Malverso Week 10

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Search Journal

Genome Paper

  • Pubmed
    • What original keyword(s) did you use? How many results did you get?
      • I used the keyword : "shewanella oneidensis genome", which gave me 185 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • After this, I went straight to advanced search.
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I searched "shewanella oneidensis genome[Title/Abstract]" so that it would search for the terms in only the titles and abstracts of the articles. This gave me only 3 results.
  • Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • I used the search term "Shewanella oneidensis genome", which gave me 7970 results.
      • The first result looked promising because it was cited 580 times, and was also an article I found using the PubMed search engine.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I did not narrow down my search using different keyword combinations or advanced search because the first article seemed to be what I was looking for.
  • Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • Again, I used the search term "Shewanella oneidensis genome". This gave me 441 results.
      • I went straight to advanced search after this.
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I refined the results by restricting the results to being only articles. This gave me 262 results.
    • Since this was still a large number, I decided to search using the keyword "Shewanella Oneidensis complete genome sequence" and again restricted the results to being articles. This gave me only 31 results.

Microarray Papers

  • Then I searched using Array Express
    • I clicked browse.
    • then I filtered by organisms > shewanella oneidensis and experiment types RNA assay and Array assay.
    • I got 20 experiments as results.
    • I looked for transcription profiling by array (all of my results fell under this category)
    • I made sure my articles of choice had a decent number of assays.
  • When I click on one of the results, what I will eventually want is the sample and data relationship file. The raw data file is where we want to find the gene Id's.
  • I looked for citations to get to the paper that corresponds to that data set.
  • I noted which results would be my responsibility to find the paper for and annotate : E-MTAB-266 and E-MTAB-319 found on this page.

Papers to Include

  1. Find genome sequence paper. Find the canonical one! This may require searching around or consulting with Dr.Dahlquist.
  2. Find microarray data papers. We are likely to find something different than the authors found even though they have already analyzed it. It is still important, however, to figure out what information has already been found out by others.

Annotated Bibliography

Citation Style

Use APA style for this bibliography. Or the style of the PeerJ - which has a downloadable citation style for the zotero program.

  • make sue to translate the citation into wiki text.

Genome Paper

Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123. doi:10.1038/nbt749

  • The abstract from PubMed.
  • The full text of the article in PubMedCentral : Not available.
  • The full text of the article from the publisher web site. (The HTML version was not available.)
  • The full PDF version of the article from the publisher web site.
  • Who owns the rights to the article?
    • The Nature Publishing Group, which is the publisher of this article, according to this site.
  • Do the authors own the rights under a Creative Commons license?
    • Yes, according to this site.
  • Is the article available “Open Access”?
    • According to this site, the article is available "Open Access".
  • What organization is the publisher of the article? What type of organization is it?
    • According to the site above, this publisher is a "Professional OA Publisher (Large)".
  • Is this article available in print or online only?
    • Online only. It was published online in November, 2002.
  • Has LMU paid a subscription or other fee for your access to this article?
    • No.
  • I performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
    • Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article I was searching for.
  • How many articles does this article cite?
    • This article has 41 cited references within the Web of Science Core Collection, according to this site.
  • How many articles cite this article?
    • It has been cited 1079 times in all databases Web of Science utilizes, and 426 within the Web of Science Core Collection, according to this site.
  • 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?
    • Examples of titles that reference the genome paper:
      • Environmental genome shotgun sequencing of the Sargasso Sea
      • Deciphering the evolution and metabolism of an anammox bacterium from a community genome
      • Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
      • More can be found by clicking this link.
    • These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.

Microarray Papers

  • Neither of the cited papers for the two results from ArrayExpress that I was assigned to were linked to the actual paper.
  • I attempted to find each of them by searching for the titles, "Transcriptome of Coculture Shewanella oneidensis and Enterococcus faecium using a graphite electrode" and "Transcriptome of Shewanella oneidensis using a graphite electrode" on Google Scholar, Web of Science, and PubMed.
  • After this did not return either of the papers, I decided to search for articles written by the authors instead.
  • This is when I noticed that both of the articles I was searching for were written by the same authors.
  • I searched for Suzanne Read, Kelvin Lau, and Franz Pichler (separately) on PubMed and Web of Science and Google Scholar. The only paper that I found to be written by some of the authors was this paper.
  • I decided not to keep searching for the rest of the authors since Suzanne Read was the head author and that searching for her should be sufficient.
  • Although Shewanella was mentioned in the abstract, after talking to Dr.Dahlquist I found that this was definitely not one of the papers I was looking for.
  • I talked to Dr.Dahlquist about what my next action should be in either searching for these two papers or looking for a new microarray data set.
  • Since all of the data sets on our ArrayExpress results had been searched for already, she explained that it was okay if our group only had three total microarray papers.
  • Therefore, I do not have an annotated microarray paper on this page.


Team Page

Heavy Metal HaterZ

Assignments

Individual Journal Entries

Shared Journal Entries

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