Information for this assignment can be found in the [[Week 10 | Week 10 assignment page]].

Information was further compiled into the group page for the [[Team_4 | Oregon Trail Survivors]].

Information was further compiled into the group page for the [[Team_4 | Oregon Trail Survivors Week 10]].

===Creating the Annotated Bibliography===

***I searched "''Shigella flexneri''" as a topic and added "genome" and "RNA" as topics. This gave me 91 results. I added the topic "cy3 cy5" for the dyes and got 2 results.

====Overview of Genome Paper====

===Overview of Genome Paper===

Dr. Dahlquist was very helpful in this portion of the assignment. First, in PubMed, I went to the [http://www.ncbi.nlm.nih.gov/pubmed/advanced Advanced Search]. Then I entered "''Shigella flexneri'' genome" and filtered by results with those keywords in the Title/Abstract. This gave me 5 results. I clicked on the first one ([https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=23&SID=1FSiDfIe2DsTtPPNrbx&page=1&doc=1 "Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence"]). I copied and pasted this into Web of Science and upon clicking on the article I saw that it had 13 cited references. I visited this reference list I found a paper called [https://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1FSiDfIe2DsTtPPNrbx&search_mode=CitedFullRecord&isickref=WOS:000182501500055 "Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T"] with 73 cited references, dated May 2003. To see if there was an older paper that this paper possibly got its original genome sequence from I visited its reference list. There was a paper dated from 2002 called [https://apps.webofknowledge.com/CitedFullRecord.do?product=WOS&colName=WOS&SID=1FSiDfIe2DsTtPPNrbx&search_mode=CitedFullRecord&isickref=WOS:000178826700021 "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157"] that looked promising and it was dated October 2002. Our group selected this paper as our genome paper as it was the oldest and most likely to be the basis for research in more recent papers.

This search yielded 7 results, but only 5 had above 3 assays and were considered viable candidates. Our group randomly assigned the data and corresponding papers to a different group member.

===~~Microarray Paper~~===

===Annotated Bibliography===

Peng J, Yang J, Jin Q (2011) An Integrated Approach for Finding Overlooked Genes in Shigella. PLoS ONE 6(4): e18509. doi: 10.1371/journal.pone.0018509