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/

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.

  • 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



  • 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

  • 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.

  • 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