Difference between revisions of "Heavy Metal HaterZ"
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===Our Genome Paper=== | ===Our Genome Paper=== | ||
| − | + | Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. ''Nature biotechnology, 20''(11), 1118-1123. doi:10.1038/nbt749 | |
| − | * | + | *The [http://www.ncbi.nlm.nih.gov/pubmed/?term=Genome+sequence+of+the+dissimilatory+metal+ion%E2%80%93reducing+bacterium+Shewanella+oneidensis abstract] from PubMed. |
| − | * | + | *The full text of the article in PubMedCentral : Not available. |
| − | *[http://www.nature.com/nbt/journal/v20/n11/full/nbt749.html | + | *The [http://www.nature.com/nbt/journal/v20/n11/full/nbt749.html full text] of the article from the publisher web site. (The HTML version was not available.) |
| − | *[http://www.nature.com/nbt/journal/v20/n11/pdf/nbt749.pdf PDF | + | *The [http://www.nature.com/nbt/journal/v20/n11/pdf/nbt749.pdf full PDF version] of the article from the publisher web site. |
| − | * | + | *Who owns the rights to the article? |
| − | * | + | **The Nature Publishing Group, which is the publisher of this article, according to this [https://s100.copyright.com/AppDispatchServlet?publisherName=NPG&publication=Nature%20Biotechnology&title=Genome%20sequence%20of%20the%20dissimilatory%20metal%20ion-reducing%20bacterium%20Shewanella%20oneidensis&author=John%20F.%20Heidelberg,%20Ian%20T.%20Paulsen,%20Karen%20E.%20Nelson,%20Eric%20J.%20Gaidos,%20William%20C.%20Nelson%20et%20al.&contentID=10.1038/nbt749&publicationDate=10/07/2002&volumeNum=20&issueNum=11&numPages=6&pageNumbers=pp1118-1123 site]. |
| − | * | + | *Do the authors own the rights under a Creative Commons license? |
| − | *Has LMU paid subscription | + | **Yes, according to this [http://oaspa.org/member/nature-publishing-group-palgrave-macmillan/ site]. |
| + | *Is the article available “Open Access”? | ||
| + | **According to [http://oaspa.org/membership/members/ this site], the article is available "Open Access". | ||
| + | *What organization is the publisher of the article? What type of organization is it? | ||
| + | **According to the site above, this publisher is a "Professional OA Publisher (Large)". | ||
| + | *Is this article available in print or online only? | ||
| + | **Online only. It was published online in November, 2002. | ||
| + | *Has LMU paid a subscription or other fee for your access to this article? | ||
| + | **No. | ||
| + | *We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar. | ||
| + | **Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for. | ||
*How many articles does this article cite? | *How many articles does this article cite? | ||
| − | ** | + | **This article has 41 cited references within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site]. |
*How many articles cite this article? | *How many articles cite this article? | ||
| − | ** | + | **It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this [https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=3&SID=3Evs6J6HvCojNOHG6K3&page=1&doc=3 site]. |
*Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? | *Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced? | ||
| − | ** | + | **Examples of titles that reference the genome paper: |
***Environmental genome shotgun sequencing of the Sargasso Sea | ***Environmental genome shotgun sequencing of the Sargasso Sea | ||
| − | |||
***Deciphering the evolution and metabolism of an anammox bacterium from a community genome | ***Deciphering the evolution and metabolism of an anammox bacterium from a community genome | ||
| − | + | ***Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments | |
| − | ***Genome of Geobacter sulfurreducens: | + | ***More can be found by clicking this [https://apps.webofknowledge.com/summary.do?product=WOS&parentProduct=UA&search_mode=CitingArticles&qid=8&SID=3Evs6J6HvCojNOHG6K3&page=1&action=sort&sortBy=LC.D;PY.D;AU.A.en;SO.A.en;VL.D;PG.A&showFirstPage=1 link]. |
| − | ** | + | **These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds. |
