BMI 633 Introduction to Bioinformatics

Course Syllabus Fall 2021

Lecturers: Drs. Jin Chen and Jong Cheol Jeong

Guest lectures: Drs. Cody Bumgardner, Qiang Cheng, Jinpeng Liu, Kangmei Zhao (Stanford), Chi Wang, and Eric Durbin

Date: Aug 23 – Dec 8 2021

Time: M/W 1-2:30 PM

Location: MDS 211

Date	Title	Lecturer(s)	Memo
Aug 23	What is bioinformatics?	Jin Chen	Introduction class; all welcome
Aug 25	Essentials of molecular biology; R programming part 1 (tutorial)	Jong Cheol Jeong Jin Chen
Aug 30	Essentials of sequencing technology; R programming part 2 (tutorial)	Jong Cheol Jeong Jin Chen
Sep 1	Sequence alignment part 1: string matching, global alignment	Jin Chen
Sep 6	NO CLASS		Labor Day
Sep 8	Sequence alignment part 2: local alignment; BLAST (tutorial)	Jin Chen	Supercomputer account setup
Sep 13	DNA-seq analysis pipeline; Galaxy part 1 (tutorial)	Jong Cheol Jeong
Sep 15	Production NGS for clinical diagnostics	Cody Bumgardner (confirmed)	Guest lecture; Coursework 1 announcement
Sep 20	Burrows-Wheeler transform; R programming part 3 (tutorial)	Jin Chen
Sep 22	Genomics applications; R programming part 4 (tutorial)	Jin Chen	Coursework 1 due
Sep 27	Genome-wide association study; PLINK lab-type application (tutorial)	Jin Chen
Sep 29	Genomics applications; R programming part 5 (tutorial)	Jin Chen
Oct 4	RNAseq analysis pipeline; Galaxy part 2 (tutorial)	Jin Chen
Oct 6	Differential expression analysis 1: RSEM	Jin Chen	Coursework 2 announcement
Oct 11	Differential expression analysis 2: Deseq2	Jin Chen
Oct 13	Differential expression analysis 3: Beyond differential expression	Jin Chen	Term project announcement; Coursework 2 due
Oct 18	Gene set enrichment analysis; GSEA tutorial	Jong Cheol Jeong
Oct 20	Mid-term exam	Jin Chen	Close-book exam
Oct 25	NO CLASS		Fall break
Oct 27	Cancer radiogenomics	Qiang Cheng (confirmed)	Guest lecture
Nov 1	Differential expression analysis 4: non-coding RNA; miRDeep (tutorial)	Jin Chen
Nov 3	Single-cell RNAseq 1: cell type detection; Seurat (tutorial)	Jin Chen	Coursework 3 announcement
Nov 8	Gut metagenomics	Jinpeng Liu (confirmed)	Guest lecture
Nov 10	Single-cell RNAseq 2: cell trajectory; Monocle (tutorial)	Jin Chen	Coursework 3 due
Nov 15	Single-cell RNAseq 3: reduce dimension and cell alignment	Jin Chen
Nov 17	Systems biology & Epigenetics	Jin Chen
Nov 23	Phenomics & exposome	Jin Chen
Nov 25	NO CLASS		Thanksgiving
Nov 30	Biological networks	Kangmei Zhao@Stanford (confirmed)	Guest online lecture; Coursework 4 announcement
Dec 1	Cancer Genomics	Chi Wang (confirmed)	Guest lecture; Coursework 4 due
Dec 6	Cancer genomics infrastructure	Eric Durbin (confirmed)	Guest lecture
Dec 8	Final project presentation		Write-up, presentation

Optional topics:

Translational bioinformatics and precision medicine (Haiquan Li)
Network biology (Jin Chen)
Metagenomics: population change over time & pathway-level variation (Jinpeng Liu)
Metagenomics, DIAMOND

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