Course: Introduction to Biomedical Informatics
Spring semester, 2013
9:10 - 12:10 Monday, 101 CSIE Building.
3 credits
Web site: http://www.csie.ntu.edu.tw/~kmchao/bioinformatics13spr
Instructor: Kun-Mao Chao (趙坤茂)
Teaching assistant: Chia-Jung Chang (張家榮) & Wu-Lung R. Yang
(楊伍隆)
[TA's office hours: 11:00 - 12:00; 15:00 - 16:00 Tuesdays]
Prerequisites: Background in biology and informatics is welcome but not required for taking this course.
Classmates: I II III IV V VI VII
課程問卷：http://ppt.cc/NgFz
Coursework:
Homework assignments and Class participation (10%)
Two midterm exams (70%; 35% each):
1. Midterm #1: April 1, 2013 Scoreboard
2. Midterm #2: May 13, 2013 Scoreboard
Oral presentation of selected papers/projects (20%)
Topics:
Sequencing and genotyping technologies
Molecular sequence analysis
Recognition of genes and regulatory elements
Comparative genomics
Gene expression
Molecular structural biology
Biological networks
Systems biology
Computational proteomics
Molecular evolution
Phylogenetic trees
Population genetics
Medical informatics
Supporting materials:
A Whirlwind Tour of Biomedical Informatics [2/18/2013] Survey
Selected Videos [2/25/2013] (Lists in HTML format)
Sequence Alignment [3/4/2013; 3/11/2013]
-- Global Alignment [3/4/2013]
-- Local Alignment [3/4/2013]
-- Various Scoring Schemes [3/4/2013; 3/11/2013]
-- An affine-gap-penalty example [3/4/2013; 3/11/2013]
-- Scoring scheme examples [3/11/2013]
-- Needleman, Saul B.; and Wunsch, Christian D. (1970). "A general method applicable to the search for similarities in the amino acid sequence of two proteins". Journal of Molecular Biology 48 (3): 443–53.
-- Smith, Temple F.; and Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences". Journal of Molecular Biology 147: 195–197.
-- Gotoh, Osamu: An improved algorithm for matching biological sequences. In: Journal of Molecular Biology. 162, 1982, S. 705-708 (PDF, 206 KB).
Space-Saving Strategies (Up to p. 13 "Local Alignment"; more about local alignment) [3/11/2013; 3/18/2013]
Suboptimal Alignments (Methods 1-5) [3/18/2013]
-- Space-Saving Strategies (pdf) [3/11/2013]
-- Eugene Myers and Webb Miller, "Optimal Alignments in Linear Space," CABIOS (Bioinformatics) 9: 169-176, 1988.
-- Chao, K. -M., Pearson, W. R. and Miller, W., 1992, Aligning Two Sequences within a Specified Diagonal Band, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 8: 481-487.
-- Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Constrained Sequence Alignment, Bulletin of Mathematical Biology, 55: 503-524.
-- Chao, K.-M., Hardison, R. C. and Miller, W., 1993, Locating Well-Conserved Regions within a Pairwise Alignment, Computer Applications in the Biosciences (CABIOS, now Bioinformatics), 9: 387-396.
-- Chao, K. -M., 1994, Computing All Suboptimal Alignments in Linear Space, Combinatorial Pattern Matching '94, Lecture Notes in Computer Science 807, 31-42, California, USA.
-- Chao, K. -M., Hardison R. C. and Miller, W., 1994, Recent Developments in Linear-Space Alignment Methods: a Survey, Journal of Computational Biology, 1: 271-291.
Multiple Sequence Alignment (Up to p. 13 "Affine Gaps") [3/18/2013]
-- Multiple Sequence Alignment (pdf) [3/18/2013]
R (by Chia-Jung Chang) [3/25/2013]
Homology Search [4/8/2013; 4/15/2013]
-- Homology Search Tools (pdf) [4/8/2013; 4/15/2013]
Genome Reconstruction (pdf, ppt) by Phillip E. C. Compeau and Pavel A. Pevzner [4/22/2013]
(For ppt, you may skip pages 125-175 & 301-350.)
-- Eulerian Tours by Christos H. Papadimitriou & Umesh Vazirani [4/22/2013]
(Exchange 10 and 01 of the left figure on Page 4)
Pattern Identification in a Haplotype Block (ppt, pdf) [4/29/2013]
Haplotype Inference (ppt, pdf) [4/29/2013]
-- Some other ways of formulation [4/29/2013]
Q&A [5/6/2013]
Connectivity Map (by Roger Yang) [5/6/2013]
Class presentations:
1. The expected number of team members: ~6;
2. Each member is required to present in turn [about 150/(the number of speakers on the same day) minutes each];
3. Revised slides should be sent to me within one week after the presentation. Please compress your figures.
4. Questions in class are always welcome.
Selected papers for presentation:
(You may access these selected articles using computers with NTU IP addresses.)
May 20, 2013
May 27, 2013
June 3, 2013
(Ind.)
Common Cold,
Uncommon Variation
Slides
Gregory A. Poland and Michael A. Barry N Engl J Med 2009; 360:2245-224
楊謹榕
(Ind.)
Full-length transcriptome assembly from RNA-seq data without a reference
genome.
Slides
Manfred G. Grabherr et al. Nature Biotechnology 29, 644–652 (May 2011)
Han Lin
(Ind.)
Transgenics: A new breed
Daniel Cressey
2 MAY 2013 | VOL 497 | NATURE | 27
薛依宸
June 10, 2013
