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BT504 : Genomics and Proteomics

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Course Info

Course Category

Biotechnology

Course Level

Undergraduate

Credit Hours

3

Pre-requisites

N/A

Instructor

Dr. Jamil Ahmed, Dr. Muhammad Nauman Aftab, Dr. Waseem Hiader
PhD, Post docs
Miscellaneous

Course Contents

Study of Omics     
Genomics, Proteomics and metabolomics     
Structure of RNA     
DNA Transcription     
Protein Translation     
Introduction to genomics     
Anatomy and organization of genome     
Gene anatomy     
Prokaryotic gene and eukaryotic gene     
Prokaryotic and Eukaryotic Expression difference     
Gene families and Gene clusters     
Types of Proteins and families     
Genome Informatics     
Prokaryotic Genome     
Eukaryotic Genomes     
Epichromosomal elements (EEs)     
Genome repeats     
Transposable Elements (TEs)     
Eukaryotic Gene Structure     
Comparative Genomics     
Functional Genomics     
Structural genomics     
Comparative genomics     
Population Genomics     
Metagenomics     
Why sequence genomes     
Genome characterization-technique used     
Genome analysis steps     
Benefits of Genomes research     
Genes and Sizes of Genomes     
Viral Genomes     
Bacterial genomes     
Yeast genome     
Mitochondrial genome     
Genomes Comparison     
Comparing distantly and closely related species     
Genome mapping     
Genetic mapping of the Genomes     
Physical mapping of the genome     
Cytogenic mapping     
FISH mapping     
Restriction mapping of the genoome     
Radiation hybrid mapping of the genome     
Clone contig mapping of the genome     
Generating Sequence of the genomes     
Human Genome Project     
Human Genome Project- Hierarchical Short Gun sequencing approach     
Human Genome Project- Whole Genome Short Gun sequencing approach     
Characteristics of our Genome part 1     
Characteristics of our Genome part 2     
Genome Browsers UCSC     
Genome Browsers ENSEMBLE     
HGP ethical and legal issues     
Genome annotations Protein coding genes     
genome annotations : transcription factors     
Arabidopsis Genome     
Mouse genome     
Comparison between mouse and human genome     
Mapping of disease genes     
Microarrays     
Types of microarray     
Microarray Formats     
Microarray-Procedure     
Microarray-chips     
Microarray – Applications     
Types of RNA and RNomics     
Non coding DNA     
Non coding RNAs     
miRNA     
Biogenesis of miRNA     
Functions of miRNA     
Mode of action miRNA     
Non coding RNA and X chromosome Silencing     
RNA Induced Silencing Complex     
siRNA     
Dicer and Drosha     
Design of siRNA     
Applications of siRNA     
Transcriptome     
Sequencing Techniques     
Automated Sequencing     
Shot Gun Sequencing     
Next Generation sequencing (NGS)  
NGS Platforms     
454 Pyrosequencing     
Illumina Sequencing     
Ion Semiconductor sequencing     
3rd Generation Sequencing     
Helicose Sequencing     
Pacbio Sequencing     
Oxford Nanopore Sequencing     
Comparison of NGS methods
Defining Genes     
Finding Genes     
Gene Prediction     
Genes predictions in prokaryotes     
Gene Predictions in Eukaryotes     
GO functional Analysis     
Gene Networks     
ORF Prediction     
ORF Finders     
TSS Prediction     
Prediction of Splice Junctions     
Prediction of Exons    
Genome Assembly     
Genome Assembly Overview     
Genome Assembly Planning     
Effect of Repeats     
Related species Assembled     
Greedy Graph Algorithm     
ALLPATHS-LG     
Lander Waterman Curve     
Assembly Pipeline1     
Assembly Pipeline2     
Quality of Assembled Genome     
Graphs     
Overlap Layout Consensus     
De Bruijn Graph     
De Bruijn Graph Example     
Assembly Issues    
Introduction to Proteomics     
Comparative Proteomics     
Between proteome comparison     
Proteomics Types and Techniques     
Characteristics of Human Proteome     
Why is Proteomics important     
Applications of Proteomics     
Chemical composition of proteins     
Primary structure of proteins     
Secondary structure of proteins     
alpha Helix     
ß- Pleated Sheets     
Tertiary Structure of Proteins     
Quaternary Structure of Proteins     
Life and Death of a Protein     
Proteins as Modular Structures     
Functional Protein Families     
Overview of Analytical Proteomics     
Extracting Proteins from Biological Samples     
Protein Separations Before Digestion     
One-Dimensional SDS-PAGE     
Two-Dimensional SDS-PAGE     
Problems of 2D SDS-PAGE     
Isoelectric Focusing     
High-Performance Liquid Chromatography     
Protein Separations After Digestion     
Tandem LC Approaches for Peptide Analysis     
Capillary Electrophoresis (CE)