Taur.vil Week 10

Week 9 Individual Journal

Lab Journal

Finding Reference Paper

1. Used PubMed and searched "Streptococcus pneumoniae" & "whole genome" & sequence to find microarray papers
2. With Kevin Meilak, found [1]
   • In the paper, identified strain R6 (accession no. NC_003098) as the reference sequence
3. Searched in UniProt for complete genome taxonomies containing Streptococcus pneumoniae and R6 (search results)
4. Found corresponding link in PubMed (link) and followed links to the original paper (link, PDF)

Finding other papers

1. In web of science, searched for "Streptococcus pneumoniae strain R6" under title and Hoskins in author to find the reference paper search
2. Only the reference paper appeared, and looked at the times cited (412 results)
3. Searched within results for microarray (56 results)
4. Selected the third option Title: "Identification of Genes That Contribute to the Pathogenesis of Invasive Pneumococcal Disease by In Vivo Transcriptomic Analysis" (link)
   • Clicked on links, found in PubMed Central, and downloaded pdf. The full article is also available online on PubMed Central and the Journal of Infection and Immunology.
   • The data is accessible at [2].
5. Went back to works citing the reference paper and restricted the search to "gene expression" and "transcription profiling" (8 results).
6. Selected a paper titled "Global transcription profiling and virulence potential of Streptococcus pneumoniae after serial passage".
   • Found journal link [3] on the LMU library links page and downloaded the pdf. The pdf is under copyright protection and can be found at [4].
   • The data is accessible at [5] and included 2 biological replicates per trial and four spot replicates.

Thoughts on Finding Papers

1. During the process of finding papers, a lot of the ones on web of science seemed to not be very useful. However, by narrowing the search criteria, I was able to limit the total amount to a small number in which it was relatively easy to find useful papers. I am sure there are many more applicable papers available, they just did not appear near the top of my search criteria.

By Tauras Vilgalys

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