Week 5 Individual Journal William P Fuchs

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Week 5 Assignment

  • This week's entry for Bioinformatics

Bibliography as a Word Document


Assignment Questions

Part A

  1. PubMed
    • I used the keywords "HIV" and "Divergence" and roughly 1000 articles show up at first glance.
    • I added some new keywords like "T-Cells" and that narrowed it down to 5 articles.
  2. Google Scholar
    • I used the keywords "HIV" and "Clones" and roughly 183,000 article registered in the search engine.
    • I added the keywords mutations and lethality and broke it down to 10,000 articles.
  3. Web of Science
    • I used the keywords "HIV" and "Divergence" and got 54 results
    • I clicked the "review articles tab on the left side of the page and got 1 result.

Part B

  1. PubMed
    • Using more specific keywords that resembles the rhetoric of the papers I'm looking for.
  2. Google Scholar
    • Clicking the modification of dates cleared many of the results.
  3. Web of Science
    • All the "Refine" tabs on the left side of the page were very useful.

Part C

  • This article sites 51 articles.
  • This article is cited 74 times.

HIV Evolution Project and Electronic Lab Notebook for Week 5


  • To initiate an investigation on the 4 subjects's strains of HIV to see if they are derived from a common source in respect to diversity and to moreover create correlation statistics to analyze that data and to search for relationships in diversity and divergence of clones of HIV-1.


  • To calculate our own sets of Theta and S Values from the sequences provided by all the progress of the HIV clones across all of subjects (6,8,9,14) across all visits of the study. However to represent those values as a function of time to calculate divergence of the env gene. The model for the Markham et. al paper will be used as a template for the %changes across each interval.
  • Conduct ClustalW multiple sequence alignment to find a the initial diversities and plot against time.
  • We will work closely with Anindita Varshneya and Mia Huddleston.
    • coordinate efforts with them to achieve sound data to run statistics for correlation.
  • Additional methods include the correlation statistics between individuals (6,8,9 and 14).

Scientific Conclusion

  • There will be a correlation of the difference categories of the variant progressives across all the clones in respect to divergence and CDT-4 declines.


I worked with classmates Colin Wikholm, Anindita Varshneya, and Mia Huddleston while we discussed partial allocation of work and general project schematics and some communication online though social media messaging. In that time we talked about the scope of the project and some minor work needs. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. William P Fuchs 20:42, 3 October 2016 (EDT)


  1. Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568
    • Publisher Full Text: [1]
    • PDF Available: [2].

Individual Journals

Class Journals


Useful Links

  1. Bio Class Page
  2. BIOL368/F16:People
  3. Will Fuchs
  4. Link to LMU: http://www.lmu.edu/