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Introduction to Genomics

Introduction to Genomics

Gerald Quon via YouTube Direct link

MCB 182 Lecture 11.5 - Co-expression networks

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MCB 182 Lecture 11.5 - Co-expression networks

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Classroom Contents

Introduction to Genomics

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  1. 1 MCB 182 Lecture 1.1 - Review - Genome content
  2. 2 MCB 182 Lecture 1.2 - Review - Gene structure
  3. 3 MCB 182 Lecture 1.3 - Review - Transcriptional regulation
  4. 4 MCB 182 Lecture 1.4 - Review - Repetitive sequences
  5. 5 MCB 182 Lecture 2.1 - DNA sequencing overview
  6. 6 MCB 182 Lecture 2.2 - Sanger sequencing
  7. 7 MCB 182 Lecture 2.3 - Shotgun sequencing
  8. 8 MCB 182 Lecture 2.4 - Illumina SBS sequencing
  9. 9 MCB 182 Lecture 2.5 - PacBio, Nanopore sequencing
  10. 10 MCB 182 Lecture 3.1 - Genome assembly - Overview
  11. 11 MCB 182 Lecture 3.2 - Genome assembly - overlap graphs
  12. 12 MCB 182 Lecture 3.3 - Genome assembly - Overlap-layout-consensus assembly
  13. 13 MCB 182 Lecture 3.4 - Genome assembly - Scaffolding contigs
  14. 14 MCB 182 Lecture 4.1 - Forward genetics
  15. 15 MCB 182 Lecture 4.2 - Reverse genetics (siRNA, antisense oligos)
  16. 16 MCB 182 Lecture 4.3 - Gene editing (non CRISPR-Cas9)
  17. 17 MCB 182 Lecture 4.4 - CRISPR-Cas9 overview
  18. 18 MCB 182 Lecture 4.5 - CRISPR-Cas9 practical considerations, applications
  19. 19 MCB 182 Lecture 5.1 - CRISPR-Cas9 genome-wide screens
  20. 20 MCB 182 Lecture 5.2 - Gene ontology structure
  21. 21 MCB 182 Lecture 5.3 - Gene ontology annotations
  22. 22 MCB 182 Lecture 5.4 - Gene ontology enrichment analysis
  23. 23 MCB 182 Lecture 6.1 - Introduction to sequence alignments
  24. 24 MCB 182 Lecture 6.2 - Scoring of sequence alignments
  25. 25 MCB 182 Lecture 6.3 - Dotplots for sequence similarity visualization
  26. 26 MCB 182 Lecture 7.1 - Overview of TF-DNA interaction assays, EMSA
  27. 27 MCB 182 Lecture 7.2 - ChIP-seq
  28. 28 MCB 182 Lecture 7.3 - SELEX, Protein Binding Microarrays (PBM), introduction to entropy
  29. 29 MCB 182 Lecture 7.4 - Absolute entropy of DNA sequences
  30. 30 MCB 182 Lecture 7.5 - Relative entropy
  31. 31 MCB 182 Lecture 7.6 - Position weight matrices, sequence logos
  32. 32 MCB 182 Lecture 7.7 - PWM applications in scanning the genome for TF binding, other applications
  33. 33 MCB 182 Lecture 8.1 - Introduction to Epigenomics
  34. 34 MCB 182 Lecture 8.2 - Histone modifications, ChIP-seq, CUT&RUN
  35. 35 MCB 182 Lecture 8.3 - DNA methylation
  36. 36 MCB 182 Lecture 8.4 - Chromatin accessibility (ATAC-seq)
  37. 37 MCB 182 Lecture 8.5 - Chromatin states
  38. 38 MCB 182 Lecture 8.6 - Massively parallel reporter assays (MPRA)
  39. 39 MCB 182 Lecture 8.7 - ChIP-seq QC metrics
  40. 40 MCB 182 Lecture 8.8 - ChIP-seq peak calling, multiple hypothesis testing
  41. 41 MCB 182 Lecture 8.9 - Narrow vs broad peaks, IDR
