1. Overview

Module Guide - HIA309 - Bioinformatics

Module Briefing

2. Reference

3. Assessment

1. Big Data, Genes, and Medicine

lecture Slides: Big Data, Genes, and Medicine

What Is a Genome and Why Do We Care? (3:29 minutes)

What Was the First Human Genome Looks Like? (12:32 minutes)

What Lessons did we Learn from the Human Genome Project? (7:31 minutes)

How Can We Use Genomes to Understand the Healthy Body and Fight Diseases? (4:39 minutes)

What is the value of Precision Medicine? (4:52 minutes)

What are the Ethical Issues Related to Genomic and Precision Medicine? (6:41 minutes)

How Does DNA Sequencing Work? (9:26 minutes)

What is Bioinformatics? (10:41 minutes)

2. Genes and Data

Lecture Slides: Genes and Data

The Central Dogma (1:48 minutes)

What Is DNA? (5:16 minutes)

What Do Proteins Do, and How? (5:10 minutes)

Genome Nuts and Bolts (5:10)

Genetic Variation and Mutation (5:10 minutes)

Gene Expression Regulation (9:49 minutes)

Epigenetic Control of Gene Expression (6:08 minutes)

Post-Translational Modifications of Proteins (12:03 minutes)

Cell Signaling and Signal Transductions (5:23 minutes)

3. Bioinformatics Database and Software Resources

lecture 3 Bioinfo database and software resources

Biological Databases (5:24 minutes)

Challenges to the Design of Biological Databases (7:46 minutes)

NCBI Gene Database (8:11 minutes)

RCSB Protein Data Bank (5:50 minutes)

Celebrating 50 Years of the Protein Data Bank Archive (by RCSBProteinDataBank) (7:27 minutes)

The Cancer Genome Atlas (TCGA) (9:31 minutes)

NCI Cancer Research Data Commons (2:19 minutes)

A Data Sharing Platform to Promote Precision Oncology (2:49 minutes)

Genomic Data Commons GDC Data Portal (9:42 minutes)

4. Bioinformatics Platforms and Resources

lecture 4 Bioinfo platform and resources

Next Generation Sequencing (NGS) (14:59 minutes)

Long-Read Sequencing (7:53 minutes)

DNA sequencing library preparation (7:22 minutes)

RNA sequencing library preparation (7:19 minutes)

Sample cleanups (3:58 minutes)

Purifying DNA Samples with Magnetic Beads (7:34 minutes)

Sample quantification and QC (6:28 minutes)

Checking Nucleic Acids with an Agilent BioAnalyzer (20:52 minutes)

Single Cell Sequencing (24:24 minutes)

Understanding Gene Coverage and Read Depth (6:05 minutes)

De novo Genome Sequencing (4:48 minutes)

Whole Genome Sequencing (WGS) (7:22 minutes)

5. Finding Mutations and Variations in DNA

lecture 5 Finding mutation and variation in DNA

Read Mapping (10:08 minutes)

Burrows-Wheeler Transform (3:52 minutes)

Using Burrows-Wheeler for Pattern Matching (5:05 minutes)

Inexact Matching (3:55 minutes)

Modeling Biological Sequences using Hidden Markov Models (7:59 minutes)

6. Practical 1: NGS raw data analysis

Practical Report 1

Submission of Practical Report 1 (Deadline: 6 April 2024, 11.59pm MYT)

Introduction to Galaxy (5:21 minutes)

Explanation - Introduction to sequencing data

Hands-on session 1: A short introduction to Galaxy

Hands-on Session 1 - A short introduction to Galaxy

Hands-on Session 2: Mapping

Hands-on Session 2 - Mapping

Hands-on session 3: Quality Control

Hands-on Session 3 - Quality Control

Hands-on session 4: Genome Assembly

Hands-on Session 4 - An Introduction to Genome Assembly

Exome sequencing data analysis for diagnosing a genetic disease

7. Functional Prediction of Genetic Variants

Lecture Slides

Overview of Functional Prediction of Genetic Variants (9:08 minutes)

Inherited vs Acquired Mutationss (1:16 minutes)

Genetic Variant Databases (5:01 minutes)

SIFT (Sort Intolerant From Tolerant) (5:14 minutes)

PolyPhen-2 (Polymorphism Phenotyping) (4:54 minutes)

PROVEAN (Protein Variation Effect Analyzer) (4:19 minutes)

RNA-Seq Mapping & Assembling (7:28 minutes)