Difference between revisions of "GÉNialOMICS Week 10"
From LMU BioDB 2015
(Added some syntax to my bibliography entry.) |
(→Ranked Microarray Papers' Annotated Bibliogrpahies: some formatting) |
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==Ranked Microarray Papers' Annotated Bibliogrpahies== | ==Ranked Microarray Papers' Annotated Bibliogrpahies== | ||
| − | '''Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. ''BMC genomics'', 12(1), 373. doi:10.1186/1471-2164-12-373''' | + | #'''Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. ''BMC genomics'', 12(1), 373. doi:10.1186/1471-2164-12-373''' |
| − | * Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator: | + | #* Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator: |
| − | ** Control: the wild-type J2315 strain | + | #** Control: the wild-type J2315 strain |
| − | ** Treatment: mutant strains which showed antibiotic resistance | + | #** Treatment: mutant strains which showed antibiotic resistance |
| − | ** Treatment: ET12 outbreak isolates, described as "pan-resistant" | + | #** Treatment: ET12 outbreak isolates, described as "pan-resistant" |
| − | * Three biological replicates were used for each experiment. | + | #* Three biological replicates were used for each experiment. |
| − | * The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the [https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2747/files/ ArrayExpress entry]. | + | #* The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the [https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2747/files/ ArrayExpress entry]. |
| − | * PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21781329 | + | #* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21781329 |
| − | * PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/ | + | #* PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/ |
| − | * Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373 | + | #* Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373 |
| − | * Publisher Full Text (PDF): http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf | + | #* Publisher Full Text (PDF): http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf |
| − | * Copyright: 2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited." | + | #* Copyright: 2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited." |
| − | * Publisher: BioMedCentral, respected Open Access organization. | + | #* Publisher: BioMedCentral, respected Open Access organization. |
| − | * Availability: Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article. | + | #* Availability: Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article. |
| − | * Did LMU pay a fee for this article: No - open access. | + | #* Did LMU pay a fee for this article: No - open access. |
| + | #*How many articles does this article cite? | ||
| + | #*How many articles cite this article? | ||
| + | #*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? | ||
| + | #Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08 | ||
| + | #* The link to the abstract from [http://www.ncbi.nlm.nih.gov/pubmed PubMed]. [http://www.ncbi.nlm.nih.gov/pubmed/18931103] | ||
| + | #* The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral]. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612433/] | ||
| + | #* The link to the full text of the article (HTML format) from the publisher web site. [http://jb.asm.org/content/191/1/261.long] | ||
| + | #* The link to the full PDF version of the article from the publisher web site. [http://jb.asm.org/content/191/1/261.full.pdf+html] | ||
| + | #* Who owns the rights to the article? '''American Society for Microbiology''' | ||
| + | #** Does the journal own the copyright? '''Yes''' | ||
| + | #** Do the authors own the copyright? '''No''' | ||
| + | #** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license? '''No''' | ||
| + | #** Is the article available “Open Access”? '''Yes''' | ||
| + | #* What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.] '''American Society for Microbiology which is a scientific society''' | ||
| + | #* Is this article available in print or online only? '''It is both available in print and online.''' | ||
| + | #* Has LMU paid a subscription or other fee for your access to this article? '''Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.''' | ||
| + | #* How many articles does this article cite? '''It has 150 cited references.''' | ||
| + | #* How many articles cite this article? '''It is cited 128 times.''' | ||
| + | #* 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? '''A lot of the papers revolved around antibiotic resistance and therapeutic strategies.''' | ||
Revision as of 03:04, 10 November 2015
Genome Paper Annotated Bibliography
The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients
- The complete bibliographic reference in the APA style (see the Writing LibGuide) You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08
- The link to the abstract from PubMed. [1]
- The link to the full text of the article in PubMedCentral. [2]
- The link to the full text of the article (HTML format) from the publisher web site. [3]
- The link to the full PDF version of the article from the publisher web site. [4]
- Who owns the rights to the article? American Society for Microbiology
- Does the journal own the copyright? Yes
- Do the authors own the copyright? No
- Do the authors own the rights under a Creative Commons license? No
- Is the article available “Open Access”? Yes
- What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here. American Society for Microbiology which is a scientific society
- Is this article available in print or online only? It is both available in print and online.
- Has LMU paid a subscription or other fee for your access to this article? Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.
- How many articles does this article cite? It has 150 cited references.
- How many articles cite this article? It is cited 128 times.
- 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? A lot of the papers revolved around antibiotic resistance and therapeutic strategies.
Ranked Microarray Papers' Annotated Bibliogrpahies
- Sass, A., Marchbank, A., Tullis, E., LiPuma, J. J., & Mahenthiralingam, E. (2011) Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis. BMC genomics, 12(1), 373. doi:10.1186/1471-2164-12-373
- Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
- Control: the wild-type J2315 strain
- Treatment: mutant strains which showed antibiotic resistance
- Treatment: ET12 outbreak isolates, described as "pan-resistant"
- Three biological replicates were used for each experiment.
- The raw data does not appear to be directly linked from the article itself. The supplement includes a summary spreadsheet, which only displays values for fold-changes that were statistically significant. However both the raw and processed data files are available on the ArrayExpress entry.
- PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/21781329
- PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155924/
- Publisher Full Text (HTML): http://www.biomedcentral.com/1471-2164/12/373
- Publisher Full Text (PDF): http://www.biomedcentral.com/content/pdf/1471-2164-12-373.pdf
- Copyright: 2011 Sass et al; licensee BioMed Central Ltd. "This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited."
- Publisher: BioMedCentral, respected Open Access organization.
- Availability: Article does not initially appear to be available in print, however, BioMedCentral's website mentions that "high quality, bound reprints" can be purchased for any published article.
- Did LMU pay a fee for this article: No - open access.
- How many articles does this article cite?
- How many articles cite this article?
- 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?
- Transcriptomic analysis was performed using the following strains, after exposure to different antibiotics in the presence of an antibiotic potentiator:
- Holden, M. T. G., Seth-Smith, H. M. B., Crossman, L. C., Sebaihia, M., Bentley, S. D., Cerdeño-Tárraga, A. M., … Parkhill, J. (2009). The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients . Journal of Bacteriology, 191(1), 261–277. http://doi.org/10.1128/JB.01230-08
- The link to the abstract from PubMed. [5]
- The link to the full text of the article in PubMedCentral. [6]
- The link to the full text of the article (HTML format) from the publisher web site. [7]
- The link to the full PDF version of the article from the publisher web site. [8]
- Who owns the rights to the article? American Society for Microbiology
- Does the journal own the copyright? Yes
- Do the authors own the copyright? No
- Do the authors own the rights under a Creative Commons license? No
- Is the article available “Open Access”? Yes
- What organization is the publisher of the article? What type of organization is it? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here. American Society for Microbiology which is a scientific society
- Is this article available in print or online only? It is both available in print and online.
- Has LMU paid a subscription or other fee for your access to this article? Well I first looked at this article through web of science which LMU does pay for but looking at the article through PubMed, PubMed central and the publisher website was free.
- How many articles does this article cite? It has 150 cited references.
- How many articles cite this article? It is cited 128 times.
- 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? A lot of the papers revolved around antibiotic resistance and therapeutic strategies.
