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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 genome, 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).