CSI 5330, Advanced Computational Biology

Fall 2017


Class Hours and Classroon: MWF 11:15am - 12:05pm @ Cashion 315

Professor: Dr. Young-Rae Cho    (email: Young-Rae_Cho@baylor.edu)
       Office: Cashion 304
       Office Hours: Mon 2:30pm - 4:00pm

Course Web Page: web.ecs.baylor.edu/faculty/cho/5330/


Description
An advanced level course to discuss computational issues on analysing biological data. The focus of this course is on design, development, and analysis of algorithms with applications to bioinformatics.

Objectives
  • To make students understand the concepts and techniques on Computational Biology and Bioinformatics.
  • To develop computational skills of designing and developing algorithms to analyse biological data.
  • To gain experience of research to develop and evaluate computational methods in Bioinformatics.

Reference Books
  • Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, by Dan Gusfield, Cambridge
  • Algorithms in Bioinformatics: A Practical Introduction, by W.-K. Sung, CRC Press
  • Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, by R. Durbin, S. Eddy, A. Krogh, and G. Mitchison, Cambridge
  • An Introduction to Bioinformatics Algorithms, by Neil C. Jones and Pavel A. Pevzner, The MIT Press
  • Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis, by I. Eidhammer, I. Jonassen, and W. R. Taylor, Wiley
  • Bioinformatics and Functional Genomics, by Jonathan Pevsner, Wiley-Liss
  • Advanced Analysis of Gene Expression Microarray Data, by Aidong Zhang, World Scientific

Topics

Assignments

Projects
  • 2 projects
  • Design, development, implementation, and evaluation of algorithms for specific biological data
  • Use of any programming language
  • Requirement: (1) presentation of previous works, (2) submission of a report (a hard copy), and (3) presentation of your work
  • Graded by (1) method (novelty and technical quality), (2) experiments (evaluation design), (3) report quality, and (4) presentation

Reports
  • Research paper style (including all five sections of Introduction, Previous Methods, Proposed Method, Experimental Results, and Conclusion)
  • At least 6 pages on the one-column format
  • Submission by email attachment
  • Submission is due at 11:59pm on the specified date. Late submission is NOT accepted.

Grading
  • Assignments: 28%   (7% each)
  • Projects: 72%   (36% each)
  • Grading scale: A (93% ~), A- (90% ~), B+ (87% ~), B+ (83% ~), B- (80% ~), C+ (77% ~), C (73% ~), C- (70% ~), D+ (67% ~), D (63% ~), D- (60% ~), F (~ 60%)

Bioinformatics Conferences
  • ISMB: Intelligent Systems for Molecular Biology
  • RECOMB: Research in Computational Molecular Biology
  • ECCB: European Conference on Computational Biology
  • PSB: Pacific Symposium on Biocomputing
  • InCoB: International Conference on Bioinformatics
  • BCB: ACM International Conferences on Bioinformatics, Computational Biology and Biomedicine
  • BIBE: IEEE International Conference on Bioinformatics and Bioengineering
  • BIBM: IEEE International Conference on Bioinformatics and Biomedicine
  • ISBRA: International Symposium on Bioinformatics Research and Application
  • BIOSTEC: International Joint Conference on Biomedical Engineering Systems and Technologies
  • EMBC: International Conference of the IEEE Engineering in Medicine and Biology Society
  • CIBCB: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
  • ICIBM: International Conference on Intelligent Biology and Medicine
  • BHI: IEEE EMBS International Conference on Biomedical and Health Informatics
  • BIOKDD: International Workshop on Biological Knowledge Discovery and Data Mining (in conjunction with DEXA)
  • BIOKDD: International Workshop on Data Mining in Bioinformatics (in conjunction with KDD)

Bioinformatics Journals
  • Bioinformatics (Oxford journal)
  • PLoS Computational Biology
  • BMC Bioinformatics
  • BMC Systems Biology
  • Briefings in Bioinformatics
  • Algorithms for Molecular Biology
  • BioData Mining
  • International Journal of Data Mining and Bioinformatics