Difference between revisions of "The Class Whoopers"

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(→‎Annotated Bibliography: ordered!)
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== Annotated Bibliography ==
 
== Annotated Bibliography ==
 
* [[Week 10]] Creation of page and combined annotated bibliography (midnight 11/10)
 
* [[Week 10]] Creation of page and combined annotated bibliography (midnight 11/10)
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===Brandon's Citations===
+
=== Genome Sequencing Papers ===
−
Genome Sequencing Paper:
+
  
−
Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11
+
*Zhang, S., Xu, Y., Zhou, Z., Wang, S., Yang, R., Wang, J., & Wang, L. (2011). Complete Genome Sequence of Bordetella Pertussis CS, a Chinese Pertussis Vaccine Strain. Journal of Bacteriology, 193(15), 4017-4018. doi: 10.1128/JB.05184-11
 
* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/21622744
 
* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/21622744
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147532/
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147532/
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* Did LMU pay a fee for this article: no
 
* Did LMU pay a fee for this article: no
  
−
Microarray Papers:
+
*Boinett, C. J., Harris, S. R., Langridge, G. C., Trainor, E. A., Merkel, T. J., & Parkhill, J. (2015). Complete genome sequence of Bordetella pertussis D420. Genome announcements, 3(3), e00657-15.
 +
*The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
 +
*The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
 +
*The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
 +
*The link to the full PDF version of the article from the publisher web site: http://genomea.asm.org/content/3/3/e00657-15.full.pdf+html
 +
*The authors won't he right of the copyright under a [http://creativecommons.org/ Creative Commons] license.
 +
*The article is available "Open Access".
 +
*Published by the American Society for Microbiology online.
 +
*Article is available online only and LMU has paid a subscription for access to this article.
  
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King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150
+
=== Microarray Papers ===
−
* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/23776625
+
−
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679012/
+
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* Publisher Full Text (HTML):  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150
+
−
* Publisher Full Text (PDF):  http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0066150&representation=PDF
+
−
* Copyright: © 2013 King et al. 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 author and source are credited. (info found [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150 here])
+
−
* Publisher: PLOS ONE (respected open access organization)
+
−
* Availability: online only
+
−
* Did LMU pay a fee for this article: no
+
−
* Web site where the data resides: [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress]
+
  
 +
===== 1 =====
 
Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE 2014;9(12):e115243. doi: 10.1371/journal.pone.0115243
 
Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE 2014;9(12):e115243. doi: 10.1371/journal.pone.0115243
 
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560  
 
* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560  
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* Web site where the data resides: [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
 
* Web site where the data resides: [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
  
−
===Lena's Citations===
+
===== 2 =====
−
Genome Sequencing Paper:
+
−
 
+
−
*Boinett, C. J., Harris, S. R., Langridge, G. C., Trainor, E. A., Merkel, T. J., & Parkhill, J. (2015). Complete genome sequence of Bordetella pertussis D420. Genome announcements, 3(3), e00657-15.
+
−
*The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
+
−
*The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
+
−
*The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
+
−
*The link to the full PDF version of the article from the publisher web site: http://genomea.asm.org/content/3/3/e00657-15.full.pdf+html
+
−
*The authors won't he right of the copyright under a [http://creativecommons.org/ Creative Commons] license.
+
−
*The article is available "Open Access".
+
−
*Published by the American Society for Microbiology online.
+
−
*Article is available online only and LMU has paid a subscription for access to this article.
+
−
 
+
−
Microarray Paper:
+
−
 
+
 
*Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11
 
*Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11
 
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
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*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
  
−
Microarray Paper:
+
===== 3 =====
 +
King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150
 +
* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/23776625
 +
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679012/
 +
* Publisher Full Text (HTML):  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150
 +
* Publisher Full Text (PDF):  http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0066150&representation=PDF
 +
* Copyright: © 2013 King et al. 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 author and source are credited. (info found [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150 here])
 +
* Publisher: PLOS ONE (respected open access organization)
 +
* Availability: online only
 +
* Did LMU pay a fee for this article: no
 +
* Web site where the data resides: [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress]
 +
 
 +
 
 +
===== 4 (note, all of these papers involve species other than Bordetella pertussis) =====
  
−
*Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785.
+
* Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785.
 
