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



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Targeted Therapy in the Pre-Systems Biology Era

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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.


High-Throughput Data Acquisition I: Gene Sequencing and Functional Genomics

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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.


High-Throughput Data Acquisition II: Proteomics

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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.


Gene Expression Analysis

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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.


Network Biology

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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).



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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.


Regression Modeling

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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.


Logic Modeling

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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.


Kinetic Modeling

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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.


Structural Biology

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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.


Synthetic Biology

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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.


Field Trip

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Systems Pharmacology and Network Medicine

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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.


Final Class

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