Ian Wright's Bioinformatics Portfolio

The goal for this assignment was to create a class shared annotated bibliography of references for the next phase of the SARS-CoV-2 research project. These references will be used in the next journal club and will kickstart research for the final COVID-19 project.

Assignment

Warm up exercise (announced in class).
- Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., ... & Hastie, K. M. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812-827.
Perform a search in Google Scholar .
1. Record the number of “hits” you found:
  - 1,130 Results
2. Record the top 10 papers, this time using APA format:
  - Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., ... & Hastie, K. M. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812-827.
  - Grubaugh, N. D., Hanage, W. P., & Rasmussen, A. L. (2020). Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell, 182(4), 794-795.
  - Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., ... & Veinotte, K. (2020). Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell.
  - Daniloski, Z., Guo, X., & Sanjana, N. E. (2020). The D614G mutation in SARS-CoV-2 Spike increases transduction of multiple human cell types. BioRxiv.
  - Hu, J., He, C. L., Gao, Q., Zhang, G. J., Cao, X. X., Long, Q. X., ... & Tang, N. (2020). The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity. BioRxiv.
  - Weissman, D., Alameh, M. G., de Silva, T., Collini, P., Hornsby, H., Brown, R., ... & Mansouri, K. (2020). D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. medRxiv.
  - Yurkovetskiy, L., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T., Wang, Y., Baum, A., ... & Egri, S. B. (2020). SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain. bioRxiv.
  - Volz, E. M., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O'Toole, A., ... & Rey, S. M. (2020). Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. MedRxiv.
  - Plante, J. A., Liu, Y., Liu, J., Xia, H., Johnson, B. A., Lokugamage, K. G., ... & Mirchandani, D. (2020). Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. bioRxiv.
  - Omotuyi, I. O., Nash, O., Ajiboye, O. B., Iwegbulam, C. G., Oyinloye, E. B., Oyedeji, O. A., ... & Okaiyeto, K. (2020). Atomistic simulation reveals structural mechanisms underlying D614G spike glycoprotein‐enhanced fitness in SARS‐COV‐2. Journal of computational chemistry, 41(24), 2158-2161.
Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
- Okell, L. C., Verity, R., Katzourakis, A., Volz, E. M., Watson, O. J., Mishra, S., ... & Ghani, A. C. (2020). Host or pathogen-related factors in COVID-19 severity?–Authors' reply. The Lancet, 396(10260), 1397.
- Gortázar, C., del-Río, F. J. R., Domínguez, L., & de la Fuente, J. (2020). Host or pathogen-related factors in COVID-19 severity?. The Lancet, 396(10260), 1396-1397.
- Díez-Fuertes, F., Iglesias-Caballero, M., Pérez, J. G., Monzón, S., Jiménez, P., Varona, S., ... & Pozo, F. (2020). A FOUNDER EFFECT LED EARLY SARS-COV-2 TRANSMISSION IN SPAIN. Journal of Virology.
- Hashemi, S. A., Ghafouri, M., Khoshi, A. H., Ghasemzadeh-moghaddam, H., Namdar-Ahmadabad, H., & Azimian, A. (2020). Is 614G mutant of SARS-CoV-2 is an agent of the third wave of COVID-19 in Iran?. Authorea Preprints.
- Meng, Q., Wang, X., Wang, Y., Dang, L., Ma, X., Chi, T., ... & Ma, P. (2020). Detect the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA. Authorea Preprints.
Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
- Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., ... & Veinotte, K. (2020). Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell.
- Grubaugh, N. D., Hanage, W. P., & Rasmussen, A. L. (2020). Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell, 182(4), 794-795.
- Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., ... & Hastie, K. M. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812-827.
- Weissman, D., Alameh, M. G., de Silva, T., Collini, P., Hornsby, H., Brown, R., ... & Mansouri, K. (2020). D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. medRxiv.
- Daniloski, Z., Guo, X., & Sanjana, N. E. (2020). The D614G mutation in SARS-CoV-2 Spike increases transduction of multiple human cell types. BioRxiv.
Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
- Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., ... & Veinotte, K. (2020). Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell.
- Grubaugh, N. D., Hanage, W. P., & Rasmussen, A. L. (2020). Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear. Cell, 182(4), 794-795.
- Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., ... & Hastie, K. M. (2020). Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell, 182(4), 812-827.
- Weissman, D., Alameh, M. G., de Silva, T., Collini, P., Hornsby, H., Brown, R., ... & Mansouri, K. (2020). D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. medRxiv.
- Daniloski, Z., Guo, X., & Sanjana, N. E. (2020). The D614G mutation in SARS-CoV-2 Spike increases transduction of multiple human cell types. BioRxiv.
We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
- - Nathan: COVID-19 and immune response: 241,000
  - Yaniv: COVID-19 and antibodies: 62,900
  - Ian: COVID-19 and immunity: 77,500
  - JT: COVID-19 and immune reaction: 104,000
  - Taylor: SARS-CoV-2 and immune response: 48,800
  - Nida: SARS-CoV-2 and antibodies: 48,200
  - Owen: SARS-CoV-2 and immunity: 57,000
  - Anna: SARS-CoV-2 and immune reaction: 97,700
  - Aiden: 2019-nCoV and immune response: 25,600
  - Fatimah: 2019-nCoV and antibodies: 17,400
  - Kam: 2019-nCoV and immunity: 24,500
  - Macie: 2019-nCoV and immune reaction: 15,500
- Record the search terms that have now been assigned specifically to you:
  - Covid-19 and immune response: 241,000 results
- Record the search terms that have now been assigned specifically to you:
  - COVID-19 and immunity
Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.
- Record the total number of hits: 6,097
- Record the top 10 papers (you don't need to do APA format for this):
  1. Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals
  2. Prevention and treatment of COVID-19 disease by controlled modulation of innate immunity
  3. COVID-19 and the immune system
  4. The laboratory tests and host immunity of COVID-19 patients with different severity of illness
  5. Treatment options for COVID-19: The reality and challenges.
  6. Gut microbiota and Covid-19- possible link and implications.
  7. Herd Immunity: Understanding COVID-19.
