SUMMER 2011 Schedule
- Faculty/senate resolution of SENSAI and your own matlab codes
- Complete tribolium manuscript
Introduction to basic biochemistry lab techniques begins Monday afternoon!!
- T.C. Bishop (2008) Geometry of the nucleosomal DNA helix. Biophysics Journal, vol 95, pp 1007—1017
- 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
- 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.
- Drendel, Echlin, Jeffers and Kilchrist (2011) Geometry of the DNA double helix. (preprint).
- Bishop (2009) VDNA: The virtual DNA plug-in for VND. Bioinformatics Advance Access. Oxford University Press?
- Introduction to python and bioinformatics code
- 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
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
Discussion sessions on Friday mornings. Announcements to follow.
Alternate with the reading discussions on Friday mornings. Announcements to follow.