VCU Bioinformatics and Bioengineering Summer Institute
Virginia Commonwealth University
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Current Research in Bioinformatics and Bioengineering
(Summer 2010)

Time: Fridays, 9:00 pm - 10:30 pm, June 11 - August 6
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizers: Various BBSI students, plus Jeff Elhai in the background
Audience: 1st and 2nd year students


  • Break the stranglehold that the bottom line has on the undergraduate mentality by focusing on individual results, how the were obtained, what we may draw from them, and what we may not.
  • Gain an appreciation of a field within bioinformatics and/or bioengineering through a dissection of several papers central to it.


  • Participants will decide on a field to which they want to devote eight sessions, a subject that can connect with the interests of all participants.
  • Each week two participants (termed conveners) will decide on one article or possibly two related articles within a field. The article will be distributed to all participants several days in advance of the session.
  • The two conveners will organize what parts of the article(s) the each of the other participants will focus on. In this way, each participant will be an expert on a small part of the article.
  • The day of the session, each convener will give a short presentation on some critical experiment. The following may be of some use:
          Hints for preparing a presentation
  • Then the entire article(s) will be thrown open for discussion, with each participant contributing his/her area of expertise.
  • The conveners will direct the flow of the discussion, aiming it towards the resolution of what they determine before the session to be key questions

Presenting difficult to understand experiments is not easy to do. People who are very good at research often not very good at making their thoughts comprehensible to a general audience. It is a learned skill. Participants in this workshop will provide feedback to facilitators, helping them see what worked and what didn't. Providing feedback is a learned skill, and an important one. The following might be of some use:
      How to critique the works of others

Schedule doi:
Fri 11 June Organization
Topics chosen for Summer 2010: Human microbiome and Phage therapy/antibiotic resistance
   Fri 18 June Conveners: Meredith Hickson and Kelly O'Briant
McVay CS, Velásquez M, Fralick JA (2007).
Phage Therapy of Pseudomonas aeruginosa Infection in a Mouse Burn Wound Model.
Antimicrob Agents Chemother 51:1934-1938.
(Focus groups)
   Fri 25 June Conveners: Stacey Houston and Jonathan Levin
Guenther S, et al. (2009).
Virulent Bacteriophage for Efficient Biocontrol of Listeria monocytogenes in Ready-To-Eat Foods.
Appl Environ Microbiol 75:93-100.
(Focus groups)
   Fri 2 July Conveners: Russell Green and Annie Lee
Singh G, et al. (2010).
Secretion of Pseudomonas aeruginosa type III cytotoxins is dependent on pseudomonas quinolone signal concentration.
Microb Pathogen (Epub ahead of print)
(Focus groups)
   Fri 9 July Conveners: Kelcey Anderson and Richard Roberts
Endy D, et al. (2000).
Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes.
Proc Natl Acad Sci USA 97:5375-5380
(Focus groups)
   Thu 15 July Conveners: Patrick Barranger and Megan Silbaugh
Giongo A, et al. (2010)
Toward defining the autoimmune microbiome for type 1 diabetes.
ISME J [Epub ahead of print]
(Focus groups)
   Thu 22 July Meredith Hickson
Annie Lee
Kelly O'Briant
Ritchie Vergara
   Thu 29 July Kelcey Anderson
Patrick Barranger
Stacey Houston
Richard Roberts
   Thu 5 Aug Russell Green
Jonathan Levin
James Ortego
Megan Silbaugh

General references

Human microbiome
The NIH Common Fund. Human Microbiome Project

Kuczynski J and 11 others (2010). Direct sequencing of the human microbiome readily reveals community differences. Genome Biol 11:210

Phage therapy and antibiotic resistance

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