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Schedule and Course Topics Aug 28 - Oct 18, 2024   McClean Historical and Recent Concepts of Genes and Genomes: Chromosomal theories, Gene theories The "Omics" World of Science Genome Sequencing Statistics Cumulative History of Plant Genome Sequencing 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 Sanger Sequencing Videos Sanger Sequencing Technology Video Illumina Sequencing Videos Illumina: Introduction to Sequencing by Synthesis The Novoseq System: Shaping the Future of Genomics Illumina NovaSeq Patterened Flow Cell Illumina NovaSeq Step-by-Step Video Illumina: NovaSeqX Series: The limits of high-throughput sequencing redefined Illumina Sequencer Statistics Illumina Sequencing: Details from an Illumina Scientist NovaSeq X and NovaSeq X Plus Technical Information> Pacific Biosciences (PacBio) Sequencing Single Molecule Real Time Sequencing - Pacific Biosciences PacBio Sequel II System Promo Video Value of PacBio Sequencing; User Perspectives PacBio Sequencing: History and CCS vs. CLR Sequel II Modes PacBio Revio System Oxford Nanopore Sequencing An Introduction to Oxford Nanopore Sequencing 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 Assembly Using PacBio Sequence Data Genome Projects and Assembly Notes-Annotated: Relevant to Original Assemblies 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 Pan-genomics and Pangenomes 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 Bacterial Genomes Organelle Genomes Eukaryotic Genomes Annotated Class Session Recordings Wednesday, August 28, 2024 Friday, August 30, 2024 Wednesday, September 4, 2024 Friday, September 6, 2024 Monday, September 9, 2024 Wednesday, September 11, 2024 Friday, September 13, 2024 Monday, September 16, 2024 Wednesday, September 18, 2024 Friday, September 20, 2024 Monday, September 23, 2024 Friday, September 27, 2024 Monday, September 30, 2024 Wednesday, October 2, 2024 Friday, October 4, 2024 Monday, October 7, 2024 Friday, October 11, 2024 Monday, October 14, 2024 This Week in Genomics Poccast stories explore unusual and surprising applications of genomics (8-29-2024) Illumina and the State of the Genomics Market (9-4-24) Bear DNA study to measure impact of conservation actions on genetic diversity (9-9-24) NHGRI Director Eric Green outlines the four chapters of human genomics (9-16-24) Green et al - Strategic vision for improving human health at the Forefront of Human Genomics (9-16-24) Genomics reveals sled dogs’ Siberian lineage (9-23-24) The untold story of the Human Genome Project: How one man’s DNA became a pillar of genetics (9-30-24) Nobel Prize in Physiology or Medicine Is Awarded to Victor Ambros and Gary Ruvkun: Awarded for their discovery of microRNA (10-7-24) Small non-coding RNAs mini class review (10-7-24) Small non-coding RNA video (10-7-24) Sept 6, 2024 "Why I Am Taking This Course" essay due Oct 4, 2024 Sequencing paper review due Oct 16, 2024 Review for exam Oct 18, 2024 Exam 1 (available October 18, 8:00 AM; due at 4:00 PM) Oct 21 - Nov 22, 2024 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 22 - Dec 13, 2024 Meinhardt 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 12 2024 Class Project Due Nov 27 - 29, 2024 No Class (Thanksgiving Holiday) Dec 16, 2022 Exam 2 available December 16, 8:00 AM; due at 4:00 PM)