AninditaVarshneya BIOL368 Week 5

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Electronic Lab Notebook

Please access this week's assignment here.

Planning Our Research Project

The following is a basic outline of procedures we will use to complete our research project as outlined in my Week 4 Individual Journal page.

  • The goal is to create a correlation analysis between CD4 T cell counts and genetic diversity.
  • In order to do this, S values and theta values will be calculated for each subject at each visit and will be plotted against their CD4 T cell count for that visit.
    • It may be worthwhile to team up with Colin Wikholm and Will Fuchs since they will most likely require similar, if not the same, data
    • S values and theta values can be used as statistical indicators of genetic diversity as they represent the differences between different strains
    • Because we will be calculating these numbers per visit, and because CD4 T cell counts are available per subject per visit, a graph can be created that plots both numbers against each other.
  • The same data will be combined into a single graph relating all S and theta values against their CD4 T cell counts.
  • Regression curves will be drawn and R^2 values will be calculated to determine which curve (if any) best represents the correlation between genetic diversity and CD4 T cell counts which represent the progression of HIV


Mia Huddleston, Colin Wikholm, Will Fuchs, and I met online on Sunday afternoon to finalize details for our future research. Mia and I met additionally to confirm our protocol, and are in agreement on the details of our research, and wrote the section titled "Planning Our Research Project" together. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source. --Anindita Varshneya 02:41, 3 October 2016 (EDT)


  1. Donovan S and Weisstein AE (2003) Exploring HIV Evolution: An Opportunity for Research. In Jungck JR, Fass MR, and Stanley ED, eds. Microbes Count! West Chester, Pennsylvania: Keystone Digital Press.
  2. 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
  3. Vlahov, D., Anthony, J.C., Munoz, A., Margolick, J., Nelson, K.E., Celentano, D.D., Solomon, L., Polk, B.F. (1991). The ALIVE study, a longitudinal study of HIV-1 infection in intravenous drug users: description of methods and characteristics of participants. NIDA Res Monogr 109, 75-100.
  4. Week 5 Assignment Page

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

Weekly Assignments Individual Journal Assignments Shared Journal Assignments

SURP 2015

Links: Electronic Lab Notebook