Readings | Network Medicine: Using Systems Biology and Signaling Networks to Create Novel Cancer Therapeutics | Biology

As you read these articles, you may find it helpful to refer to the suggested paper reading strategy, and questions to consider.

Course readings.
WEEK #	TOPICS	READINGS
1	Introduction See the Lecture Summary	No readings
2	Targeted Therapy in the Pre-Systems Biology Era See the Lecture Summary	Schechter, A. L., D. F. Stern, et al. "The Neu Oncogene: an Erb-B-related Gene Encoding a 185,000-Mr Tumour Antigen." Nature 312, no. 5994 (1984): 513–6. Konopka, J. B., S. M. Watanabe, et al. "Cell Lines and Clinical Isolates Derived From Ph1-positive Chronic Myelogenous Leukemia Patients Express C-abl Proteins With a Common Structural Alteration." Proceedings of the National Academy of Science of the United States of America 82, no. 6 (1985): 1810–4.
3	High-Throughput Data Acquisition I: Gene Sequencing and Functional Genomics See the Lecture Summary	Yan, H., D. W. Parsons, et al. "IDH1 and IDH2 Mutations in Gliomas." The New England Journal of Medicine 360, no. 8 (2009): 765–73. Sun, T., N. Aceto, et al. "Activation of Multiple Proto-oncogenic Tyrosine Kinases in Breast Cancer via Loss of the PTPN12 Phosphatase." Cell 144, no. 5 (2011): 703–18.
4	High-Throughput Data Acquisition II: Proteomics See the Lecture Summary	Bantscheff, M., D. Eberhard, et al. "Quantitative Chemical Proteomics Reveals Mechanisms of Action of Clinical ABL Kinase Inhibitors." Nature Biotechnology 25, no. 9 (2007): 1035–44. Bendall, S. C., E. F. Simonds, et al. "Single-cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum." Science 332, no. 6030 (2011): 687–96.
5	Gene Expression Analysis See the Lecture Summary	Mao, M., M. J. Marton, et al. "Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer". Nature 415, no. 6871 (2001): 530–6. Venet, D., J. E. Dumont, et al. "Most Random Gene Expression Signatures are Significantly Associated With Breast Cancer Outcome." PLoS Computational Biology 7, no. 10 (2011): e1002240.
6	Network Biology See the Lecture Summary	Goh, K. I., M. E. Cusick, et al. "The Human Disease Network." Proceedings of the National Academy of Science of the United States of America 104, no. 21 (2007): 8685–90. Chuang, H. Y., E. Lee, et al. "Network-based Classification of Breast Cancer Metastasis." Molecular Systems Biology 3, no. 140 (2007).
7	Clustering See the Lecture Summary	Huang, P. H., A. Mukasa, et al. "Quantitative Analysis of EGFRvIII Cellular Signaling Networks Reveals a Combinatorial Therapeutic Strategy for Glioblastoma." Proceedings of the National Academy of Science of the United States of America 104, no. 31 (2007): 12867–72. Jiang, H., J. R. Pritchard, et al. "A Mammalian Functional-genetic Approach to Characterizing Cancer Therapeutics." Nature Chemical Biology 7, no. 2 (2011): 92–100.
8	Regression Modeling See the Lecture Summary	Gaudet, S., K. A. Janes, et al. "A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines." Molecular and Cellular Proteomics 4, no. 10 (2005): 1569–90. Lau, K. S., A. M. Juchheim, et al. "Vivo Systems Analysis Identifies Spatial and Temporal Aspects of the Modulation of TNF-alpha-induced Apoptosis and Proliferation by MAPKs." Science Signaling 4, no. 165 (2011): ra16.
9	Logic Modeling See the Lecture Summary	Poltz, R., R. Franke, et al. "Logical Network of Genotoxic Stress-induced NF-kappaB Signal Transduction Predicts Putative Target Structures for Therapeutic Intervention Strategies." Advances and Applications in Bioinformatics and Chemistry 2 (2009): 125–38. Morris, M. K., J. Saez-Rodriguez, et al. "Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli." PLoS Computational Biology 7, no. 3 (2011): e1001099.
10	Kinetic Modeling See the Lecture Summary	Santos, S. D., R. Wollman, et al. "Spatial Positive Feedback at the Onset of Mitosis." Cell 149, no. 7 (2012): 1500–13. Batchelor, E., C. S. Mock, et al. "Recurrent Initiation: a Mechanism for Triggering p53 Pulses in Response to DNA Damage." Molecular Cell 30, no. 3 (2008): 277–89.
11	Structural Biology See the Lecture Summary	Shan, Y., M. P. Eastwood, et al. "Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization." Cell 149, no. 4 (2012): 860–70. Rasmussen, S. G., B. T. DeVree, et al. "Crystal Structure of the Beta2 Adrenergic Receptor-Gs Protein Complex." Nature 477, no. 7366 (2011): 549–55.
12	Synthetic Biology See the Lecture Summary	Sallee, N. A., B. J. Yeh, et al. "Engineering Modular Protein Interaction Switches by Sequence Overlap." Journal of the American Chemical Society 129, no. 15 (2007): 4606–11. Rutherford, B. J., R. H. Dahl, et al. "Functional Genomic Study of Exogenous N-butanol Stress in Escherichia Coli." Applied and Environmental Microbiology 76, no. 6 (2010): 1935–45.
13	Field Trip See the Lecture Summary	No readings
14	Systems Pharmacology and Network Medicine See the Lecture Summary	Duncan, J. S., M. C. Whittle, et al. "Dynamic Reprogramming of the Kinome in Response to Targeted MEK Inhibition in Triple-negative Breast Cancer." Cell 149, no. 2 (2012): 307–21. Barretina, J., G. Caponigro, et al. "The Cancer Cell Line Encyclopedia Enables Predictive Modelling of Anticancer Drug Sensitivity." Nature 483, no. 7391 (2012): 603–7.
15	Final Class See the Lecture Summary	No readings