BMI_633_F21

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