  8. COVID-19: what has been learned and to be learned about the novel coronavirus disease.
  9. Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic.
  10. The Long Road Toward COVID-19 Herd Immunity: Vaccine Platform Technologies and Mass Immunization Strategies.
Perform a title/abstract search on your assigned keywords.
- Record the total number of hits: 353
- Record the top 10 papers (you don't need to do APA format for this):
  1. The impact of nutrition on COVID-19 susceptibility and long-term consequences. Review
  2. Gut microbiota and Covid-19- possible link and implications. Review
  3. Herd Immunity: Understanding COVID-19. Review
  4. COVID-19 and Asthma: Reflection During the Pandemic. Review
  5. Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals
  6. Deployment of convalescent plasma for the prevention and treatment of COVID-19
  7. COVID-19 and diabetes mellitus: An unholy interaction of two pandemics. Review
  8. Prevention and treatment of COVID-19 disease by controlled modulation of innate immunity. Review
  9. Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.
  10. BCG-induced trained immunity: can it offer protection against COVID-19? Review
Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
- Do you find any new articles that you did not find before on PubMed?
  - Yes
- List up to 5 new articles that were found on the author name search:
  1. T Follicular Helper Cells Regulate Humoral Response for Host Protection against Intestinal Citrobacter rodentium Infection
  2. Corrigendum to 'Cyclic AMP-Responsive element-binding protein (CREB) is critical in autoimmunity by promoting Th17 but inhibiting treg cell differentiation': [EBioMedicine 25 (2017) 165-174]
  3. The Coppery Age: Copper (Cu)-Involved Nanotheranostics
  4. Daphnetin ameliorates glucocorticoid-induced osteoporosis via activation of Wnt/GSK-3β/β-catenin signaling
  5. Momentum dependent [Formula: see text] band splitting in LaFeAsO
Now access the Web of Science database. Perform an unrestricted search on your assigned keywords.
- Record the total number of hits: 998
- Record the top 10 papers (you don't need to use APA format for this):
  1. New approximations, and policy implications, from a delayed dynamic model of a fast pandemic
  2. Network pharmacology analysis of the therapeutic mechanisms of the traditional Chinese herbal formula Lian Hua Qing Wen in Corona virus disease 2019 (COVID-19), gives fundamental support to the clinical use of LHQW
  3. Corona-Like Illness: Did we get it before WHO Announcement of the Disease? A Cross-sectional Survey
  4. COVID-19 vaccine and boosted immunity: Nothing ad interim to do?
  5. Caregiver willingness to vaccinate their children against COVID-19: Cross sectional survey
  6. SARS-CoV-2-specific virulence factors in COVID-19
  7. Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2-Infected Syrian Hamsters
  8. SARS-CoV-2 infections in children and young people
  9. Micronutrients as immunomodulatory tools for COVID-19 management
  10. On the genetics and immunopathogenesis of COVID-19
We will now create a shared bibliography for the entire class. Go through the search results that you have found and add articles to the class shared bibliography page.
- Only add articles that are unique (everyone will be adding to the page and we do not want redundant articles)
- Put review articles and primary research articles in their respective sections. If the article does not fit either of those two categories, place it in the other articles section.
- Add the articles in APA format (re-find them in Google Scholar to easily obtain APA format, if necessary). Add your wiki signature to the end of the citation.
- Ideally, each student will contribute 2-3 unique articles.
Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format: Ling, Y., Xu, S. B., Lin, Y. X., Tian, D., Zhu, Z. Q., Dai, F. H., ... & Hu, B. J. (2020). Persistence and clearance of viral RNA in 2019 novel coronavirus disease rehabilitation patients. Chinese medical journal.
- In Web of Science, search for the specific article that you have been assigned.
  - How many cited references does that article have?
    - 14
  - How many articles have cited the article you have been assigned?
    - 180
What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.
- Google Scholar: advantages
  - Simple citing mechanism. Can copy article citation in multiple formats. Can see how many times the article is cited and what papers cite it. Can click link to authors profile including all papers they've contributed to.
- Google Scholar: disadvantages
  - Advanced search is limited. There is author and publication date functionality but no options to query abstract/titles or editors etc. There is also no abstract to the articles included within google scholar itself.
- PubMed: advantages
  - Detailed advanced search and good filtering system in results page. Sharing papers with colleagues is simple and supported. Abstract included within the site. Similar articles, conflict of interest, abstract, title, and other information are neatly arranged. Figures are presented in the PubMed website.
- Pubmed: disadvantages
  - Full text links are not as smooth as google scholar. Google scholar will give you the option of moving straight to pdf format where PubMed will send you to the journal website first. Difficult citing system.
- Web of Science: advantages
  - Advanced search system is very detailed. Filter system in results page is helpful. The 'Hot Pages in the Field' option is useful. Keywords, author information, other metadata is easily accessible and useful. Citations in the paper are directly available to the user. Very helpful. Number of times the paper has been cited is also accessible.
- Web of Science: disadvantages
  - Difficult to find full text and even includes a button to search google scholar to find text. I guess this maybe an advantage but also, it'd be smoother to go directly to full text through WebofScience itself.
What impact does choice of keywords have on your results?
- More keywords brings up fewer and more refined results. The difference between using 'coronavirus', 'COVID-19', '2019-nCoV', and 'SARS-CoV-2' produces very different results. 'SARS-CoV-2' and 'COVID-19' produces the most quality results.
For your Conclusion section, write a short reflection about what you learned by doing this exercise. Include in your answer what you knew previously about searching the biological literature, and what you learned that was new today.

