2021 CBB Qualifier Exam on COVID-19 and Network Biology

Read the following papers or preprints and their supplementary materials:

1. Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell discovery, 6(1), 1-18.
2. Zhou, Y., Hou, Y., Shen, J., Mehra, R., Kallianpur, A., Culver, D. A., … & Fiocchi, C. (2020). A network medicine approach to investigation and population-based validation of disease manifestations and drug repurposing for COVID-19. PLoS Biology, 18(11), e3000970.
3. Gysi, D. M., Valle, Í. D., Zitnik, M., Ameli, A., Gan, X., Varol, O., … & Barabási, A. L. (2020). Network medicine framework for identifying drug repurposing opportunities for COVID-19. arXiv preprint arXiv:2004.07229.
4. Ding, J., Lugo-Martinez, J., Yuan, Y., Kotton, D. N., & Bar-Joseph, Z. (2020). Reconstructing SARS-CoV-2 response signaling and regulatory networks. bioRxiv preprint
5. Fiscon, G., Conte, F., D'Offizi, G., Farina, L., & Paci, P. (2020). SAveRUNNER: a network-based algorithm for drug repurposing and its application to COVID-19. arXiv preprint arXiv:2006.03110.

Write a critical review and comparison of these papers focusing on their similarities and differences. Consider only the computational analyses and their results. You can ignore the experimental approaches, if there are any. Points you should consider include:

• What is the biological goal of each paper?
• How does each paper achieve this goal computationally? Are any analyses similar in all papers?
• Are there differences between the methods used or developed by these papers?
• What are the similarities and differences between the results presented in these papers?

You may consider additional questions that occur to you as you read these papers. You may use images from the papers to make your points. I expect that you will need to read related papers. Be sure to provide appropriate citations and a complete bibliography. Use 11 point font, single-spaced text, with 1" margins. Your review should be about eight-ten pages long.