Difference between revisions of "GÉNialOMICS Week 10"

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(→‎Ranked Microarray Papers' Annotated Bibliogrpahies: bolded citations)
(→‎Ranked Microarray Papers' Annotated Bibliogrpahies: added Anu's biblio)
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#* How many articles cite this article? '''It is cited 128 times.'''
 
#* 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.'''
 
#* 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.'''
 +
# '''Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. ''PLoS One'', 8(3), e58943.'''
 +
#* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
 +
#* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
 +
#* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
 +
#**Cannot find HTML format on publisher web site.
 +
#* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
 +
#* Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
 +
#* 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? Yes.
 +
#* Is the article available “Open Access”? Yes.
 +
#* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
 +
#* Is this article available in print or online only? Available in print and online.
 +
#* Has LMU paid a subscription or other fee for your access to this article? No.
 +
#* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 +
#* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
 +
#* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
 +
#* How many articles does this article cite? This article has 34 cited references.
 +
#* How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
 +
#* 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? Most of the articles are related to  antimicrobial therapy, tolerance, and resistance.
 +
# Mira, N. P., Madeira, A., Moreira, A. S., Coutinho, C. P., & Sá-Correia, I. (2011). Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients’ airways and antimicrobial therapy. PLoS One, 6(12), e28831.
 +
#* The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Genomic+Expression+Analysis+Reveals+Strategies+of+Burkholderia+cenocepacia+to+Adapt+to+Cystic+Fibrosis+Patients%27+Airways+and+Antimicrobial+Therapy
 +
#* The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3244429/
 +
#* The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028831
 +
#**Cannot find HTML format on publisher web site.
 +
#* The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0028831&representation=PDF
 +
#* Who owns the rights to the article? Authors of the article: Nuno P. Mira, Andreia Madeira, Ana Sílvia Moreira, Carla P. Coutinho, Isabel Sá-Correia
 +
#* 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? Yes.
 +
#* Is the article available “Open Access”? Yes.
 +
#* What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
 +
#* Is this article available in print or online only? Available in print and online.
 +
#* Has LMU paid a subscription or other fee for your access to this article? No.
 +
#* Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-809/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 +
#* What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The "treatments" strains were collected from a cystic fibrosis patient. The strain "IST439" was collected first, and the strain "IST4113" was collected 3 years later. The control for this experiment is reference data of Burkholderia cenocepacia.
 +
#* Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? There were 3 replicates of each of the 2 strains and 6 replicates of the reference strain. It is unclear whether these are biological or technical replicates.
 +
#* How many articles does this article cite? This article has 75 cited references.
 +
#* How many articles cite this article? This article has been cited 22 times in All Databases, and 22 times in Web of Science Core Collection.
 +
#* 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? Most articles are related to Burkholderia's pathogenesis and antibiotic resistance.

Revision as of 03:40, 10 November 2015

Ranked Microarray Papers' Annotated Bibliogrpahies

  1. 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?
  2. 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.
  3. Van Acker, H., Sass, A., Bazzini, S., De Roy, K., Udine, C., Messiaen, T., ... & Coenye, T. (2013). Biofilm-grown Burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species. PLoS One, 8(3), e58943.
    • The link to the abstract from PubMed: http://www.ncbi.nlm.nih.gov/pubmed/?term=Biofilm-Grown+Burkholderia+cepacia+Complex+Cells+Survive+Antibiotic+Treatment+by+Avoiding+Production+of+Reactive+Oxygen+Species
    • The link to the full text of the article in PubMedCentral: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596321/
    • The link to the full text of the article (HTML format) from the publisher web site: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
      • Cannot find HTML format on publisher web site.
    • The link to the full PDF version of the article from the publisher web site: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0058943&representation=PDF
    • Who owns the rights to the article? Authors of the article: Heleen Van Acker, Andrea Sass, Silvia Bazzini, Karen De Roy, Claudia Udine, Thomas Messiaen, Giovanna Riccardi, Nico Boon, Hans J. Nelis, Eshwar Mahenthiralingam, Tom Coenye
    • 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? Yes.
    • Is the article available “Open Access”? Yes.
    • What organization is the publisher of the article? What type of organization is it? Public Library of Science, Professional OA Publisher, Member of Open Access Scholarly Publishers Association
    • Is this article available in print or online only? Available in print and online.
    • Has LMU paid a subscription or other fee for your access to this article? No.
    • Where does MicroArray Data reside? https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3532/?keywords=&organism=Burkholderia+cenocepacia&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
    • What experiment was performed? What was the "treatment" and what was the "control" in the experiment? The experiment hoped to test whether persister cells are present in Burkholderia cepacia complex (Bcc) biofilms, what the molecular basis of antimicrobial tolerance in Bcc persisters is, and how persisters can be eradicated from Bcc biofilms. Burkholderia cenocepacia biofilms were treated with 1024 µg/ml of tobramycin in the treatment group. The control group did not receive any tobramycin.
    • Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each? 2 technical replicates were made across 5 biological replicates for the control, and 2 technical replicates of 3 biological replicates of the treatments.
    • How many articles does this article cite? This article has 34 cited references.
    • How many articles cite this article? This article is cited 17 times in All Databases, and 17 time in Web of Science Core Collection.
    • 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? Most of the articles are related to antimicrobial therapy, tolerance, and resistance.
  4. Mira, N. P., Madeira, A., Moreira, A. S., Coutinho, C. P., & Sá-Correia, I. (2011). Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients’ airways and antimicrobial therapy. PLoS One, 6(12), e28831.
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