| − | === | + | ===Microarray Papers=== |
| − | * | + | *Datasets can be found at this [https://www.ebi.ac.uk/arrayexpress/browse.html?keywords=&organism=Shewanella+oneidensis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array= link]. |
| − | + | ||
*E-GEOD-15334 - Emily | *E-GEOD-15334 - Emily | ||
*E-GEOD-21044 - Josh | *E-GEOD-21044 - Josh | ||
Revision as of 02:15, 10 November 2015
Contents
Shewanella oneidensis
Our Gene Database Testing Report
Group Paper - File:Final Report 20151218 2 HMH.docx
Group Members
- Coder: Mary Alverson
- GenMAPP User & Project Manager: Ron Legaspi
- Quality Assurance: Josh Kuroda
- GenMAPP User: Emily Simso
Important Links
Our Files
Our Deliverables
| Gene Database Project Links | |||||||
|---|---|---|---|---|---|---|---|
| Overview | Deliverables | Reference Format | Guilds | Project Manager | GenMAPP User | Quality Assurance | Coder |
| Teams | Heavy Metal HaterZ | The Class Whoopers | GÉNialOMICS | Oregon Trail Survivors | |||
| Individual Journal Entries | ||||
|---|---|---|---|---|
| Mary Alverson | Week 11 | Week 12 | Week 14 | Week 15 |
| Emily Simso | Week 11 | Week 12 | Week 14 | Week 15 |
| Ron Legaspi | Week 11 | Week 12 | Week 14 | Week 15 |
| Josh Kuroda | Week 11 | Week 12 | Week 14 | Week 15 |
Week 10 Assignment : Annotated Bibliography
Individual Biographies
Our Genome Paper
Heidelberg, J. F., Paulsen, I. T., Nelson, K. E., Gaidos, E. J., Nelson, W. C., Read, T. D., ... & Fraser, C. M. (2002). Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis. Nature biotechnology, 20(11), 1118-1123. doi:10.1038/nbt749
- The abstract from PubMed.
- The full text of the article in PubMedCentral : Not available.
- The full text of the article from the publisher web site. (The HTML version was not available.)
- The full PDF version of the article from the publisher web site.
- Who owns the rights to the article?
- The Nature Publishing Group, which is the publisher of this article, according to this site.
- Do the authors own the rights under a Creative Commons license?
- Yes, according to this site.
- Is the article available “Open Access”?
- According to this site, the article is available "Open Access".
- What organization is the publisher of the article? What type of organization is it?
- According to the site above, this publisher is a "Professional OA Publisher (Large)".
- Is this article available in print or online only?
- Online only. It was published online in November, 2002.
- Has LMU paid a subscription or other fee for your access to this article?
- No.
- We performed a search in the ISI Web of Science/Knowledge database by typing in the title "Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis" to the search bar.
- Three articles came up as results. The first two articles title's did not exactly match, and were cited under 15 times each. The third article was the article we were searching for.
- How many articles does this article cite?
- This article has 41 cited references within the Web of Science Core Collection, according to this site.
- How many articles cite this article?
- It has been cited 1079 times in all databases, and 426 within the Web of Science Core Collection, according to this site.
- Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
- Examples of titles that reference the genome paper:
- Environmental genome shotgun sequencing of the Sargasso Sea
- Deciphering the evolution and metabolism of an anammox bacterium from a community genome
- Genome of Geobacter sulfurreducens: Metal reduction in subsurface environments
- More can be found by clicking this link.
- These papers include studying within in the species, finding out the genomes of other species, as well as the metabolic versatility of microorganisms and metal ion reduction in environments. This shows that a sequenced genome can aide in experiments of many kinds.
- Examples of titles that reference the genome paper:
Microarray Papers
- Datasets can be found at this link.
- E-GEOD-15334 - Emily
- E-GEOD-21044 - Josh
- E-GEOD-15657 - Ron
- E-MTAB-266 - Mary
- E-MTAB-319 - Mary
