Nanguiano Week 10

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Annotated Bibliography of Genomics Papers for your Species

  1. The journal article which describes the results of the whole genome sequencing for your species. (Note that you will be giving a journal club presentation on this article for your Week 11 assignment.)
    • Use a keyword search for each of these databases/tools and answer the following:
      • PubMed
        • What original keyword(s) did you use? How many results did you get?
          • First, I searched "pertussis", and got 29,674 results. Realizing that was too broad, I searched for "bordetella pertussis", and got 11,829 results. After, I searched "bordetella pertussis genome", and got 757 results, then I searched "bordetella pertussis genome sequence", and got 530 results.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • Searching "bordetella pertussis genome sequence" was the most useful combination to narrow the search. It reduced the number of results from 29,674 to 530. An advanced search would likely decrease the number of results further.
      • Google Scholar
        • What original keyword(s) did you use? How many results did you get?
          • I began by using the same combinations of keywords as I used for Pubmed to see how Google Scholar would compare. A search for "pertussis" resulted in 336,000 results, which was noticeably more than Pubmed. Searching "bordetella pertussis" resulted in 54,900 results. "bordetella pertussis genome" resulted in 22,500 results, and "bordetella pertussis genome sequence" resulted in 20,500 results. It was apparent that there were far too many results to be useful with the search results that I'd used before on Pubmed. However, I knew that it an advanced search would be necessary in order to narrow down the results further.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • Similarly to Pubmed, the search for "bordetella pertussis genome sequence" resulted in the fewest results. However, it was still 22,500 results, which was far too many to work with. This was much more manageabel than the 336,000 results initially returned by the "pertussis" search, but still far too many. An advanced search would be necessary.
      • Web of Science
        • What original keyword(s) did you use? How many results did you get?
          • I used the same keywords that I'd used above for both Pubmed and Google Scholar. The search for "pertussis" returned 111,582 results, a value much larger than the number of results returned from Pubmed, but much less than Google Scholar. A search for "bordetella pertussis" returned 34,582 results. "bordetella pertussis genome" returned 415 results, and "bordetella pertussis genome sequence" returned 285 results.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • The search for "bordetella pertussis genome sequence" returned 285 results, significantly less than both Pubmed and Google Scholar.
    • Use the advanced search functions for each of these three databases/tools and answer the following:
      • PubMed
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          • The very first search I conducted was "Title/Abstract" containing "bordetella pertussis genome", which returned 7 results. A search for "bordetella pertussis genome sequence" in the title or abstract returned 19 results. The fact that the latter search returned more results was surprising to me, but it seemed that the results were more related to what I was looking for in comparison to the results returned by the former.
      • Google Scholar
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          • The first search I conducted was "bordetella pertussis genome", where all the words were contained in the title. There were 40 results. I then searched "bordetella pertussis genome sequence" with the same filters, predicting that it would result in more results than the previous search. However, I was incorrect. This search resulted in only 10 results.
      • Web of Science
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          • I first searched "bordetella pertussis genome" with the "title" filter on. This resulted in 38 results. A search for "bordetella pertussis genome sequence" with the same filter gave 26 results.
    • After searching, I selected a paper from Pubmed that contained information about the Bordetella pertussis genome.
  2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
    • Give an overview of the results of the search.
      • How many articles does this article cite?
        • 13
      • How many articles cite this article?
        • 1
      • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
        • It's difficult to say, since only one article cited the paper. The paper seems to be a review article discussing pertussis strains and pediatrics. From this, I can assume that the main direction has been discussing how to treat whooping cough.
  3. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
    • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
    • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
    • State what you used as search terms and what type of search terms they were.
    • Give an overview of the results of the search.
      • On array express, I searched by organism "Bordetella pertussis", "RNA Assay", and "Array Assay".
      • How many results did you get?
        • 13.
      • Give an assessment of how relevant the results were.
        • Only the top 3 results were for purely Bordetella pertussis. The rest were varying combinations of pertussis and other strains of Bordetella.
    • For each article, please provide all of the same information that you provided for the genome article above.
    • In addition, you must also link to the web site where the microarray data resides.
    • Bibliography 1: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/
    • Bibliography 2: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
      • Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
        1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
        2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

Links

Nicole Anguiano
BIOL 367, Fall 2015

Assignment Links
Individual Journals
Shared Journals
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