Does any resource help with this course?

• Mastering Reinforcement Learning
• 蘑菇书EasyRL
• JoyRL Book

Does any resource help with this course?

1. Algorithm Design by Kleinberg and Tardos
2. Algorithms by Jeff Erickson
3. Linear Programming
4. Design of Approximation Algorithms

Prerequisites 1. Introduction to Genomics 基因组学

• eukaryotes, prokaryotes, viruses
  • 真核生物、原核生物、病毒
  • water 70%, protein 15%, RNA 6%, DNA 1%
• genome 基因组
  • bacterium, human, plant, virus
  • 细菌、人类、植物、病毒
  • chromosome 染色体
  • plasmid 质粒
  • mitochondria 线粒体
  • chloroplast 叶绿体
• ploidy 倍性
  • 2 copies of the same chromosome, one from each parent
  • haploid 单倍体
  • diploid 二倍体
  • polyploid, triploid, tetraploid
• molecular biology 分子生物学
  • DNA, RNA, protein
  • nucleotide 核苷酸, amino acid 氨基酸
  • gene, genome, transcriptome 转录组, proteome 蛋白质组
• DNA: A-T, C-G
  • double helix 双螺旋
  • sugar-phosphate backbone 糖磷酸骨架
  • 5' to 3' direction
  • chromosome, gene, exon 外显子, intron 内含子, promoter 启动子, enhancer 增强子, terminator 终止子
• protein
  • encoded by gene
  • polymer of amino acid monomers 氨基酸单体聚合物
  • cellular functions 细胞功能
    • catalysis 催化
    • structure 结构
    • signalling 信号
• amino acid
  • 20 types
  • 3-letter and 1-letter code
  • hydrophobic 疏水, hydrophilic 亲水, charged 带电
• central dogma
  • DNA -> RNA -> protein
  • transcription 转录, translation 翻译
  • U (uracil) in RNA instead of T (thymine) in DNA
  • ribosome 核糖体, tRNA, mRNA
• reserve transcription 逆转录
  • mRNA -> DNA
  • reverse transcriptase 逆转录酶
  • retrovirus 逆转录病毒
• gene
  • unit of heredity 遗传单位
  • 2% of human genome codes for genes
  • promoter, 5' UTR, coding sequence, 3' UTR, terminator
  • coding sequence: exon, intron
• variation
  • sequence variation
    • single nucleotide variation (SNV) 单核苷酸变异
    • single nucleotide polymorphism (SNP) 单核苷酸多态性
    • indels: insertion, deletion
  • structural variation
    • large-scale (>50bp)
    • involving entire sections of DNA
    • gain or loss of fucntion (GoF, LoF)
  • conservation
• sequencing technology
  • DNA/RNA extraction -> library preparation -> sequencing -> export fastq files -> QC/analysis
  • Illumina, Nanopore
• FASTQ files, reads
  • 4 lines per read
    • identifier - unique name
    • sequence - AGTC
    • spacer - +
    • quality - confidence score for each DNA base
• sequencing strategies
  • whole genome sequencing (WGS)
    • all DNA in cells
  • whole exome sequencing (WES)
    • all exons
    • cheap, capture importants
  • RNA sequencing (RNA-seq)
    • all RNA in cells
  • scRNA-seq
    • all RNA but idividual cells
  • Amplicon
    • use PCR target specific region
  • Pair-end
    • sequence both ends of DNA fragment