Cancelled Classes (tentative):
Note that some of these classes may be covered by Guest Lectures.
Topic of Modules 1 & 2
Biology, Genomics, Algorithms and Data Structures.
By the end of this module, the students will have familiarity with
basic concepts of biology in terms genomics, transcriptomics and
proteomics and how they are used in formulating combinatorial problems
leading to data science algorithms and their complexity. The students
will also have a historical perspectives.
[Reading 1] https://en.wikipedia.org/wiki/Algorithm;
https://en.wikipedia.org/wiki/Muhammad_ibn_Musa_al-Khwarizmi
[Reading 2] https://en.wikipedia.org/wiki/Genomics;
https://en.wikipedia.org/wiki/Human_Genome_Project
Topic of Module 3, 4, 5 & 6
Objective(s)
By the end of this module, the students will have familiarity with
basic concepts of Graph Theory and ability to devise new graph
algorithms for bioinformatics applications. Topic of interest: Graph
Representation, Trees, DeBruijn Graph, DFS and BFS, Shortest Paths,
Eulerian Paths, Hamiltonian Paths, Applications to Genomics
[Reading 1] Cormen et al. Chapters 23 and 25.
[Reading 2] https://en.wikipedia.org/wiki/Hamiltonian_path;
https://en.wikipedia.org/wiki/Eulerian_path
Topic of Module 7, 8 & 9.
Strings & Stringology.
By the end of this module, the students will have familiarity with
basic concepts of sequence analysis and will be able to devise new
string theoretic algorithms to manipulate data structures involving
strings over finite alphabets. Topics of interest: Suffix Trees and
Suffix Arrays, String Matching, Edit Distance, Alignment, BLAST, BLAT.
[Reading 1] Cormen et al. Chapter 34
[Reading 2] https://en.wikipedia.org/wiki/BLAST
Topic of Module 10, 11 & 12
Sorting and Searching
By the end of this module, the students will have familiarity with
basic concepts of representation of bioinformatics statistics and data
and will be able to devise algorithms to search, organize and analyze
data using efficient algorithms. Topics of interest: Order Statistics,
Sorting, Binary Search, Merge Sort, Heap Sort, Quick Sort, Selection
and Median.
[Reading 1] Cormen et al., Chapters 7, 8, 9, & 10.
[Reading 2] https://en.wikipedia.org/wiki/Sorting_algorithm;
https://en.wikipedia.org/wiki/Search_algorithm
Topic of Module 13
Computational Complexity Analysis
By the end of this module, the students will have familiarity with
basic concepts of complexity theory and will be able to understand,
devise and solve recurrence equations for expressing the time
complexity of an algorithm.
[Reading 1] Cormen et al. Chapters 2, 3 and 4.
[Reading 2] https://en.wikipedia.org/wiki/Recurrence_relation
Topic of Module 14
Future!