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20.440

Analysis of Biological Networks

6-0-9 units · Graduate

Explores computational and experimental approaches to analyzing complex biological networks and systems. Includes genomics, transcriptomics, proteomics, metabolomics and microscopy. Stresses the practical considerations required when designing and performing experiments. Also focuses on selection and implementation of appropriate computational tools for processing, visualizing, and integrating different types of experimental data, including supervised and unsupervised machine learning methods, and multi-omics modelling. Students use statistical methods to test hypotheses and assess the validity of conclusions. In problem sets, students read current literature, develop their skills in Python and R, and interpret quantitative results in a biological manner. In the second half of term, students work in groups to complete a project in which they apply the computational approaches covered.

Fall 2004 · Analysis of Biological Networks (BE.440)

Topics

  • Decoding Information I (Transcription Regulation)
  • Decoding Information II (Translation)
  • Roundtable Discussion
  • Examination 1
  • How to Write an NIH Grant Proposal
  • Analysis of the Interferon Network (The JAK/STAT System)
  • Analysis of the Interferon Network
  • Analysis of the Interferon Network (cont.)
  • Roundtable 1: Students Present Model Projects on Apoptosis
  • Epithelial Cell Morphogenesis Signaling Hierarchy I
  • Epithelial Cell Morphogenesis Signaling Hierarchy II
  • Round Table Discussion
  • Epithelial Cell Morphogenesis Signaling Hierarchy III
  • Examination 2
  • Roundtable 3
  • Changes in Lung Epithelium During Pathogenesis I
  • Changes in Lung Epithelium During Pathogenesis II
  • Network Example: Functional Glycomics
  • Final Papers Due