  42. 42 MCB 182 Lecture 9.1 - Introduction to RNA-seq, motivation
  43. 43 MCB 182 Lecture 9.2 - Bulk RNA-seq fundamentals
  44. 44 MCB 182 Lecture 9.3 - RNA-seq read mapping strategies
  45. 45 MCB 182 Lecture 9.4 - RNA-seq quantification
  46. 46 MCB 182 Lecture 9.5 - RNA-seq differential gene expression, batch effects
  47. 47 MCB 182 Lecture 9.6 - ncRNA (miRNA, lncRNA, eRNA)
  48. 48 MCB 182 Lecture 9.7 - Introduction to single cell RNA sequencing (scRNA-seq)
  49. 49 MCB 182 Lecture 9.8 - Analysis goals of scRNA-seq
  50. 50 MCB 182 Lecture 9.9 - scRNA-seq technologies
  51. 51 MCB 182 Lecture 9.10 - scRNA-seq experimental design, dropout noise
  52. 52 MCB 182 Lecture 9.11 - More on scRNA-seq dropout noise
  53. 53 MCB 182 Lecture 9.12 - Introduction to PCA (scRNA-seq)
  54. 54 MCB 182 Lecture 9.13 - scRNA-seq applications (trajectory inference, visualization)
  55. 55 MCB 182 Lecture 10.1 - Overview of the physical organization of the genome
  56. 56 MCB 182 Lecture 10.2 - DamID for mapping protein-DNA interactions
  57. 57 MCB 182 Lecture 10.3 - Chromatin conformation capture (3C, 4C) assays
  58. 58 MCB 182 Lecture 10.4 - Chromatin conformation capture (Hi-C) assays
  59. 59 MCB 182 Lecture 10.5 - Visualization of Hi-C data, bias in the Hi-C assay
  60. 60 MCB 182 Lecture 10.6 - Topologically associated domains (TADs), A/B compartments
  61. 61 MCB 182 Lecture 10.7 - Chromatin looping, loop extrusion model
  62. 62 MCB 182 Lecture 10.8 - Choosing 3C assay, genome assembly with Hi-C
  63. 63 MCB 182 Lecture 11.1 - Introduction to molecular interaction networks
  64. 64 MCB 182 Lecture 11.2 - Protein-protein interaction (PPI) networks
  65. 65 MCB 182 Lecture 11.3 - Genetic interaction (GI) networks
  66. 66 MCB 182 Lecture 11.4 - Regulatory interaction networks
  67. 67 MCB 182 Lecture 11.5 - Co-expression networks
  68. 68 MCB 182 Lecture 11.6 - Centrality measures of node importance in a gene network
  69. 69 MCB 182 Lecture 11.7 - Network structural motifs and scale-free property
  70. 70 MCB 182 Lecture 11.8 - Modularity of gene networks, guilt by association principles
  71. 71 MCB 182 Lecture 12.1 - Introduction to human genetic variation
  72. 72 MCB 182 Lecture 12.2 - Mendelian versus complex trait genetics
  73. 73 MCB 182 Lecture 12.3 - GWAS for binary phenotypes
  74. 74 MCB 182 Lecture 12.4 - Q-Q plots, types of genetic architectures of complex traits
  75. 75 MCB 182 Lecture 12.5 - GWAS for continuous phenotypes, effect size versus statistical significance
  76. 76 MCB 182 Lecture 12.6 - Confounding factors in GWAS
  77. 77 MCB 182 Lecture 12.7 - More on detecting, visualizing + correcting for population structure in GWAS
  78. 78 MCB 182 Lecture 12.8 - PCA for analysis of population structure in GWAS, multiple hypothesis testing
  79. 79 MCB 182 Lecture 12.9 - Fine-mapping causal variants based on GWAS associations
  80. 80 MCB 182 Lecture 12.10 - Epistasis, missing heritability in GWAS

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