附件８

國立陽明大學　　　　94　學年度第　2　學期　　　　授課進度表

授課系級：生物資訊研究所 1-3年級　負責教師姓名：趙淑妙

時間：每週二下午7, 8節(15:30-17:20) 聯絡電話：(02) 2789-2887

地　　點：陽明大學第一教學大樓的123室　　　　　　　　e-mail: smchaw@sinica.edu;

日期

講題

時數

教師姓名（中文）

2/21

3/07

2/28

3/14

3/21

3/28

4/04

4/11

4/17-21

4/25

5/02

5/09

5/16

5/23

5/30

6/06

6/13

6/20

Chap1：Gene structure, Genetic codes, and Mutation

Chap2：Dynamics of Genes in Populations

228 Memorial Day- No class

Quiz /Chap3：Evolutionary change in nucleotide sequence

Chap4：Rates and pattern of nucleotide substitution

Quiz/Chap4-1：Molecular clocks and Relative rate test

校際活動週

Chap5-1：Methods of tree reconstruction

Chap5-2：Molecular phylogenetic examples

期中考 (Take home assignment)

Chap6-1：Types of gene duplication

Chap6-2：Molecular tinkering

Quiz/Chap7-1：Transposable elements

Chap7-2：Genetic and evolutionary effects of transposition

Quiz/Chap8-1：Genome evolution

Chap8-2：Organelle evolution

Quiz/ Paper presentations/ Discussions (Articles 1, 2, 3)

Paper presentations and Discussions (Articles 4,5,6)

Paper Discussions/Current topics (Articles 7,8,9, 10)

趙淑妙

王達益*

趙淑妙/曾雲輝*

趙淑妙

趙淑妙/王達益

趙淑妙

趙淑妙/曾雲輝

趙淑妙

王達益

趙淑妙/曾雲輝*

趙淑妙

教科書名：1. Fundamentals of Molecular Evolution 2.Molecular Evolution and phylogenetics

3. The phylogenetic Handbook A Practical Approach to DNA and Protein Phylogeny

4. Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids

作　　者：1. Grauer D. and Li W.-H. 2.Masatoshi Nei and Sudhir Kumar 3. Marco Salemi and Anne-Mieke Vandamee 4. Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison

出版社：1. Sinauer 2.Oxford University 3.Cambridge University 4.Cambridge University

*王達益: 中央研究院生物多樣性中心助研究員; 2789-3863 x 221; dywang@gate.sinica.edu.tw

*曾雲輝：中央研究院基因體中心博士後; 2789-9930 x 309 : yunhuei@gate.sinica.edu.tw

Reading assignments (Jun 6, 13, 20)

1. Irie-Kushiyama S, Asano-Miyoshi M, Suda T, Abe K, Emori Y. (2004) Identification of 24 genes and two pseudogenes coding for olfactory receptors in Japanese loach, classified into four subfamilies: a putative evolutionary process for fish olfactory receptor genes by comprehensive phylogenetic analysis. Gene 325: 123-135.

2. Yang J, Su AI, Li WH. (2005) Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes. Mol Biol Evol. 22(10):2113-21188. Epub 2005 Jun 29.

3. Yang J, Li WH (2004) Developmental constraint on gene duplicability in fruit flies and nematodes. Gene. 340:237-40.

4. Nei M, Gojobori T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.

5. Easteal S, Collet C. (1994) Consistent variation in amino-acid substitution rate, despite uniformity of mutation rate: protein evolution in mammals is not neutral. Mol Biol Evol. 11: 643-647.

6. Nekrutenko A, Makova KD, Li WH (2002). The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res. 12:198-202.

7. Erickson DL, Smith BD, Clarke AC, Sandweiss DH, Tuross N. (2005) An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proc Natl Acad Sci U S A.102:18315-18320.

8. Bardeleben C, Moore RL, Wayne RK. (2005) A molecular phylogeny of the Canidae based on six nuclear loci. Mol Phylogenet Evol. 37:815-831.

9. Kazazian HH Jr. (2004) Mobile elements: drivers of genome evolution. Science. 303(5664):1626-32. Review.