Zachary T. Goldstein Week 5

HIV Evolution Project

Annotated Bibliography

File:Annotated Bib Bioinformatics Zgoldste.pdf

Database Questions

PubMed

1. What original keyword(s) did you use? How many results did you get?
   • I searched "dN/dS" AND "HIV" as a keyword search and got 34 results.
2. Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
   • Using the specific keyword "dN/dS" was the best way to narrow down my search because it immediately filtered out articles that didn't talk about the ratios we were searching for. Since the initial number of articles was already relatively low I did not have to further refine my search; there were still 34 results.
3. Which advanced search functions were most useful to narrow down the search? How many results did you get?
   • The title/abstract search function, and publication date search function were the most useful...when I added these to the search it narrowed it down to 30 articles, many of which were applicable to our topic

GoogleScholar

1. What original keyword(s) did you use? How many results did you get?
   • Using the same keyword parameters as PubMed "dN/dS" AND "HIV" Google Scholar produced a little under 3,000 results.
2. Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
   • I found that when using Google Scholar to search for a very specific keyword/topic, it is best to only include that topic in the search bar, and not include broad topics such as HIV because it will limit the results to a much more reasonable number. In this case deleting "HIV" filtered out almost 3,000 articles.
3. Which advanced search functions were most useful to narrow down the search? How many results did you get?
   • Using the "where my words occur" advanced function to force google to look for the words in the title of the articles narrowed my search down to only 24 articles.

Web of Science

1. What original keyword(s) did you use? How many results did you get?
   • I did not actually use any keywords while searching for an article in Web of Science. Instead I was looking for the same article I found on PubMed and I used the exact title and author to find it. I got 1 result.
2. Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
   • Combining portions of the "topic" with the year published enabled me to narrow down my search to just 1 result.
3. Which advanced search functions were most useful to narrow down the search? How many results did you get?
   • My favorite part of Web of Science is after finding one paper that fits your topic, you can go to the summary screen and click "times cited" to find other papers that cited that paper. This was how I was able to find articles related to my subject so quickly. My first article was cited 6 times so it gave me 6 new results.

Prospective Search on Markham et al. (1998) Article

1. How many articles does the Markham et al. (1998) article cite?
   • The Markham article cited 51 other articles within Web of Science Core Collection
2. How many articles cite the Markham et al. (1998) article?
   • 74 articles have cited it within the Web of Science Core Collection

Electronic Journal

Purpose

• The purpose of this weeks assignment is to finalize our question, methods, and prediction for our project. Our aim is to create an brief outline of the methods, procedures, and steps we will use to analyze our data and answer our question so we are prepared to be productive in class during Week 6

Methods/Results

• Updated hypothesis in Week 4 to include predictions about θ values
• Changed prediction from 2 groups to 3 groups
• We plan on selecting cut-offs for dN/dS ratio numbers that we will use to classify the new groups: nonprogressor, moderate progressor, and rapid progressor
• Re-rank subjects based on dN/dS ratios
• We will use Biology Workbench to calculate "S" and θ values to determine genetic diversity between subjects
• A chi-squared test will be run on the θ values to determine statistical significance between the three groups
• We will make an unrooted tree with the expectation that subjects of the new groups will be branched more closely together, and the groups as a whole will be noticeably isolated from each other
• We will organize all data in tables
• We will save all data/files at least 2 different ways and begin to work on the powerpint

Data/Files

• none

Scientific Conclusion

• We established steps and a specific plan of action that we will use in class during week 6 to begin our research and powerpoint. We concluded that a chi-squared test should be run to compare θ values between the new groups, and that we will need assistance with determining cutoff points for dN/dS ratios.

Acknowledgements

• I would like to acknowledge the help of my partner User:Shivum A Desai on the completion of this assignment. I received help from him in class in learning how to properly create citations, understand journals, and identify key pieces of information for the bibliography. We also met outside of class in the Lab to discuss our electronic notebook assignment and prepare for next week's class.
• I would like to acknowledge the help of User:Kam D. Dahlquist in requesting a primary article from an outside source and with helping me identify what kind of publisher the paper originated from. She also assisted me with clarifying questions about format of uploaded articles within the assignment via email.
• I would also like to acknowledge the help of Glenn Johnson on instructing the class on how to properly and efficiently use the databases listed below.
• While I received help on this assignment everything completed on this page is my own work and was not copied from anyone else.

Zachary T. Goldstein 16:58, 29 September 2016 (EDT)Zachary T. Goldstein

References

LibGuides

PubMed

Google Scholar

Web of Science

LMU Library Journal Catalog

Week 5 Assignment

handout

APA Citations

BIOL368/F16

All class assignments:

• Week 1 Assignment
• Week 2 Assignment
• Week 3 Assignment
• Week 4 Assignment
• Week 5 Assignment
• Week 6 Assignment
• Week 7 Assignment
• Week 8 Assignment
• Week 9 Assignment
• Week 10 Assignment
• Week 11 Assignment
• Week 14 Assignment
• Week 15 Assignment

All individual assignments:

• Zachary T. Goldstein Week 2
• Zachary T. Goldstein Week 3
• Zachary T. Goldstein Week 4
• Zachary T. Goldstein Week 5
• Zachary T. Goldstein Week 6
• Zachary T. Goldstein Week 7
• Zachary T. Goldstein Week 8
• Zachary T. Goldstein Week 9
• Zachary T. Goldstein Week 10
• Zachary T. Goldstein Week 11
• Zachary T. Goldstein Week 14
• Zachary T. Goldstein Week 15

All shared journals:

• BIOL368/F16:Class Journal Week 1
• BIOL368/F16:Class Journal Week 2
• BIOL368/F16:Class Journal Week 3
• BIOL368/F16:Class Journal Week 4
• BIOL368/F16:Class Journal Week 5
• BIOL368/F16:Class Journal Week 6
• BIOL368/F16:Class Journal Week 7
• BIOL368/F16:Class Journal Week 8
• BIOL368/F16:Class Journal Week 9
• BIOL368/F16:Class Journal Week 10
• BIOL368/F16:Class Journal Week 11
• BIOL368/F16:Class Journal Week 14
• BIOL368/F16:Class Journal Week 15

User: Zachary T. Goldstein