology and statistics as well as programming experience (Perl, C, or C++) are assumed. Prerequisite courses are BCB 567, BBMB 301, Biol 315, Stat 430, and credit or enrollment in Gen 411.
Please address any special needs or special accommodations with the instructor at the beginning of the semester or as soon as you become aware of your needs. Those seeking accommodations based on disabilities should obtain a Student Academic Accommodation Request (SAAR) from the Disability Resources (DR) office (515-294-6624). DR is located in Room 1076 of the Student Services Building.
Assignments
Homework assignments will be posted regularly to deepen understanding of the lecture material. Written answers will be due two weeks after the assignment is posted (unless specified otherwise).
Grading
Grading will be based on two in-class midterm examinations (weighted 30% each) and the final written examination (40% weight). The examination questions will review material covered in class up to the examination date.
Selected journals
Students will be expected to read current research literature in the field. The following list provides a selected relevant journals that are electronically accessible from ISU accounts. For more choices, see e-Journals @ ISU.