|Course title||Algorithms for Bioinformatics
|Course description||This course describes some algorithms commonly used in contemporary bioinformatics. After a brief introduction to basic molecular biology and genetics, four main topics will be covered with corresponding lists of algorithms:
1. Sequence alignment and assembly: dynamic programming for optimal sequence alignment, FASTA and BLAST for heuristic alignment of long sequences, tree-based methods for multiple sequence alignment, suffix-tree, suffix-array and Burrows-Wheeler Transform for short read alignment, and algorithms based on de Bruijn graphs for sequence assembly
2. Statistical modeling: forward, backward, Viterbi and Baum-Welch algorithms for hidden Markov models, Gibbs sampling for sequence motif discovery, and Bayesian classifiers, logistic regression and expectation-maximization for data classification and clustering
3. Phylogenetics: methods based on Jukes-Cantor and Kimura models for divergence time estimation, maximum parsimony, UPGMA, Neighbor-joining and maximum likelihood methods for phylogenetic tree reconstruction.
4. High-throughput data analysis: Hierarchical clustering and k-means for data clustering, and algorithms for selected problems such as signal peak calling, detection of gene fusion, haplotype phasing. Other topics such as RNA secondary structure prediction may also be covered depending on the available time.
1. 序列對準及組裝：為最佳化對準的動態規劃；為對準長序列的FASTA和BLAST；為多序列對準的樹狀方法；為短序列的後綴樹、後綴數組和Burrows-Wheeler變換；以及為序列組裝，基於de Bruijn圖形的算法
|Semester||1 or 2|
|Grade Descriptors||A/A-: EXCELLENT – exceptionally good performance and far exceeding expectation in all or most of the course learning outcomes; demonstration of superior understanding of the subject matter, the ability to analyze problems and apply extensive knowledge, and skillful use of concepts and materials to derive proper solutions.
B+/B/B-: GOOD – good performance in all course learning outcomes and exceeding expectation in some of them; demonstration of good understanding of the subject matter and the ability to use proper concepts and materials to solve most of the problems encountered.
C+/C/C-: FAIR – adequate performance and meeting expectation in all course learning outcomes; demonstration of adequate understanding of the subject matter and the ability to solve simple problems.
D+/D: MARGINAL – performance barely meets the expectation in the essential course learning outcomes; demonstration of partial understanding of the subject matter and the ability to solve simple problems.
F: FAILURE – performance does not meet the expectation in the essential course learning outcomes; demonstration of serious deficiencies and the need to retake the course.
|Learning outcomes||At the end of the course of studies, students will be able to
1. Explain the problems studied in both biological and computational terms.
2. Explain the details of the studied algorithms.
3. Apply the learned algorithms to solving both problems in bioinformatics and other domains.
4. Study new algorithms proposed for the same problems.
5. Understand contents of other classes in computational biology and bioinformatics.
(for reference only)
|Recommended Reading List||1. Wing-Kin Sung, Algorithms in Bioinformatics: A Practical Introduction, Chapman & Hall, 2009 (and corresponding online materials at http://www.comp.nus.edu.sg/~ksung/algo_in_bioinfo/)
2. Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT Press, 2004
|CSCIN programme learning outcomes||Course mapping|
|Upon completion of their studies, students will be able to:|
|1. identify, formulate, and solve computer science problems (K/S);||TP|
|2. design, implement, test, and evaluate a computer system, component, or algorithm to meet desired needs (K/S);
|3. receive the broad education necessary to understand the impact of computer science solutions in a global and societal context (K/V);||TP|
|4. communicate effectively (S/V);
|5. succeed in research or industry related to computer science (K/S/V);
|6. have solid knowledge in computer science and engineering, including programming and languages, algorithms, theory, databases, etc. (K/S);||TP|
|7. integrate well into and contribute to the local society and the global community related to computer science (K/S/V);|
|8. practise high standard of professional ethics (V);|
|9. draw on and integrate knowledge from many related areas (K/S/V);
|Remarks: K = Knowledge outcomes; S = Skills outcomes; V = Values and attitude outcomes; T = Teach; P = Practice; M = Measured|