Difference between revisions of "Hhinsch Week 11"

Revision as of 06:28, 14 November 2017

Bibliography Notes

• You must use these three databases/tools to find the references that you include in your bibliography: PubMed, GoogleScholar, and Web of Science. Answer the following questions as part of your assignment:
• Use a keyword search for the first three databases/tools and answer the following:
  • PubMed
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". The search keywords produced six results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I didn't need to narrow down the results because there were only six results from the original search.
  • Google Scholar
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". I got 31,400 results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I then used the keywords: "yeast cold shock microarray data over time". There were still over 20,000 results so I added a constraint that only showed articles published post 2017. The search narrowed down to 1,530 results.
  • Web of Science
    • What original keyword(s) did you use? How many results did you get?
      • I originally used the keywords: "yeast cold shock microarray". The search keywords produced ten results.
    • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
      • I didn't need to narrow down the results because there were only ten results from the original search.
• 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?
      • Again, I didn't feel like I needed to narrow down the search because there were only six results from the original search.
  • Google Scholar
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I used the allintitle: Saccharomyces cerevisiae microarray cold shock response data function in order to narrow down the search. I got one result. Most of the other keywords I tried didn't satisfy a narrow search and came up with zero results, or came up with too many.
  • Web of Science
    • Which advanced search functions were most useful to narrow down the search? How many results did you get?
      • I used the (TS=(microarray AND data AND saccharomyces AND cerevisiae AND cold AND shock)) AND DOCUMENT TYPES: (Article) advanced search booleans for the Web of Science and came up with seven results. This narrowed down the topics of the articles.
  • Perform a prospective search on the following three review articles in Web of Science and answer the following:
    • Aguilera, J., Randez-Gil, F., & Prieto, J.A. (2007). Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews, 31, 327–341. doi: 10.1111/j.1574-6976.2007.00066.x
      • How many articles does this article cite?
        • This article cites 144 references.
      • How many articles cite this article?
        • 77 articles cite this article.
    • Al-Fageeh, M.B. & Smales, C.M. (2006). Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal, 397, 247–259. doi: 10.1042/BJ20060166
      • How many articles does this article cite?
        • This article cites 108 references.
      • How many articles cite this article?
        • 125 articles cite this article.
    • Thieringer, H.A., Jones, P.G.,& Inouye, M. (1998). Cold shock and adaptation. BioEssays, 20, 49–57. doi: 10.1002/(SICI)1521-1878(199801)20:1<49::AID-BIES8>3.0.CO;2-N
      • How many articles does this article cite?
        • This article cites 76 references.
      • How many articles cite this article?
        • 258 articles cite this article.

Bibliography

Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., & Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/26420504
• PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/
• Publisher Full Text (HTML): https://link.springer.com/article/10.1007/s11538-015-0092-6
• Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf
• Copyright: The Author(s) 2015. Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
• Publisher: Bulletin of Mathematical Biology(scientific society)
• Availability: Online
• Did LMU pay a fee for this article: No
• Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip

Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/16989656
• PubMed Central: N/A
• Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1
• Publisher Full Text (PDF): http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf
• Copyright: Copyright © 2007, Oxford University Press; Open Access after time has elapsed: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. You must ask permission from the publisher to use the article.
• Publisher: Published by Oxford University Press(respected open access organization)
• Availability: Online and in print
• Did LMU pay a fee for this article: No
• Data: I couldn't find any supplementary data other than the data provided in the article.

Acknowledgments

1. Dr. Dahlquist helped the QA's and Data Analysts learn what to look for and how to navigate Web of Science.
2. I worked with Mary Balducci over text and in class in order to complete the deliverables of this assignment.
3. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.Hhinsch (talk) 22:28, 13 November 2017 (PST)

References

1. Web of Science. (2017). Retrieved November 13, 2017, from https://login.webofknowledge.com/error/Error?Error=IPError&PathInfo=%2F&RouterURL=https%3A%2F%2Fwww.webofknowledge.com%2F&Domain=.webofknowledge.com&Src=IP&Alias=WOK5
2. LMU BioDB 2017. (2017). Week 11. Retrieved November 13, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
3. PubMed. (2017). Retrieved November 13, 2017 from https://www.ncbi.nlm.nih.gov/pubmed
4. Google Scholar. (2017). Retrieved November 13, 2017 from https://scholar.google.com/
5. Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x
6. Dahlquist, K. D., Fitzpatrick, B. G., Camacho, E. T., Entzminger, S. D., & Wanner, N. C. (2015). Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae. Bulletin of Mathematical Biology, 77(8), 1457–1492. http://doi.org/10.1007/s11538-015-0092-6

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