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Schedule and Course Topics Aug 23 - Oct 13, 2023   McClean Historical and Recent Concepts of Genes and Genomes: Chromosomal theories, Gene theories The "Omics" World of Science Genome Sequencing Statistics History of Genetics and Genomics Historical Timeline of Genetics and Central Dogma of Molecular Genetics Historical Timeline of Genome Sequencing Related Discoveries Mendel, the Chromosomal Theory of Inheritance, and DNA as the Hereditary Material Mendel, the Chromosomal Theory of Inheritance, and DNA as the Hereditary Material-Annotated Whole Genome Sequencing: Sanger Sequencing; Next Generation Sequencing; DNA structure; Clone-based vs. shotgun sequencing; Assembly of genomes Sequencing the SARS-CoV-2 (COVID-19) Virus Sequencing the SARS-CoV-2 (COVID-19) Virus - Annotated Genomic Sequencing: Background and Technologies Genomic Coverage Explained Effect of Modern Sequencing Technology on Genome Completeness NovaSeq X and NovaSeq X Plus Technical Information Sanger Sequencing Videos Sanger Sequencing Technology Video Illumina Sequencing Videos Illumina Sequencing Technology Video Illumina NovaSeq Patterened Flow Cell Illumina NovaSeq Promo Video Illumina NovaSeq Step-by-Step Video Illumina NovaSeqX Series Video Illumina Sequencer Statistics Illumina Sequencing: Details from an Illumina Scientist Pacific Biosciences (PacBio) Sequencing PacBio Sequencing Video PacBio Sequel II System Promo Video PacBio Sequencing: History and CCS vs. CLR Sequel II Modes Oxford Nanopore Sequencing Oxford Nanopore Technology Sequencing Promo Video Oxford Nanopore Technology Sequencing Video Oxford Nanopore Technology: How Basecalling Works Ion Torrent Sequencing Ion Torrent Sequencing Notes Ion Torrent Sequencing Video Genome Projects and Assembly Genome Projects and Assembly Notes-Annotated Simple Assembly Explanation - de Bruijn Graphs DeBruijn Graph Concept Assembly Problems Genome Annotation: Gene number, Categories of functional genes, Distribution of sequence classes, SNP discovery Genome Annotation: Defining the Content of a Reference Genome Sequence-annotated Comparative Genomics: Common features of genomes, Genomic features specific to individual species, Genomic features shared by bacterial genomes, Genomic features shared by eukaryotic genomes, Variation among eukaryotic genomes, Genome evolution Viral Genomes Viral Genomes-Annotated Bacterial Genomes Organelle Genomes Eukaryotic Genomes Annotated Class Session Recordings Wednesday,August 23, 2023 Friday,August 25, 2023 Monday,August 28, 2023 Wednesday,August 30, 2023 Friday, September 1, 2023 Wednesday, September 6, 2023 Friday, September 8, 2023 Wednesday, September 13, 2023 Friday, September 15, 2023 Monday, September 18, 2023 Wednesday, September 20, 2023 Friday, September 22, 2023 Monday, September 25, 2023 Wednesday, September 27, 2023 Friday, September 29, 2023 Monday, October 2, 2023 Wednesday, October 4, 2023 Friday, October 6, 2023 Monday, October 9, 2023 Wednesday, October 9, 2023 This Week in Genomics Human X Chroosome Sequenced (8-28-23) Human BioBank Interviews (9-6-23) The Utility of the UAE Genome Program (9-13-23) The Einkorn Wheat Genome (9-18-23) Predicting Disease Causing Mutations (9-25-23) 1000 Genomes Sequenced (10-2-23) Sept 29, 2023 Sequencing paper review due Oct 11, 2023 Review for exam Oct 13, 2023 Exam 1 (available October 13, 8:00 AM; due at 5:00 PM) Oct 16 - Nov 17, 2023 Li Functional Genomics: Forward and reverse genetics, tools used, methods employed to identify the genes of interest Gene Expression: Large scale expression studies, RNA-seq and other methods; Expression study designs, Appropriate controls Lecture 2.1: Introduction to Functional Genomics Lecture 2.2: Induced Mutations Lecture 2.3: Gene-index Catalogue for Induced Mutants Lecture 3: Gene Silencing Lecture 4: Linkage Mapping and Map Based Cloning Nov 21 - Dec 9, 2022 To be determined Proteomes: Protein structure and functions, Protein isolation and characterization, Biochemical approaches to studying protein-protein interactions, Computational approaches to studying protein-protein interactions, Applications Lecture 1 - Introduction Lecture 1 - Notes Lecture 2- Gel Electrophoresis Lecture 2 - Notes Lecture 3 - Mass Spectrometry Lecture 3 - Notes Analysis Program Mass Spectrometry-based Proteomics Antibody Screening with Microarrays Personalized Cancer Management Prostate Signaling Microarray Protein DNA Interactions Microarray Protein Microarray Review Protein Microarray Technology Proteochips Fluorescence Resonance Energy Transfer Microscopy (Paper) Proteomics (Powerpoint presentation) Lecture 3 Notes Lecture 4 Protein Microarrays Notes Lecture 4 Protein Microarrays Lecture 5 Protein-Protein Interactions notes Lecture 5 Protein Protein Interactions Nov 17 2023 Class Project Due Nov 24, 2022 No Class (Thanksgiving Holiday) Dec 16, 2022 Exam 2 available December 16, 8:00 AM; due at 4:00 PM)