Instructor: Dr. Jin Chen

Institute for Biomedical Informatics

BMI 633 Course Syllabus

Date	Title	Lecturer	Memo
Jan 25	What is bioinformatics?	Jin Chen	Term project announcement
Jan 27	Essentials of molecular biology	JC Jeong	Guest lecture
Feb 1	Sequence alignment 1: string matching, global alignment	Jin Chen
Feb 3	Sequence alignment 2: local alignment, BLAST	Jin Chen
Feb 8	NGS 1: DNA-seq analysis pipeline	JC Jeong	Guest lecture
Feb 10	NGS 2: Burrows-Wheeler transform; BWA	Jin Chen	Coursework 1 announcement
Feb 15	Metagenomics, DIAMOND; R tutorial Part 1	Jin Chen
Feb 17	Genome-wide association study; R tutorial Part 2	Jin Chen	Coursework 1 due
Feb 22	Genome-wide association study; PLINK lab-type application; R tutorial Part 3	Jin Chen
Feb 24	Genomics applications; R tutorial Part 4	Jin Chen
Mar 1	Essentials of molecular biology (RNA)	Jin Chen
Mar 3	Differential expression analysis 1: RSEM	Jin Chen	Coursework 2 announcement
Mar 8	Differential expression analysis 2: Deseq2	Jin Chen
Mar 10	Differential expression analysis 3: Galaxy	Jin Chen	Coursework 2 due
Mar 15	Gene set enrichment analysis; GSEA	JC Jeong	Guest lecture
Mar 17	Test prep review	Jin Chen
Mar 22	Mid-term exam		Mid-term exam
Mar 24	Differential expression analysis 4: non-coding RNA; miRDeep	Jin Chen	Term project explained
Mar 29	Single-cell RNAseq 1: cell type detection; Seurat	Jin Chen
Mar 31	Production NGS for clinical diagnostics	Cody Bumgardner	Coursework 3 announcement, Guest lecture
Apr 5	Single-cell RNAseq 2: cell trajectory; Monocle	Jin Chen
Apr 7	Translational bioinformatics and precision medicine	TBD	Coursework 3 due; Guest lecture
Apr 12	Single-cell RNAseq 3: reduce dimension and cell alignment	Jin Chen
Apr 14	Systems biology & Epigenetics	Jin Chen
Apr 19	Cancer genomics infrastructure	Eric Durbin	Guest lecture
Apr 21	Biological networks	Jin Chen	Coursework 4 announcement
Apr 26	Phenomics & exposome	Jin Chen
Apr 28	Cancer Genomics	Chi Wang	Guest lecture; Coursework 4 due on Nov 19
May 3	Radiogenomics	Jin Chen
May 5	Final project presentation		Write-up, presentation, and demonstration

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