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本課程網頁中的 .M 檔案需由MATLAB®軟體運行。
MATLAB® software is required to run the .m files in this section.

生物學建議閱讀資料
Suggested Readings in Biology

以下Bruce Alberts等著,《細胞分子生物學》第四版中的部分,New York: Garland Science, 2002.。
The following sections from Alberts, Bruce, et al. Molecular Biology of the Cell. 4th ed. New York: Garland Science, 2002. ISBN: 0815332181, are suggested:

  • RNA和蛋白質的合成
    RNA and Protein Synthesis
  • 基因調控概述
    Overview of Gene Control
  • 基因如何調控其工作
    How Genetic Switches Work
  • 細胞訊息傳導的基本原理
    General Principles of Cell Signaling
以下課程講義由Alexander van Oudenaarden教授及其他下列所提及的作者提供。
Downloadable course notes are included courtesy of Prof. Alexander van Oudenaarden as well as any additional authors noted in the table below.
LEC # 課程單元 閱讀資料
第一部分:系統微生物學-將細胞視成一個完全攪拌反應器
Part I: Systems Microbiology - 'The Cell as a Well-stirred Bioreactor'
1 簡介
Introduction

酵素動力學
Michaelis-Menten Kinetics
2 平衡結合
Equilibrium Binding

合作現象
Cooperativity
Michaelis-Menten酵素動力學
Michaelis-Menten Kinetics (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)
3 λ嗜菌體
Lambda Phage

多穩定性
Multistability
λ嗜菌體的基因開關
A Genetic Switch in Lamba Phage (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)

Hasty, Jeff, Joel Pradines, Milos Dolnik, and J. J. Collins. 〈基因的干擾基底開關和放大器〉,《美國國家科學學會公報》
Hasty, Jeff, Joel Pradines, Milos Dolnik, and J. J. Collins. "Noise-based Switches and Amplifiers for Gene Expression." Proc. Natl. Acad. Sci. USA 97, no. 5 (Feb 29, 2000): 2075-80.
4 多穩定性(繼續上次課程)
Multistability (cont.)
Isaacs, Farren J., Jeff Hasty, Charles R. Cantor, and J. J. Collins.〈自我調節基因模組的預測及測量〉,《美國國家科學學會公報》 100, no. 13 (June 24, 2003):7714-19。
Isaacs, Farren J., Jeff Hasty, Charles R. Cantor, and J. J. Collins. "Prediction and Measurement of an Autoregulatory Genetic Module." PNAS 100, no. 13 (June 24, 2003): 7714-19.
5 合成基因開關
Synthetic Genetic Switches
合成基因開關
Synthetic Genetic Switches (PDF)

Gardner, Timothy S., Charles R. Cantor, and James J. Collins. 〈在大腸桿菌中建構一個基因搖頭開關〉 ,《自然》403, no. 6767 (January 20, 2000):339-42。
Gardner, Timothy S., Charles R. Cantor, and James J. Collins. "Construction of a Genetic Toggle Switch in Escherichia coli." Nature 403, no. 6767 (January 20, 2000): 339-42.
6 穩定性分析
Stability Analysis
穩定性分析
Stability Analysis (PDF)
7 大腸桿菌的趨化性介紹
Introduction E. coli Chemotaxis
8 格式化和穩健形趨化性模型的比較
Fine-tuned versus Robust Chemotaxis Models
大腸桿菌的趨化性建模
Modeling Escherichia coli chemotaxis (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)

Spiro, Peter A., John S. Parkinson, and Hans G. Othmer. 〈細菌趨化性中的刺激及適應模型〉,《美國國家科學學會公報》 94, no. 14 (July, 1997):7263–68。
Spiro, Peter A., John S. Parkinson, and Hans G. Othmer. "A Model of Excitation and Adaptation in Bacterial Chemotaxis." Proc. Natl. Acad. Sci. USA 94, no. 14 (July, 1997): 7263–68.
9 掩飾趨化性
Wrapping up Chemotaxis
生物震盪器
Biological Oscillators (PDF)
10 基因震盪器
Genetic Oscillators
生物震盪器
Biological Oscillators (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)

Elowitz, Michael B., and Stanislas Leibler. 〈轉路調控的合成震盪網路〉,《自然》403, no. 6767 (January 20, 2000):335-8。
Elowitz, Michael B., and Stanislas Leibler. "A Synthetic Oscillatory Network of Transcriptional Regulators." Nature 403, no. 6767 (January 20, 2000): 335-8.
11 基因震盪器(繼續上次課程)
Genetic Oscillators (cont.)
Routh-Hurwitz測試法
Routh-Hurwitz (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)

