for - quote - better approach than gene sequence as universal panecea

quote - better approach than gene sequence as universal panecea - (see quote below)

• Look at the high-level organization of the system
  • the living system
• Locate what is going wrong there and then work down to find what you might do
• at lower levels with a drug or any other kind of treatment for that matter to put it right
• That works much better than trying to go the other way because
  • going the other way, the space for
    • possible molecules and
    • possible effects and
    • even more possible combinations of effects
  • because those complex diseases are going to require combinations of treatment
  • There are too many
  • You can't do clinical trials on all of those possibilities
  • It's just far too expensive
  • So I think we just take need to take a different approach to medical research
    • to try to benefit from the human genome sequencing
    • in a way that's different from what they originally promised

967F primer

very crisp summary

weak sequencing - reduces to: - or: - parallel (simultaneous) - strict sequencing

Varmus, H. (2021, August 31). Covid has revealed the need for genomic sequencing around the world. Financial Times. https://www.ft.com/content/342fd3c3-5a22-49a0-9cef-135f2ccd8700

ReconfigBehSci. (2021, November 26). RT @PeterHotez: …this info is more relevant than immune escape. For instance the B.1.351 from ZA last year never really took off. So transm… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1464240155070447632

Davis, N., & correspondent, N. D. S. (2022, January 21). Covid reinfection: How likely are you to catch virus multiple times? The Guardian. https://www.theguardian.com/world/2022/jan/21/covid-reinfection-how-likely-are-you-to-catch-virus-multiple-times

Eric Topol. (2021, November 27). View of key mutations of Omicron’s 50, with 30 in the spike protein, 15 in its receptor binding domain https://ft.com/content/42c5ff3d-e676-4076-9b9f-7243a00cba5e http://covariants.org @EllingUlrich @_b_meyer https://t.co/onMoNFVLFJ [Tweet]. @EricTopol. https://twitter.com/EricTopol/status/1464452102382448643

Maxmen, A. (2021). Omicron blindspots: Why it’s hard to track coronavirus variants. Nature. https://doi.org/10.1038/d41586-021-03698-7

Cauchemez, S., & Bosetti, P. (2021). A reconstruction of early cryptic COVID spread. Nature. https://doi.org/10.1038/d41586-021-02989-3

COVID-19 Patients Not Allowed to Know Which Variant Infected Them. (n.d.). Retrieved September 7, 2021, from https://www.businessinsider.com/covid-patients-cant-know-which-variant-infected-them-delta-2021-8?r=US&IR=T

Mallapaty, S. (2021). India’s neighbours race to sequence genomes as COVID surges. Nature, 593(7860), 485–486. https://doi.org/10.1038/d41586-021-01287-2

Morgan, O. W., Aguilera, X., Ammon, A., Amuasi, J., Fall, I. S., Frieden, T., Heymann, D., Ihekweazu, C., Jeong, E., Leung, G. M., Mahon, B., Nkengasong, J., Qamar, F. N., Schuchat, A., Wieler, L. H., & Dowell, S. F. (2021). Disease surveillance for the COVID-19 era: Time for bold changes. The Lancet, 0(0). https://doi.org/10.1016/S0140-6736(21)01096-5

Xu, G., Qi, F., Li, H., Yang, Q., Wang, H., Wang, X., Liu, X., Zhao, J., Liao, X., Liu, Y., Amit, I., Liu, L., Zhang, S., & Zhang, Z. (2020). The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. MedRxiv, 2020.08.15.20175638. https://doi.org/10.1101/2020.08.15.20175638

Guo, L., Boocock, J., Tome, J. M., Chandrasekaran, S., Hilt, E. E., Zhang, Y., Sathe, L., Li, X., Luo, C., Kosuri, S., Shendure, J. A., Arboleda, V. A., Flint, J., Eskin, E., Garner, O. B., Yang, S., Bloom, J. S., Kruglyak, L., & Yin, Y. (2020). Rapid cost-effective viral genome sequencing by V-seq. BioRxiv, 2020.08.15.252510. https://doi.org/10.1101/2020.08.15.252510

Xu, G., Qi, F., Li, H., Yang, Q., Wang, H., Wang, X., Liu, X., Zhao, J., Liao, X., Liu, Y., Amit, I., Liu, L., Zhang, S., & Zhang, Z. (2020). The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. MedRxiv, 2020.08.15.20175638. https://doi.org/10.1101/2020.08.15.20175638

Addetia, A., Crawford, K. H., Dingens, A., Zhu, H., Roychoudhury, P., Huang, M., Jerome, K. R., Bloom, J. D., & Greninger, A. (2020). Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. MedRxiv, 2020.08.13.20173161. https://doi.org/10.1101/2020.08.13.20173161

How coronavirus mutations can track its spread—And disprove conspiracies. (2020, March 26). Science. https://www.nationalgeographic.com/science/2020/03/how-coronavirus-mutations-can-track-its-spread-and-disprove-conspiracies/

Behrmann, Ole, and Martin Spiegel. ‘COVID-19: From Rapid Genome Sequencing to Fast Decisions’. The Lancet Infectious Diseases 0, no. 0 (14 July 2020). https://doi.org/10.1016/S1473-3099(20)30580-6.

Hiatt, J., Patwardhan, R., Turner, E. et al. Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7, 119–122 (2010). https://doi.org/10.1038/nmeth.1416

Varmus, H. (2020, May 9). The World Doesn’t Yet Know Enough to Beat the Coronavirus. The Atlantic. https://www.theatlantic.com/ideas/archive/2020/05/lack-testing-holding-science-back/611422/

Pinto, S. F., & Ferreira, R. S. (2020). Analyzing course programmes using complex networks. ArXiv:2005.00906 [Physics]. http://arxiv.org/abs/2005.00906

inference of "%diploid coverage"