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Algorithms in Bioinformatics


Fall 2014


Lectures

Time: Friday 10:00AM - 11:40AM
Location: 2-403 Dong Zhong Yuan

Lab

Time: Wednesday(Even week) 10:00AM - 11:40AM
Location: 4-302 Biology Building, The computer lab of the department of Bioinformatics and Biostatistics

Office Hour

Friday 12:30 to 1:30 PM
Location: Room 4-221-05 , School of Life Sciences and Biotechnology.

Syllabus

Week Date Teacher Topics Labs & Guides
1 Sept. 19 Chaochun Wei Introduction to the course Lecture PPTs:
2 Sept. 24,26 Chaochun Wei Introduction to the computing environment and run a search program Lecture PPTs:
3 Oct. 3 Chaochun Wei Cancelled due to National Day Holiday
4 Oct. 8, 10 Chaochun Wei Praobality theory for Biological Sequence analysis Lecture PPTs: Homework(Due on Oct 17th):
5 Oct. 17 Chaochun Wei Algorithm Complexity Analsysis Lecture PPTs:
6 Oct. 22, 24 Chaochun Wei Dynamic Programming Lecture PPTs: Homework(Due on Oct 31): Lecture PPTs:
7 Oct. 31 Chaochun Wei Sequence Alignment

This class will be in the computer lab (4-302)

8 Nov.5, 7 Chaochun Wei Hidden Markov Model Lecture PPTs: Lab Homework (Due on Nov. 21):
9 Nov.14 Chaochun Wei Hidden Markov Model
10 Nov.19,21 Chaochun Wei Multiple sequence alignment Lecture PPTs:

Note: The course on Nov. 21 will be canceled due to the annual sports game of SJTU.

11 Nov. 28 Chaochun Wei Motif Finding, Metagenomics sequencing classification Lecture PPTs: Homework (Due on Dec. 26, 2014):
16 January 4, 2015 Chaochun Wei Course review and homework review Lecture PPTs:

Office hour has been changed to Thursday afternoon, January 8, 2015.

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    References: "Unix and Perl Primer for Biologists" .


    * Some parts of this course is from Sean Eddy 's course ( "Introduction to Computational Molecular Biology", School of Medicine, Washington University in St. Louis. Its current course master is Prof. Michael Brent).

     

    ©2013 Chaochun Wei