Conclusion

Before this exercise, I was only comfortable using Google Scholar as a scholarly search engine.I now feel comfortable using all three in tandem. Each of the databases have their advantages and each can be used for these qualities. PubMed and WebofScience can be used for advanced searching, Scholar can be used for finding full text and citations, and WebofScience can be used to easily access references within the article. It's possible to use all three together. I did not know very much about advanced searching before this exercise and now feel more empowered in my searching skills, especially through the Title/Abstract search function. I did not know that PubMed provided figures and WebofScience reference data, which will be extremely useful in my future research endeavors. My experience prior was limited to google scholar, searching keywords without advanced parameters, and using the citation button. This exercise has most definitely expanded my comfort zone.

Acknowledgements

Assignment questions was copied from BIOL368/F20:Week_10
Purpose section copied and edited from assignment section of BIOL368/F20:Week_10
User:Aiden_Burnett provided invaluable assistance and alleviated crippling confusion in regards to which article to perform a search upon for citation data. This document would not be what it is without the partnership of User:Aiden_Burnett.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Ian R. Wright (talk) 11:50, 12 November 2020 (PST)

References

Google Scholar . Google Scholar. https://scholar.google.com/schhp?hl=en&as_sdt=0,5
PubMed. PubMed. https://pubmed.ncbi.nlm.nih.gov/
WebofScience. WebofScience. http://apps.webofknowledge.com.electra.lmu.edu/WOS_GeneralSearch_input.do?product=WOS&search_mode=GeneralSearch&SID=7Ftokdc43TAK7aYpgPm&preferencesSaved=
Dahlquist K., Adinulos A. (2020, September 8). BIOL368/F20:Week_10. OpenWetWare. BIOL368/F20:Week_10

Ian R. Wright Week 10

Contents

Ian Wright's Bioinformatics Portfolio

Assignment Pages

Individual Journal Entries

Class Journals

Purpose

Assignment

Conclusion

Acknowledgements

References

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