Readings

  • Hunter, Peter J., and Thomas K. Borg. “Integration from Proteins to Organs: The Physiome Project.” Nature Reviews 4 (March 2003): 237-243.
    Listed reading
  • Kitano, Hiroaki. “Systems Biology: A Brief Overview.” Science 295 (March 1, 2002): 1662-1664.
    Listed reading
  • McAdams, Harley H., et al. “The Evolution of Genetic Regulatory Systems in Bacteria.” Nature Reviews (Genetics) 5 (March 2004): 1-9.
    Listed reading
  • Denamur, Erick, et al. “Evolutionary Implication of the Frequent Horizontal Transfer of Mismatch Repair Genes.” Cell 103 (November 22, 2000): 711-721.
    Listed reading
  • Sancar, Aziz, et al. “Molecular Mechanisms of Mammalian DNA Replain and the DNA Damage Checkpoints.” Annu. Rev. Biochem. 73 (2004): 39-85.
    Listed reading
  • Katze, Michael G., et al. “Viruses and Interferon: A Fight for Supremacy.” Nature Reviews 2 (September 2002): 675-687.
    Listed reading
  • Pawson, Tony, and Piers Nash. “Assembly of Cell Regulatory Systems Through Protein Interaction Domains.” Science 300 (April 18, 2003): 445-452.
    Listed reading
  • Chen, Xiaomin, et al. “Crystal Structure of a Tyrosine Phosphorylated STAT-1 Dimer Bound to DNA.” Cell 93 (May 29, 1998): 827-839.
    Listed reading
  • LEC #: 11 · TOPICS: Analysis of the Interferon Network (cont.) · READINGS: Taniguchi, Tadatsugu, et al. “IRF Family of Transcription Factors as Regulators of Host Defense.” Ann. Rev. Immunol. 19 (2001): 623-655.
    Reading assignment
  • LEC #: 12 · TOPICS: Analysis of the Interferon Network (cont.) · READINGS: Example Paper on NO from Last Year
    Reading assignment
  • Webre, Daniel J., et al. “Bacterial Chemotaxis.” Current Biology 13, no. 2, pp. 47-49.
    Listed reading
  • Levit, Mikhail N., and Jeffry B. Stock. “Receptor Methylation Controls the Magnitude of Stimulus-response Coupling in Bacterial Chemotaxis.” The Journal of Biological Chemistry 277, no. 29 (September 27, 2002): 36769-36765.
    Listed reading
  • Alon, U., et al. “Robustness in Bacterial Chemotaxis.” Nature 397 (January 14, 1999): 168-171.
    Listed reading
  • Taniguchi, Tadatsugu, et al. “IRF Family of Transcription Factors as Regulators of Host Defense.” Ann. Rev. Immunol. 19 (2001): 623-655.
    Listed reading
  • Berg, Howard C. “The Rotary Motor of Bacterial Flagella.” Annual Review of Biochemistry 72 (2003): 19-54.
    Listed reading
  • Schmeichel, Karen L., and Mina J. Bissell. “Modeling Tissue-specific Signaling and Organ Function in Three Dimensions.” Journal of Cell Science 116, no. 12: 2377-2388.
    Listed reading
  • Davies, Jamie A. “Extracellular Matrix.” In Encyclopedia of Life Sciences. Nature Publishing Group, 2001.
    Listed reading
  • Dow, Julian A. T., and Shireen A. Davies. “Integrative Physiology and Functional Genomics of Epithelial Function in a Genetic Model Organism.” Physiol. Rev. 83 (2003): 657-729.
    Listed reading
  • Parmar, Hema, and Gerald R. Cunha. “Epithelial-stromal Interactions in the Mouse and Human Mammary Gland in Vivo.” Endocrine-Related Cancer 11 (2004): 437-458.
    Listed reading
  • Taddei, Ilaria, et al. “Integrins in Mammary Gland Development and Differentiation of Mammary Epithelium.” Journal of Mammary Gland Biology and Neoplasia 8, no. 4 (October 2003): 383-394.
    Listed reading
  • Liu, Hong, et al. “Polarity and Proliferation are Controlled by Distinct Signaling Pathwaysdownstream of PI3-kinase in Epithelial Tumor Cells.” Journal of Cell Biology 164, no. 4 (February 16, 2004): 603-612.
    Listed reading
  • Brisken, Cathrin, et al. “IGF-2 is a Mediator of Prolactin-induced Morphogenesis in the Breast.” Developmental Cell 3 (December 2002): 877-887.
    Listed reading
  • Brinckerhoff, Constance E., and Lynn M. Matrisian. “Matrix Metalloproteinases: A Tail of a Frog that became a Prince.” Nature Reviews (Molecular Cell Biology) 3 (March 2002): 207-214.
    Listed reading
  • Leist, Marcel, and Marja Jaattela. “Four Deaths and a Funeral: From Caspases to Alternative Mechanisms.” Nature Reviews (Molecular Cell Biology) 2 (August 2001): 1-10.
    Listed reading
  • Krissansen, Geoffrey Wayne. “Integrin Superfamily.” In Encyclopedia of Life Sciences. Nature Publishing Group, 2001.
    Listed reading
  • Miranti, Cindy K., and Joan S. Brugge. “Sensing the Environment: A Historical Perspective on Integrin Signal Transduction.” Nature Cell Biology 4 (April 2002): 83-90.
    Listed reading
  • Insall, Robert, and Laura Machesky. “Cytoskeleton.” In Encyclopedia of Life Sciences. New York: Nature Publishing Group, 2001.
    Listed reading
  • Sasisekharan, Ram, and James R. Myette. “The Sweet Science of Glycobiology.” American Scientist 91 (September-October 2003): 432-441.
    Listed reading
  • Ridley, Anne J., et al. “Cell Migration: Integrating Signals From Front to Back.” Science 302 (December 5, 2003): 1704-1709.
    Listed reading
  • Chodosh, Lewis et al. “Protein Kinase Expression during Murine Mammary Development.” Developmental Biology 219 (2000): 259-276.
    Listed reading
  • Padera, Robert, et al. “FGF-2/Fibroblast Growth Factor Receptor/Hepartin-like Glycosaminoglycan Interactions: A Compensation Model for FGF-2 Signaling.” The FASEB Journal 13 (October 1999): 1677-1687.
    Listed reading
  • Tan, John L., et al. “Cells Lying on a Bed of Microneedles: An Approach to Isolate Mechanical Force.” Proceedings of the National Academy of Sciences 100, no. 4 (18 February, 2003): 1484-1489.
    Listed reading
  • Wiseman, Paul W., et al. “Spatial Mapping of Integrin Interactions and Dynamics During Cell Migration by Image Correlation Microscopy.” Journal of Cell Science 117, no. 23, pp. 5521-5534.
    Listed reading
  • Corry, David B. “Emerging Immune Targets for the Therapy of Allergic Asthma.” Nature Reviews (Drug Discovery) 1 (January 2002): 55-64.
    Listed reading
  • Niiro, Hiroaki, and Edward A. Clark. “Regulation of B-cell Fate by Antigen-receptor Signals.” Nature Reviews (Immunology) 2 (December 2002): 945-956.
    Listed reading
  • Koretzky, Gary A., and Peggy S. Myung. “Positive and Negative Regulation of T-cell Activation by Adaptor Proteins.” Nature Reviews (Immunology) 1 (November 2001): 95-97.
    Listed reading

Prerequisites & course information

Prereq: 20.420[J] and permission of instructor G (Spring) 6-0-9 units

Sources