Aaron Arvey

Papers

Heme controls the regulation of protein tyrosine kinases Jak2 and Src
Xiao Yao, Parimaladevi Balamurugan, Aaron Arvey, Christina Leslie, Li Zhang
Biochemical and Biophysical Research Communications, November 2010.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions
Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina Leslie
PLoS Computational Biology, 6(9):e1000916, September 2010.

Target mRNA abundance dilutes microRNA and siRNA activity
Aaron Arvey, Erik Larsson, Chris Sander, Christina S Leslie and Debora S Marks
Molecular Systems Biology 6:363, April 2010
PDF Supp    ISMB Slides: (PDF) (PPT)    Keystone Slides: (PDF) (PPT)

Minimizing off-target signals in RNA fluorescent in situ hybridization
Aaron Arvey*, Anita Hermann*, Cheryl C. Hsia, Eugene Ie, Yoav Freund, and William McGinnis (* Joint first authors)
Nucleic Acids Research, February 2010.
Software PDF Supp Slides (PDF), Slides (ODP),

Detection of genomic islands via segmental genome heterogeneity.
Aaron Arvey, Rajeev Azad, Alpan Raval, and Jeffrey Lawrence.
Nucleic Acids Research, July 2009.
Software PDF Supp

ResBoost: characterizing and predicting catalytic residues in enzymes.
Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjolander.
BMC Bioinformatics 10:197, June 2009.
PDF

Software

I've been part of a few large software projects. If you have any questions, don't hesitate to email me, or the appropriate mailing list. All projects are either posted on SourceForge or are in the process of being posted.

• JBoost is an implementation of several popular boosting algorithms using alternating decision tree. It is very effective at producing reliable, easy to use, and easy to visualize classifiers.
• RepeatMap is client/server pair of programs to determine very specific probes for in situ hybridizations and microarray experiments. You can use the client provided, set up a server of your own, or write your own client.

Misc Presentations

Be sure to download the OpenOffice.org if you want to edit some of my presentations: .
OpenOffice exports to almost all formats (including PowerPoint) and is entirely open source.
Unfortunately in more recent years, I've caved in and started using PowerPoint as my primary presentation editor :-(

• Introduction to Boosting and Alternating Decision Trees [PDF], [ODP],

I'll add links to more presentations at some point in time...