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University of California, Davis

MCB 182: Introduction to Genomics

University of California, Davis via YouTube

Syllabus

MCB 182 Lecture 1.1 - Review - Genome content.
MCB 182 Lecture 1.2 - Review - Gene structure.
MCB 182 Lecture 1.3 - Review - Transcriptional regulation.
MCB 182 Lecture 1.4 - Review - Repetitive sequences.
MCB 182 Lecture 2.1 - DNA sequencing overview.
MCB 182 Lecture 2.2 - Sanger sequencing.
MCB 182 Lecture 2.3 - Shotgun sequencing.
MCB 182 Lecture 2.4 - Illumina SBS sequencing.
MCB 182 Lecture 2.5 - PacBio, Nanopore sequencing.
MCB 182 Lecture 3.1 - Genome assembly - Overview.
MCB 182 Lecture 3.2 - Genome assembly - overlap graphs.
MCB 182 Lecture 3.3 - Genome assembly - Overlap-layout-consensus assembly.
MCB 182 Lecture 3.4 - Genome assembly - Scaffolding contigs.
MCB 182 Lecture 4.1 - Forward genetics.
MCB 182 Lecture 4.2 - Reverse genetics (siRNA, antisense oligos).
MCB 182 Lecture 4.3 - Gene editing (non CRISPR-Cas9).
MCB 182 Lecture 4.4 - CRISPR-Cas9 overview.
MCB 182 Lecture 4.5 - CRISPR-Cas9 practical considerations, applications.
MCB 182 Lecture 5.1 - CRISPR-Cas9 genome-wide screens.
MCB 182 Lecture 5.2 - Gene ontology structure.
MCB 182 Lecture 5.3 - Gene ontology annotations.
MCB 182 Lecture 5.4 - Gene ontology enrichment analysis.
MCB 182 Lecture 6.1 - Introduction to sequence alignments.
MCB 182 Lecture 6.2 - Scoring of sequence alignments.
MCB 182 Lecture 6.3 - Dotplots for sequence similarity visualization.
MCB 182 Lecture 7.1 - Overview of TF-DNA interaction assays, EMSA.
MCB 182 Lecture 7.2 - ChIP-seq.
MCB 182 Lecture 7.3 - SELEX, Protein Binding Microarrays (PBM), introduction to entropy.
MCB 182 Lecture 7.4 - Absolute entropy of DNA sequences.
MCB 182 Lecture 7.5 - Relative entropy.
MCB 182 Lecture 7.6 - Position weight matrices, sequence logos.
MCB 182 Lecture 7.7 - PWM applications in scanning the genome for TF binding, other applications.
MCB 182 Lecture 8.1 - Introduction to Epigenomics.
MCB 182 Lecture 8.2 - Histone modifications, ChIP-seq, CUT&RUN.
MCB 182 Lecture 8.3 - DNA methylation.
MCB 182 Lecture 8.4 - Chromatin accessibility (ATAC-seq).
MCB 182 Lecture 8.5 - Chromatin states.
MCB 182 Lecture 8.6 - Massively parallel reporter assays (MPRA).
MCB 182 Lecture 8.7 - ChIP-seq QC metrics.
MCB 182 Lecture 8.8 - ChIP-seq peak calling, multiple hypothesis testing.
MCB 182 Lecture 8.9 - Narrow vs broad peaks, IDR.
MCB 182 Lecture 9.1 - Introduction to RNA-seq, motivation.
MCB 182 Lecture 9.2 - Bulk RNA-seq fundamentals.
MCB 182 Lecture 9.3 - RNA-seq read mapping strategies.
MCB 182 Lecture 9.4 - RNA-seq quantification.
MCB 182 Lecture 9.5 - RNA-seq differential gene expression, batch effects.
MCB 182 Lecture 9.6 - ncRNA (miRNA, lncRNA, eRNA).
MCB 182 Lecture 9.7 - Introduction to single cell RNA sequencing (scRNA-seq).
MCB 182 Lecture 9.8 - Analysis goals of scRNA-seq.
MCB 182 Lecture 9.9 - scRNA-seq technologies.
MCB 182 Lecture 9.10 - scRNA-seq experimental design, dropout noise.
MCB 182 Lecture 9.11 - More on scRNA-seq dropout noise.
MCB 182 Lecture 9.12 - Introduction to PCA (scRNA-seq).
MCB 182 Lecture 9.13 - scRNA-seq applications (trajectory inference, visualization).
MCB 182 Lecture 10.1 - Overview of the physical organization of the genome.
MCB 182 Lecture 10.2 - DamID for mapping protein-DNA interactions.
MCB 182 Lecture 10.3 - Chromatin conformation capture (3C, 4C) assays.
MCB 182 Lecture 10.4 - Chromatin conformation capture (Hi-C) assays.
MCB 182 Lecture 10.5 - Visualization of Hi-C data, bias in the Hi-C assay.
MCB 182 Lecture 10.6 - Topologically associated domains (TADs), A/B compartments.
MCB 182 Lecture 10.7 - Chromatin looping, loop extrusion model.
MCB 182 Lecture 10.8 - Choosing 3C assay, genome assembly with Hi-C.
MCB 182 Lecture 11.1 - Introduction to molecular interaction networks.
MCB 182 Lecture 11.2 - Protein-protein interaction (PPI) networks.
MCB 182 Lecture 11.3 - Genetic interaction (GI) networks.
MCB 182 Lecture 11.4 - Regulatory interaction networks.
MCB 182 Lecture 11.5 - Co-expression networks.
MCB 182 Lecture 11.6 - Centrality measures of node importance in a gene network.
MCB 182 Lecture 11.7 - Network structural motifs and scale-free property.
MCB 182 Lecture 11.8 - Modularity of gene networks, guilt by association principles.
MCB 182 Lecture 12.1 - Introduction to human genetic variation.
MCB 182 Lecture 12.2 - Mendelian versus complex trait genetics.
MCB 182 Lecture 12.3 - GWAS for binary phenotypes.
MCB 182 Lecture 12.4 - Q-Q plots, types of genetic architectures of complex traits.
MCB 182 Lecture 12.5 - GWAS for continuous phenotypes, effect size versus statistical significance.
MCB 182 Lecture 12.6 - Confounding factors in GWAS.
MCB 182 Lecture 12.7 - More on detecting, visualizing + correcting for population structure in GWAS.
MCB 182 Lecture 12.8 - PCA for analysis of population structure in GWAS, multiple hypothesis testing.
MCB 182 Lecture 12.9 - Fine-mapping causal variants based on GWAS associations.
MCB 182 Lecture 12.10 - Epistasis, missing heritability in GWAS.

Taught by

Gerald Quon

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