Teaching
EECS730: Introduction to Bioinformatics (Fall 2016)
Syllabus
08/23/2016: IntroductIon to the human genome project and medical genetics [slides]
Further readings: [IHGSC] [Celera]
Video: Cracking the code of life
08/25/2016: Molecular Biology Primer [slides]
08/30/2016: Algorithm Primer [notes]
09/01/2016: Sequence comparison with edit distance [slides]
09/05/2016: More on sequence alignment [slides]
09/08/2016: Indexed alignment [slides]
09/08/2016: Homework 1: Implementing sequence alignment algorithms (due 11:59PM Sep 30th) [HW1] [human_hemoglobin_alpha.fasta] [mouse_hemoglobin_alpha.fasta]
09/13/2016: KUMC visit, no class
09/15/2016: Indexed alignment and BLAST, cont.
09/20/2016: Multiple Sequence Alignments [slides]
09/22/2016: Hidden Markov Model and Profile HMM [slides]
09/27/2016: Viterbi algorithm and Forward-backward algorithm
09/29/2016: ab initio Gene Finding [slides]
10/04/2016: RNA secondary structure prediction [slides]
10/06/2016: Mid-term review, RNA secondary structure folding with Zuker-Sankoff energy model
10/11/2016: No class (Fall break)
10/13/2016: Mid-term exam (closed book, closed notes)
10/13/2016: Homework 2: Implementing Viterbi algorithm for profile HMM (due 11:59PM Nov 11th) [HW2] [AAA.hmm] [AAA_test.fasta]
10/18/2016: RNA secondary structure Alignment [slides]
10/20/2016: Structured RNA element discovery [slides]
10/24/2016: Final Exam (in-class presentation Dec. 1st, 6th, and 8th; final paper due 11:59PM Dec 16th) [Final paper]
10/25/2016: Structured RNA element discovery (cont.)
10/27/2016: Protein secondary structure prediction [slides]
11/01/2016: Protein threading [slides]
11/03/2016: Microarray data [slides]
11/08/2016: Microarray data (cont.)
11/10/2016: Gene clustering [slides]
11/15/2016: Gene clustering (cont.)
11/17/2016: Next-generation sequencing [slides]
11/22/2016: Next-generation sequencing cont.
11/28/2016: Next-generation sequencing cont.
12/01/2016: Final paper presentation
12/06/2016: Final paper presentation
12/08/2016: Final paper presentation