BIOL398-01/S10:HIV Evolution

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BIOL398-01: Bioinformatics Laboratory

Loyola Marymount University

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Contents

Background

References

  1. Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, and Yu XF. . pmid:9770526. PubMed HubMed [Paper1]
  2. Vlahov D, Anthony JC, Munoz A, Margolick J, Nelson KE, Celentano DD, Solomon L, and Polk BF. . pmid:1661376. PubMed HubMed [Paper2]
All Medline abstracts: PubMed HubMed

Week 3

Lecture

  • Introduction to online biological databases

Activity

Preparation for Week 4 Journal Club

"Science... is a process taking place in the minds of living scientists," (Curtis, 1983). The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings are others). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research. This is the first of three journal club discussions we will have this semester. For this first journal club, the entire class will read and present the Markham et al. (1998) paper referenced above. Each student will create an individual wiki journal page for their Week 3 assignment and also contribute to the shared journal page in preparation for the presentation in class on February 9.

  1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). Links to online biological dictionaries can be found on the course Google Site. List the citation(s) for the dictionary(s) you use.
  2. Write a 1-2 page outline of the article. Your outline can be in any form you choose. It does not have to be complete sentences, but it should answer the questions listed below and have enough information so that I can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures and tables.
    • How do the results of this study compare to the results of previous studies (See Discussion).
  3. Each group of students will be assigned one table or figure. The pair will be responsible for explaining the table/figure in detail to the class.

Online Biological Dictionaries

Week 4

Week 5

Week 6

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