Note final ps For question 2(a)the value of k'in the final equation(Eq 3b) needs to be rescaled Tuesday lecture will be for questions on the last problem set Juan)

发育生物学中的一些基本原理；发育生物学中的动物模型；发育生物学中的现代技术。 胚胎的早期发育：卵裂、原肠作用、神经胚作用。 细胞分化的机制：侧重基因表达的调控对组织器官形成和分化的影响。 果蝇躯体轮廓发育的分子机制 四肢动物的肢体的发育 性别决定与生殖细胞

一、果蝇胚胎发育概况 二、胚胎躯体轴线的建立由母体基因决定 三、受精后合子基因的表达 四、Pair-rule基因的表达界定胚胎的类体节 五、体节极性基因(segment polarity genes)与细胞谱系的建立 六、不同体节的发育命运决定于 homeotic selector genes

一、什么是系统生物学? 二、什么是生物系统? 三、系统生物学的研究内容 四、系统生物学的技术和方法 五、系统组学(Systeome) 六、癌的系统生物学 七、系统生物学对医学的影响 八、小结

Outline Multiple Sequence AlignmentCarillo-& Lipman, Clustal(W) Position-Specific Scoring Matrices(PSSM) Information content, Shannon entropy Sequence logos Hidden Markov Models Other approaches: Genetic algorithms, expectation maximization, MEME, Gibbs sampler

Outline FASTA, Blast searching, Smith-Waterman Psi-Blast Review of Genomic DNA structure Substitution patterns and mutation rates Synonymous and non-Synonymous substitutions Jukes-Cantor Model Kimura's Two-Parameter Model

The Language of genomics CDNAS, ESTS. BACS Alus. etc Dideoxy Method Shotgun Sequencing The 'shotgun coverage equation(Poisson) Flavors of blast BLASTIPNXJ, TBLASTINXI Statistics of High Scoring Segments

Review of DNA Seq. Comparison/Alignment Target frequencies and mismatch penalties Eukaryotic gene structure Comparative genomics applications Pipmaker(2 species comparison) Phylogenetic Shadowing(many species) Intro to DNA sequence motifs

Markov Hidden markov models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs

Review of markov HMM Models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs