Difference between revisions of "Jkuroda Week 10"

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=== Annotated Bibliography of Genomics Papers for ''Shewanella oneidensis'' ===
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* Use a keyword search for each of these databases/tools and answer the following: 
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** '''PubMed'''
 +
*** What original keyword(s) did you use?  How many results did you get?
 +
**** <code>"Shewanella oneidensis"</code>
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**** 793 results.
 +
*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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**** <code>(("shewanella"[MeSH Terms] OR "shewanella"[All Fields]) AND oneidensis[All Fields]) AND ("2010/11/07"[PDat] : "2015/11/05"[PDat] AND English[lang])</code>
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**** 387 results
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** '''Google Scholar'''
 +
*** What original keyword(s) did you use?  How many results did you get?
 +
**** <code>"Shewanella oneidensis"</code>
 +
**** 13,200 results
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*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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**** <code>"Shewanella oneidensis genomics"</code> ''since 2014''
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**** 1,430 results
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** '''Web of Science'''
 +
*** What original keyword(s) did you use?  How many results did you get?
 +
**** <code>"Shewanella oneidensis"</code>
 +
**** 6,383 results
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*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
 +
**** <code>TOPIC: (Shewanella oneidensis) Refined by: LANGUAGES: ( ENGLISH ) AND RESEARCH DOMAINS: ( SCIENCE TECHNOLOGY ) AND LANGUAGES: ( ENGLISH ) AND RESEARCH AREAS: ( BIOCHEMISTRY MOLECULAR BIOLOGY OR MICROBIOLOGY OR GENETICS HEREDITY OR BIOTECHNOLOGY APPLIED MICROBIOLOGY OR SCIENCE TECHNOLOGY OTHER TOPICS OR ENVIRONMENTAL SCIENCES ECOLOGY OR CHEMISTRY OR CELL BIOLOGY )</code>
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**** 5,835 results
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==Microarray Paper==
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* Used ArrayExpress and searched for relevant microarray papers using filters.
 +
* Wanted to find papers with bigger assay numbers so I sorted by that column.
 +
* Among our group members we decided which papers to focus on.
 +
* I chose <code>E-GEOD-21044 - delta-arcS versus wild-type</code>
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===Bibliographic Entry===
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* '''APA:''' Lassak J, Henche AL, Binnenkade L, Thormann KM. (2010). ArcS is the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. ''Applied and Environmental Microbiology'', 76(10), 3263-3274.
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* [http://www.ncbi.nlm.nih.gov/pubmed/?term=ArcS+is+the+cognate+sensor+kinase+in+an+atypical+Arc+system+of+Shewanella+oneidensis+MR-1 '''PubMed''']
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* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2869118/ '''PMC''']
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* [http://aem.asm.org/content/76/10/3263.full '''Full Text''']
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* [http://aem.asm.org/content/76/10/3263.full.pdf+html '''PDF Version''']
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* The American Society for Microbiology owns the copyright. The article is not open-access.
 +
* The publisher is the American Society for Microbiology. It is a scientific society.
 +
* This article is available in the printed and on-line journals.
 +
* LMU has not paid for my access.
 +
* This article has 76 citations.
 +
* According to the ''Web of Science'', this article is cited by 35 other articles.
 +
* Looking at the titles of the other articles, it seems like most research has been focused on a two-component system present in shewanella oneidensis as well as anaerobic and aerobic respiration.
 +
* [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21044/E-GEOD-21044.raw.1.zip '''Raw microarray data''']
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* [https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-21044/E-GEOD-21044.processed.1.zip '''Processed microarray data''']
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* The experiment looked to find more information about the Arc two-component system of shewanella oneidensis by shifting oxygen levels. The treatment in the experiment was the changing levels of oxygen.  The control were strains of shewanella oneidensis MR-1 wild type cells.
 +
* Expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells.
  
 
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Latest revision as of 04:58, 9 November 2015

Annotated Bibliography of Genomics Papers for Shewanella oneidensis

  • 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?
        • "Shewanella oneidensis"
        • 793 results.
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • (("shewanella"[MeSH Terms] OR "shewanella"[All Fields]) AND oneidensis[All Fields]) AND ("2010/11/07"[PDat] : "2015/11/05"[PDat] AND English[lang])
        • 387 results
    • Google Scholar
      • What original keyword(s) did you use? How many results did you get?
        • "Shewanella oneidensis"
        • 13,200 results
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • "Shewanella oneidensis genomics" since 2014
        • 1,430 results
    • Web of Science
      • What original keyword(s) did you use? How many results did you get?
        • "Shewanella oneidensis"
        • 6,383 results
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • TOPIC: (Shewanella oneidensis) Refined by: LANGUAGES: ( ENGLISH ) AND RESEARCH DOMAINS: ( SCIENCE TECHNOLOGY ) AND LANGUAGES: ( ENGLISH ) AND RESEARCH AREAS: ( BIOCHEMISTRY MOLECULAR BIOLOGY OR MICROBIOLOGY OR GENETICS HEREDITY OR BIOTECHNOLOGY APPLIED MICROBIOLOGY OR SCIENCE TECHNOLOGY OTHER TOPICS OR ENVIRONMENTAL SCIENCES ECOLOGY OR CHEMISTRY OR CELL BIOLOGY )
        • 5,835 results

Microarray Paper

  • Used ArrayExpress and searched for relevant microarray papers using filters.
  • Wanted to find papers with bigger assay numbers so I sorted by that column.
  • Among our group members we decided which papers to focus on.
  • I chose E-GEOD-21044 - delta-arcS versus wild-type

Bibliographic Entry

  • APA: Lassak J, Henche AL, Binnenkade L, Thormann KM. (2010). ArcS is the cognate sensor kinase in an atypical Arc system of Shewanella oneidensis MR-1. Applied and Environmental Microbiology, 76(10), 3263-3274.
  • PubMed
  • PMC
  • Full Text
  • PDF Version
  • The American Society for Microbiology owns the copyright. The article is not open-access.
  • The publisher is the American Society for Microbiology. It is a scientific society.
  • This article is available in the printed and on-line journals.
  • LMU has not paid for my access.
  • This article has 76 citations.
  • According to the Web of Science, this article is cited by 35 other articles.
  • Looking at the titles of the other articles, it seems like most research has been focused on a two-component system present in shewanella oneidensis as well as anaerobic and aerobic respiration.
  • Raw microarray data
  • Processed microarray data
  • The experiment looked to find more information about the Arc two-component system of shewanella oneidensis by shifting oxygen levels. The treatment in the experiment was the changing levels of oxygen. The control were strains of shewanella oneidensis MR-1 wild type cells.
  • Expression profiles of three independent replicates of Shewanella oneidensis MR-1 delta-arcS were compared to three independent replicates of Shewanella oneidensis MR-1 wild type cells.

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