Flexible and Extendable Scientific Undergraduate Experience

SUMMER 2011 Schedule

Disease cluster

  1. Faculty/senate resolution of SENSAI and your own matlab codes
  2. Complete tribolium manuscript

Structural biology

Introduction to basic biochemistry lab techniques begins Monday afternoon!!

  1. Reading
    1. T.C. Bishop (2008) Geometry of the nucleosomal DNA helix. Biophysics Journal, vol 95, pp 1007—1017
    2. Morozov,  Fortney,  Gaykalova, Studitsky, Widom and Siggia (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies, Nucleic Acids Research, vol 37, pp 4707—4772
    3. Sereda and Bishop (2009) Evaluation of elastic rod models with long range interactions for predicting nucleosome stability. Journal of Biomolecular Structure & Dynamics, vol 27, pp 867—887.
    4. Drendel, Echlin, Jeffers and Kilchrist (2011) Geometry of the DNA double helix. (preprint).
    5. Bishop (2009) VDNA: The virtual DNA plug-in for VND. Bioinformatics Advance Access. Oxford University Press?


  1. Introduction to python and bioinformatics code
  2. Meet in Asa Ben Hur’s office at 10:00am on Tuesday 5/17


Barbazuk, Fu and McGinnis (2008),  Genome-wide analyses of alternative splicing in plants: Opportunities and challenges, Genome Research, vol 18, pp 1381—1392. Available at the link http://genome.cshlp.org/content/18/9/1381.full

Daily logs

Since there are multiple, independent clusters you will be required to maintain daily hour-by-hour logs. The purpose is not for time-keeping, but so that you have a record of your progress. I will be reviewing these logs on a weekly basis.

Liberal Arts reading

  • "Cadillac Desert", by Marc Reisner (1993)
  • "How to lie with statistics", by Darrell Huff (1993)
  •  “Seven Clues to the Origin of Life: a Scientific Detective Story” by A.G. Cairns-Smith
  • “Merchants of doubt”, by Oreskes and Conway

Painting by: Michael Garfield

Discussion sessions on Friday mornings. Announcements to follow.

Professional Development

Alternate with the reading discussions on Friday mornings.  Announcements to follow.