注意 : 授課時間:每星期四上午09:10 ~12:00

授課地課:台大資工系107教室

生物資訊 Bioinformatics Spring 2007

授課負責教師

謝叔蓉


中央研究院統計科學研究所副研究員 國立臺灣大學工所兼任副教授

 

Syllabus

Office:

Institute of Stat. Sci. 305, Academia Sinica

 

 

Lecture time and place:

9:10~12:00 AM Thur. , 台灣大學資訊工程系107教室.

 

 

Office hour:

to be announced 

 

 

Pre-requisite:

C and one Statistics course (eg. Statistics, Regression Analysis , Multivariate Stat., etc.) for science and engineerin background students, Statistics and Molecular and Cell Biology for biology background students, or consent of the organizer.

 

 

Grading:

Homework (30%), Midterm (40%), Term Project (30%).

 

 

 

參考書:

1.      DNA from the BEGINNING : chaps. 16~41

2.      A Primer of Genome Science, Greg Gibson and Spencer V. Muse, Sinauer Associates, 2002

3.      Molecular Cell Biology, Lodish et al. 4th edition, NY: Freeman, 2000.

4.      Biologist's Guide to Analysis of DNA Microarray Data and Microarray Analysis Set, M. Schena, Wiley, 2002

5.      The Analysis of Gene Expression Data, G. Parmigiani and E. S. Garrett, Springer, 2006

 

授課時間:

Thursday, 9:10 - 12: 00 A.M.

授課地點

台灣大學資訊工程系107教室

 


課程目標:

這個生物資訊課程為跨領域的課程。希望理工背景的學生能由此獲得分生與生化基礎。而生物背景的學生能學得如何應用統計方法、資訊軟體與網路上資源,以奠定將來 從事生物資訊這領域研究的基礎,及獲得服務於生物科技企業界的基本訓練。

課程內容:


 

這課程第一部份涵蓋細胞分子生物學、生化學、癌症基因學、基因網絡(networks)、Biochemical pathways。第二部分為微晶片數據之介紹與分析、相關的統計方法與計算軟體(叢聚、分類等)的應用及基因網路的建構。第三部分將由客座講員主講基因功能學及蛋白體學方面的專門研究課題。

    • 主題 1: Organization of the course ( 1hr ); 
              Molecular Biology I ( 2hrs )
      授課教師: 任志鴻 (Genome center, N. Yang-ming Univ.)
      授課日: Thursday, March 1st, 2007   Lecture 1

       
    • 主題 2: Molecular Biology II
      授課教師: 任志鴻 (Genome center, N. Yang-ming Univ.)
      授課日: Thursday, March 8th, 2007     Lecture 2

       
    • 主題 3: Molecular Biology for reconstructing genetic networks
      授課教師任志鴻 (Genome center, N. Yang-ming Univ.)
      授課日: Thursday, March 15th, 2007   Lecture

       
    • 主題 4: Microarray gene expression data
      授課教師謝叔蓉
      授課日: Thursday, March 22th, 2007   Lecture1  Lecture2  R introduction  Exercise

       
    • 主題 5: Data Preprocessing for Affymetrix GeneChip Data
      授課教師: 吳漢銘
      授課日: Thursday, March 29th, 2007   Preprocessing Oligo    Filtering and MissingValues  Exercise 
       
        
    • No class on April 5th, 2007

       
    • 主題 6: Finding Differential Expressed Genes (including Case study using LimmaGUI and affylmGUI)
      授課教師: 吳漢銘 (中研院統計所)
      授課日: Thursday, April 12th, 2007  Finding DEGenes Exercise

       
    • 主題 7: Analysis of cDNA microarray Data
      授課教師: 謝叔蓉
      授課日: Thursday, April 19th, 2007  Normalization and clustering Analysis of Multi-array data R for microarray
      Exercise 7

 

    • 主題 9: Classification methods and their applications:
      Classify functions of genes and predict functions of unannotated genes.
      授課教師: 謝叔蓉
      授課日: Thursday, May 3th, 2007  classification   R_classification


    • 主題 10: Mid-Term Exam, Thursday, May 10th, 2007(Mid-Term Exam will include "Clustering" course)

       
    • 主題 11: Yeast genomics
      授課教師: 高承福 (Institute of Cellular and Organismic Biology, Academia Sinica)
      授課日: Thursday, May 17th, 2007   Yeast genomics

 

    • 主題 12: Reconstructing gene networks and pathways I  GNW_LDE  GNW_TIGP
      授課教師: 謝叔蓉
      授課日: Thursday, May 24th, 2007

       
    • 主題 13: Gene Networks: past, present and future  Gene Networks
      授課教師: 喻秋華 (NHRI, 分子基因醫學組)
      授課日: Thursday, May 31th, 2007


    • 主題 14: Reconstructing gene networks and pathways II  Fuzzy
      授課教師: 謝叔蓉
      授課日: Thursday, June 7th, 2007

    • 主題 15: Systems biology
      授課教師王學偉 (陽明大學微免所)
      授課日: Thursday, June 14th, 2007


       
    • 主題 16: Project presentation II Project1-1 Project1-2  Project2      
      授課日: Thursday, June 21th, 2007
      地點:中央研究院統計科學研究所308會議室
       


 

FINAL EXAM : Term project.

Related Websites:

Data sets: 

GOOD LUCK AND HAVE A GREAT SEMESTER!

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