) &
Kevin Lin (ªL¬f§Ê;
)[TA's office hours: 3:00-5:00 PM, Tuesdays; Venue: R432]
Course: Introduction to Biomedical Informatics
Spring semester, 2014
9:10 - 12:10 Monday, 101 CSIE Building.
3 credits
Web site: http://www.csie.ntu.edu.tw/~kmchao/bioinformatics14spr
Instructor: Kun-Mao Chao (»¯©[Z)
Teaching assistant: Chia-Jung Chang (±i®aºa;
) &
Kevin Lin (ªL¬f§Ê;
)
[TA's office hours: 3:00-5:00 PM, Tuesdays; Venue: R432]
Prerequisites: Background in biology and informatics is welcome but not required for taking this course.
Classmates: I II III IV V VI VII
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Coursework:
Homework assignments and Class participation (10%)
Two midterm exams (70%; 35% each):
1. Midterm #1: March 31, 2014 partial_solutions; grading criteria; grade_statistics
2. Midterm #2: May 5, 2014 grade_statistics
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 Survey [2/17/2014]
Selected Videos [2/24/2014]
NCBI [2/24/2014]
Basic Algorithmic Strategies [3/3/2014]
-- Basic Algorithmic Strategies [3/3/2014]
Sequence Alignment [3/3/2014; 3/10/2014]
-- Global Alignment [3/3/2014; 3/10/2014]
-- Local Alignment [3/10/2014]
-- Various Scoring Schemes [3/10/2014]
-- An affine-gap-penalty example [3/10/2014]
-- Scoring scheme examples [3/10/2014]
-- 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¡V53.
-- Smith, Temple F.; and Waterman, Michael S. (1981). "Identification of Common Molecular Subsequences". Journal of Molecular Biology 147: 195¡V197.
-- 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. 14 "Local Alignment") [3/10/2014; 3/17/2014]
Suboptimal Alignments (Methods 1-5) [3/17/2014; 3/24/2014]
-- Space-Saving Strategies (pdf) [3/10/2014; 3/17/2014; 3/24/2014]
-- 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.
-- Chao, K.-M. and Miller, W., 1995, Linear-Space Algorithms that Build Local Alignments from Fragments, Algorithmica, 13: 106-134.
Multiple Sequence Alignment (Up to p. 13 "Affine Gaps") [3/24/2014]
-- Multiple Sequence Alignment (pdf) [3/24/2014]
-- Homology Search Tools (pdf) []
R: An Introduction; More Details (by Chia-Jung Chang) [4/7/2014]
Genome Reconstruction by Phillip E. C. Compeau and Pavel A. Pevzner [4/14/2014]
pdf (the first
one in the link),
ppt (the third
one in the link)
(For ppt, you
may skip pages 125-175 & 301-350.)
-- B(2,3) [4/14/2014]
-- Eulerian Tours by Christos H. Papadimitriou & Umesh Vazirani [4/14/2014]
(Exchange 10 and 01 of the left figure on Page 4)-- An example for fragment assembly as an Eulerian cycle problem [4/28/2014]
Pattern Identification in a Haplotype Block (ppt, pdf) [4/21/2014]
-- An example [4/28/2014]
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Haplotype Inference (ppt,
pdf) [4/21/2014]
(Read the problem formulation on pp. 1262-1263 of the pdf
file)
-- Some other ways of formulation [4/28/2014]
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HLA Simulation (by Chia-Jung Chang) [4/28/2014]
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Class presentations:
1. The expected number of team members: <8;
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.
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Selected papers for presentation:
(You may access these selected articles using computers with NTU IP addresses.)
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May 12, 2014
David Sankoff, "The
early introduction of dynamic programming into computational biology," Bioinformatics (2000) 16 (1): 41-47.
[Slides]
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BLAST [Slides]
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402.
BLAST@NCBI
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May 19, 2014
May 26, 2014
16. Innovative bioinformatic approaches
for developing peptide-based vaccines against hypervariable viruses
Danylo Sirskyj, Francisco Diaz-Mitoma,
Ashkan Golshani, Ashok Kumar and Ali Azizi
Immunology and Cell Biology (2011)
89, 81¡V89
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June 9, 2014
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