Difference between revisions of "QLanners Week 11"

Revision as of 08:26, 14 November 2017

Bibliography Entries

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. doi: 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%2Fs11538-015-0092-6
• Publisher Full Text (PDF): https://link.springer.com/content/pdf/10.1007%2Fs11538-015-0092-6.pdf
• Copyright: 2015 by The Authors (information found on PDF version of article); article is Open Access at Springerlink.com
• Publisher: Springer Nature (research, educational and professional publisher)
• Availability: in print and online
• Did LMU pay a fee for this article: no
• Is dataset available: Yes: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip

Becerra, M., Lombardia, L.J., Gonzalez-Siso, M.I., Rodriguez-Belmonte, E., Hauser, N.C., & Cerdan, M.E. (2003). Genome-wide analysis of the yeast transcriptome upon heat and cold shock. Comparative and Functional Genomics, 4(4), 366-375. doi: 10.1002/cfg.301

• PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/18629074
• PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447359/
• Publisher Full Text (HTML): N/A
• Publisher Full Text (PDF): http://downloads.hindawi.com/journals/ijg/2003/175356.pdf
• Copyright: 2003 Hindawi Publishing Corporation (information found on https://www.hindawi.com/journals/ijg/2003/175356/abs/); article is Open Access at Hindawi.com
• Publisher: Hindawi (for-profit, peer-reviwed publisher)
• Availability: online
• Did LMU pay a fee for this article: no
• Is dataset available: unable to find

Keyword Search Results

PubMed

• Search Query: "yeast cold shock"
  • Search Results: 211
• Search Query: "microarray data yeast cold shock"
  • Search Results: 3
• Adding "microarray data" to the query greatly limited the search results. However, this query may have been too strict as there was only three results. Although I did find one article "Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae" which I have chosen to use in the bibliography.

Google Scholar

• Search Query: "yeast cold shock"
  • Search Results: About 288,000
• Search Query: "microarray data yeast cold shock"
  • Search Results: About 30,700
• Search Query: "microarray data of cold shock in Saccharomyces cerevisiae"
  • Search Results: About 15,400
• Google Scholar provided much more results than PubMed. Thus, more specific search queries were able to be used to find papers that were very closely matched to the topic. The last query seemed to offer a number of results pertaining to the topic.

Web Of Science

• Search Query: "yeast cold shock"
  • Search Results: 218
• Search Query: "microarray data yeast cold shock"
  • Search Results: 4
• For both searches, the query was selected to be "topic" in the right-hand box. Similar to PubMed, adding "microarray data" to the query greatly reduced the number of search results. In this more specific query, I found a research article titled "Genome-wide analysis of the yeast transcriptome upon heat and cold shock" that I used in my bibliography.

Advanced Search Results

PubMed

• Search: (yeast[Title]) AND cold shock[Title]
  • Search Results: 5
• Search: ((yeast[Title]) AND cold[Title]) AND shock[Title]
  • Search Results: 5
• Search: ((yeast[Title]) AND cold shock[Title]) AND microarray[Title]
  • Search Results: 0
• Specififying yeast and cold shock to be in the title returned significantly less results (and more appropriate results), then just using these terms in a query. However, when microarray being in the title was added to the advanced search, no results were returned (meaning the search was too specific).

Google Scholar

• Search: allintitle: yeast cold shock
  • Search Results: 18
• Search: allintitle: yeast cold shock microarray
  • Search Results: 5
• Using the search for yeast and cold shock in the title returned a good amount more articles than this sam advances search in PubMed. However, once again, when microarray being in the title was added to the search specifications, there was again no results.

Web of Science

• Search: TI=(yeast) AND TI=(cold shock)
  • Search Results: 8
• Search: TI=(yeast) AND TI=(cold) AND TI=(shock)
  • Search Results: 8
• Search: TI=(yeast) AND TI=(cold shock) AND TI=(microarray)
  • Search Results: 0
• This advanced search created very similar results to the advanced search from PubMed. In this query, the TI= indicated that the text in the parentheses was in the title. The first two searches resulted in fairly relevant articles, although most appeared to already have been found. However, adding microarray to the title made the search too restrictive to yield any results.

Prospective Search Results

• 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?
    • 144
  • How many articles cite this article?
    • 77
• 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?
    • 125
  • How many articles cite this article?
    • 108
• 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?
    • 76
  • How many articles cite this article?
    • 258

Acknowledgements

1. I worked in class with my teammate Antonio to find relevant articles to use in the annotated bibliography. I also texted Antonio during the weekend to clear up some confusion regarding how to fill out different parts of the bibliography entries.
2. I checked base with my teammates Simon and Eddie in class on Thursday to make sure our team page was filled out correctly, and also that they knew were to enter their information each week on the page.
3. Dr. Dahlquist for providing information on how to properly fill out the annotated bibliography.
   

Qlanners (talk) 00:26, 14 November 2017 (PST)

References

LMU BioDB 2017. (2017). Week 11. Retrieved November 9, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11

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