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
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* Did LMU pay a fee for this article: yes
 
* Did LMU pay a fee for this article: yes
 
*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
−
 
−
=== Nicole Anguiano ===
 
  
 
* Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81
 
* Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81
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# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 
# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 
* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/
 
* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/
−
 
  
 
* Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
 
* Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
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* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
 
* Link to microarray data: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
  
−
===Mahrad Saeedi===
+
*King, Audrey J et al. “Comparative Genomic Profiling of Dutch Clinical Bordetella Pertussis isolates Using DNA Microarrays: Identification of Genes Absent from Epidemic Strains.” BMC Genomics 9 (2008): 311. PMC. Web. 10 Nov. 2015.
−
 
+
−
Genome Sequencing Paper:
+
−
 
+
−
King, Audrey J et al. “Comparative Genomic Profiling of Dutch Clinical Bordetella Pertussis isolates Using DNA Microarrays: Identification of Genes Absent from Epidemic Strains.” BMC Genomics 9 (2008): 311. PMC. Web. 10 Nov. 2015.
+
−
 
+
 
* PubMed Abstract:  http://www.biomedcentral.com/1471-2164/9/311#abs
 
* PubMed Abstract:  http://www.biomedcentral.com/1471-2164/9/311#abs
 
* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/>
 
* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481270/>
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* Did LMU pay a fee for this article: no
 
* Did LMU pay a fee for this article: no
  
−
Microarray Paper:
+
*Nakamura, Mari M. et al. “Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella Pertussis  .” Infection and Immunity 74.10 (2006): 5537–5548. PMC. Web. 10 Nov. 2015.
−
 
+
−
Nakamura, Mari M. et al. “Growth Phase- and Nutrient Limitation-Associated Transcript Abundance Regulation in Bordetella Pertussis  .” Infection and Immunity 74.10 (2006): 5537–5548. PMC. Web. 10 Nov. 2015.
+
−
 
+
 
* PubMed Abstract:  <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/?report=reader#__abstractid499869title>
 
* PubMed Abstract:  <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/?report=reader#__abstractid499869title>
 
* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/>
 
* PubMed Central: <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1594893/>
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* Availability: online access
 
* Availability: online access
 
* Did LMU pay a fee for this article: no
 
* Did LMU pay a fee for this article: no
−
 
  
 
== Deliverables ==
 
== Deliverables ==

Revision as of 04:26, 10 November 2015

The Class Whoopers Crew Page

The_Class_Whoopers

  • Species: Bordetella pertussis

Crew Members

Team Goals for the Week of 11/3

  • For all:
    • Make an annotated bibliography of 1-2 articles (preferably 2) on Bordetella pertussis following the instructions here, and post them on your individual journal page!
    • Once everyone has done their bibliographies, we'll discuss a ranking of which we think are the best ones and list them below in ranked order. Try to find different articles from everyone else so we have the maximum number of options.

Meetings!

  • Monday, November 9, 8pm, Seaver 120

Annotated Bibliography

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)

Genome Sequencing Papers

Microarray Papers

1

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE 2014;9(12):e115243. doi: 10.1371/journal.pone.0115243

2
3

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150


4 (note, all of these papers involve species other than Bordetella pertussis)
  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?
  1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
  2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

Deliverables

  • GenMAPP Gene Database for assigned species (.gdb)
  • ReadMe file to accompany the Gene Database (.pdf)
  • Sample ReadMe in Word format: ReadMe_Vc-Std_External_20131122.zip
  • Include Gene Database Schema diagram in ReadMe
  • Sample schema in Adobe Illustrator format: Vibrio_schema_20101022.zip
  • Gene Database Testing Report for final submitted Gene Database (print from wiki to .pdf file)
  • Processed and analyzed DNA microarray dataset (.xls)
  • GenMAPP Expression Dataset file (.gex)
  • Filtered MAPPFinder Results (.xls)
  • Sample MAPP file of a relevant biological pathway for your species (.mapp)
  • Group Report describing the creation of the Gene Database and the biological analysis of the data (.doc or .pdf)
  • PowerPoint presentation (.ppt, given on Tuesday, December 15)


Links

GenMAPP Analysis of Bordetella pertussis Microarray Data

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

Journal Entries

Class Whoopers Individual Journal Entries
Brandon Klein Week 11 Week 12 Week 14 Week 15
Lena Olufson Week 11 Week 12 Week 14 Week 15
Mahrad Saeedi Week 11 Week 12 Week 14 Week 15
Team Entries Week 11 Week 12 Week 14 Week 15

Group Members

Team Weekly Assignments

  • Week 10 Creation of page and combined annotated bibliography (midnight 11/10)
  • Week 11 (midnight 11/17)
  • Week 12 (midnight 11/24)
  • Week 14 (midnight 12/8)
  • Week 15 (midnight 12/15)
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