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Computer Science Course Information
|Course No.||CIS 786||Sections||115|
|Title||Computational Approach in BioInformatics & Related Area|
|Prerequisite(s)||Basic knowledge of data structures, algorithms, and heuristic search methodologies— a previous bioinformatics course is preferred but not required.|
|Instructor|| Usman Roshan
|Instructor Office Hours|
|Description||The lectures will cover computational approaches used in comparative bioinformatics with an emphasis on heuristic techniques. Some of the topics to be covered are phylogenetics, sequence alignment, microarray analysis, protein structure and function prediction and analysis, phylogeny-centric methods in comparative proteomics, and some statistical modelingsuch as hidden markov models. The required biology will be covered.
Course goals This course will expose you to various bioinformatics problems and how to solve them in practice using heuristics. You will learn various heuristic techniques (which can be applied to related areas as well), various software programs which implement these heuristics, and also learn how to analyze and interpret the results of these programs. The course project will give you further depth in a particular area of bioinformatics
09/07/05 Heuristic methods—complexity, local moves, local search
iterated local search, ant colony optimization, TSP, SAT
09/14/05 Phylogenetics—distance based methods, likelihood
parsimony, heuristic searches
09/21/05 Phylogenetics—large-scale phylogeny reconstruction
divide-and-conquer methods, parallel methods, supertree methods
09/28/05 Sequence alignment—pairwise, heuristic pairwise, FASTA, BLAST
10/05/05 Multiple sequence alignment—various heuristics
including progressive and iterative approaches
10/12/05 Phylogenetic motifs—methods, implications, real data analysis
10/19/05 Correlated mutation analysis
10/26/05 Student presentations
11/02/05 Student presentations
11/09/05 Student presentations
11/16/05 Student presentations
11/23/05 Student presentations
11/30/05 Student presentations
12/07/05 Student presentations
|Text Book(s)||The course will be based upon lecture notes and journal and conference publications.
The following textbooks may be used for reference:
_ Algorithms on strings, trees, and sequences: computer science and computational biology, Dan Gusfield
_ Introduction to computational molecular biology, Setubal and Medianis
_ Introduction to bioinformatics, Arthur Lesk
_ An Introduction to Bioinformatics Algorithms, Neil Jones and Pavel Pevzner
_ Biological sequence analysis: probabilistic models of proteins and nucleic acids, Durbin et. al.
_ Protein bioinformatics, Eidhammer et. al.
All the textbooks are available from the NJIT library and Amazon.
|Time & Place||Wednesday 6:00 PM - 9:05 PM, Info 4415|
|Other Info||Course grade This will be depend upon a course project and a paper presentation. The course project can be, (1) an experimental performance study where you apply existing software for solving a problem and then analyze and interpret the results, or (2) a programming project where you implement an algorithm or heuristic and report on its performance. Other projects which may not fall under this category can also be considered. After completion, the project must be described in a report complete with methodology, results, and conclusion. The presentation should describe a recent published conference or journal paper. The paper must be approved by the instructor before presentation
Cheating The NJIT Honor Code will be upheld and any violations will be brought to the immediate attention of the Dean of Students
Changes to syllabus Students will be consulted and must agree to any modifications or deviations from the syllabus throughout the course (major deviations are not expected).