Difference between revisions of "The Class Whoopers"

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(Updated Team Goals)
(Updated Genome Sequencing Paper)
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Neither of these papers is the ''first'' to report the genome sequence of ''B. pertussis.''  The paper that you will want to use is [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html this one].  I found it by looking at the introduction and references of the Zhang et. al (2011) paper.  For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003).  You will use the Parkhill paper for your project.  ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:54, 10 November 2015 (PST)''
 
Neither of these papers is the ''first'' to report the genome sequence of ''B. pertussis.''  The paper that you will want to use is [http://www.nature.com/ng/journal/v35/n1/full/ng1227.html this one].  I found it by looking at the introduction and references of the Zhang et. al (2011) paper.  For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003).  You will use the Parkhill paper for your project.  ''— [[User:Kdahlquist|Kdahlquist]] ([[User talk:Kdahlquist|talk]]) 09:54, 10 November 2015 (PST)''
  
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*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
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Note: revise/complete this citation
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* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/21622744
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* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147532/
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* Publisher Full Text (HTML):  http://jb.asm.org/content/193/15/4017.long
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* Publisher Full Text (PDF):  http://jb.asm.org/content/193/15/4017.full.pdf+html
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* Copyright: © 2011, American Society for Microbiology (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication.
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* Publisher: American Society for Microbiology (scientific society)
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* Availability: in print and online
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* Did LMU pay a fee for this article: no
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(''Note'': The below paper is very similar to the genome sequencing paper listed above but more recent. We were unsure how to designate which of the two would be a better paper. If possible, feedback regarding which to choose would be appreciated. Otherwise, we would like to use the above genome sequencing paper.)
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*Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
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*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.
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* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
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*The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
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* PubMed Central: Not available on PubMed Central (?)
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*The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
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* Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
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*The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
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* Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
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*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
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* Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication (?)
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*The authors won't he right of the copyright under a [http://creativecommons.org/ Creative Commons] license.
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* Publisher: Nature Publishing Group (for profit?)
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*The article is available "Open Access".
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* Availability: in print and online
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*Published by the American Society for Microbiology online.
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* Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal ''Nature Genetics''.
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*Article is available online only and LMU has paid a subscription for access to this article.
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=== Microarray Paper ===
 
=== Microarray Paper ===

Revision as of 01:32, 11 November 2015

The Class Whoopers Crew Page

The_Class_Whoopers

  • Species: Bordetella pertussis

Crew Members

Team Goals for the Week of 11/10

  • For all:
    • Outline your assigned paper on your user page and include a list of 10 defined terms from the paper.
  • Nicole & Brandon
    • Prepare Journal Club presentation on the designated genome sequencing article
    • Slides Due: by midnight, Tuesday, November 17
    • Presentation Date: Tuesday, November 24
  • Lena & Mahrad
    • Prepare Journal Club presentation on the designated microarray paper
    • Slides Due: by midnight, Tuesday, November 17
    • Presentation Date: Tuesday, November 17

Meetings!

  • Monday, November 9, 8pm, Seaver 120

Annotated Bibliography

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

Genome Sequencing Paper

Neither of these papers is the first to report the genome sequence of B. pertussis. The paper that you will want to use is this one. I found it by looking at the introduction and references of the Zhang et. al (2011) paper. For your Week 11 assignment, please remove your annotated bibliography entries for the two papers below and create one for this new paper by Parkhill et al. (2003). You will use the Parkhill paper for your project. — Kdahlquist (talk) 09:54, 10 November 2015 (PST)

Note: revise/complete this citation

  • Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., et al. (2003). Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nature genetics, 35(1), 32-40. doi:10.1038/ng1227
  • PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12910271
  • PubMed Central: Not available on PubMed Central (?)
  • Publisher Full Text (HTML): http://www.nature.com/ng/journal/v35/n1/full/ng1227.html
  • Publisher Full Text (PDF): http://www.nature.com/ng/journal/v35/n1/pdf/ng1227.pdf
  • Copyright: ©2003 Nature Publishing Group (information found on PDF version of article). This article is not Open Access, but it is freely available 6 months after publication (?)
  • Publisher: Nature Publishing Group (for profit?)
  • Availability: in print and online
  • Did LMU pay a fee for this article: Yes, LMU pays a subscription fee for access to the journal Nature Genetics.

Microarray Paper

This paper is suitable for your project. — Kdahlquist (talk) 10:04, 10 November 2015 (PST)

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, 9(12):e115243. doi: 10.1371/journal.pone.0115243


Project Progress

Week 11

Include "Executive Summaries" for each individual's progress here.

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)

Individual Journal Entries

Class Whoopers Individual Journal Entries
Nicole Anguiano Week 11 Week 12 Week 14 Week 15
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
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