Atkinson, Mariette R., Michael A. Savageau, Jesse T. Myers, and Alexander J. Ninfa.〈大腸桿菌中基因線路展示搖頭開關或震盪行為的發展〉,《細胞》 113, no. 5 (May 30, 2003):597-607。
Atkinson, Mariette R., Michael A. Savageau, Jesse T. Myers, and Alexander J. Ninfa. "Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli." Cell 113, no. 5 (May 30, 2003): 597-607.
12 隨機化學動力學
Stochastic Chemical Kinetics
生化系統中干擾的來源和結果
The Origin and Consequences of Noise in Biochemical Systems (PDF) (Courtesy of Alexander van Oudenaarden and Mukund Thattai. Used with permission.)
13 隨機化學動力學(繼續上次課程)
Stochastic Chemical Kinetics (cont.)
第二部分:細胞系統生物學-將細胞視成一個既有濃度梯度的分隔系統
Part II: Cell Systems Biology - 'The Importance of Diffusion and Gradients for Cellular Regulation'
14 細胞系統生物學簡介
Introduction Cell Systems Biology

Fick法則
Fick's Laws
15 局部刺激
Local Excitation

整體抑制理論
Global Inhibition Theory
局部刺激,整體抑制理論
Local Excitation, Global Inhibition Model (PDF)
16 局部刺激(繼續上次課程)
Local Excitation (cont.)

整體抑制理論(繼續上次課程)
Global Inhibition Theory (cont.)
17 大腸桿菌中快速極間震盪
Rapid Pole-to-pole Oscillations in E. coli
Howard, Martin, Andrew D. Rutenberg, and Simon de Vet. 〈細菌的動力學隔間:大腸桿菌中正確的分隔〉,《物理評論通訊》 87, no. 27 (December 31, 2001)。
Howard, Martin, Andrew D. Rutenberg, and Simon de Vet. "Dynamic Compartmentalization of Bacteria: Accurate Division in E. Coli." Physical Review Letters 87, no. 27 (December 31, 2001).
18 大腸桿菌中快速極間震盪(繼續上次課程)
Rapid Pole-to-pole Oscillations in E. coli (cont.)
19 真核生物的梯度感應模型
Models for Eukaryotic Gradient Sensing
真核生物的梯度感應模型
Models for Eukaryotic Gradient Sensing (PDF)

相關MATLAB®檔案
Associated MATLAB® code file (M)

Narang, Atul, K. K. Subramanian, and D. A. Lauffenburger. 〈以受體調控的磷脂膜訊息傳導動力學為基礎的梯度感應趨化性數學模型〉,《生醫工程年鑑》 29, no. 8 (2001):677-91。
Narang, Atul, K. K. Subramanian, and D. A. Lauffenburger. "A Mathematical Model for Chemoattractant Gradient Sensing based on Receptor-regulated Membrane Phospholipid Signaling Dynamics." Annals of Biomedical Engineering 29, no. 8 (2001): 677-91.
20 真核生物的梯度感應模型(繼續上次課程)
Models for Eukaryotic Gradient Sensing (cont.)
Postma, Marten, and Peter J. M. Van Haastert. 〈趨化性細胞梯度感應的擴散易位模型〉,《生物物理期刊》81, no. 3 (September, 2001):1314-23。
Postma, Marten, and Peter J. M. Van Haastert. "A Diffusion–Translocation Model for Gradient Sensing by Chemotactic Cells." Biophysical Journal 81, no. 3 (September, 2001): 1314-23.
21 細胞骨架動力學建模
Modeling Cytoskeleton Dynamics
Dogterom, Marileen, and Stanislas Leibler.〈物理層面的微管結構生長與調控〉,《物理評論通訊》 70, no. 9 (March 1, 1993)。
Dogterom, Marileen, and Stanislas Leibler. "Physical Aspects of the Growth and Regulation of Microtubule Structures." Physical Review Letters 70, no. 9 (March 1, 1993).
22 細胞骨架動力學建模(繼續上次課程)
Modeling Cytoskeleton Dynamics (cont.)
Cytrynbaum, E. N., V. Rodionov, and A. Mogilner.〈動力蛋白依賴性自我組織微管星狀體的數值模型〉,《細胞科學期刊》117, no. 8 (March 15, 2004):1381-97。
Cytrynbaum, E. N., V. Rodionov, and A. Mogilner. "Computational Model of Dynein-dependent Self-organization of Microtubule Asters." Journal of Cell Science 117, no. 8 (March 15, 2004): 1381-97.
第三部分:發育系統生物學-由單一細胞建構一個生物體
Part III: Developmental Systems Biology - 'Building an Organism Starting From a Single Cell'
23 數量感應
Quorum Sensing
You, Lingchong, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold.〈胞間訊息傳遞和調控性殺戮的計畫形群體控制〉,《自然》 428, no. 6985 (April 22, 2004):868-71。
You, Lingchong, Robert Sidney Cox III, Ron Weiss, and Frances H. Arnold. "Programmed Population Control by Cell-Cell Communication and Regulated Killing." Nature 428, no. 6985 (April 22, 2004): 868-71.
24 期末題組諮詢時間
Final Problem Set Question Hour
25 果蠅發育學
Drosophila Development
Houchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler.〈早期果蠅胚胎發育精準度和比例的建立〉,《自然》 415, no. 6873 (February 14, 2002):798-802。
Houchmandzadeh, Bahram, Eric Wieschaus, and Stanislas Leibler. "Establishment of Developmental Precision and Proportions in the Early Drosophila embryo." Nature 415, no. 6873 (February 14, 2002): 798-802.

 
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