Aaron Arvey

About Me

Research interests include inference in machine learning, cancer biology, and regulatory mechanics of miRNA. I am a PhD student at Cornell Weill and Sloan Kettering. I am currently working in Christina Leslie's Transcriptional Inference Lab, utilizing flexible modelling techniques to integrate disparate data sources. I also work in the Altan-Bonnet Immunology Dynamics Lab on a variety of problems in normal and pathological immunology.

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.

Papers

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, 2010.
Software PDF Supp

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

Presentations

Be sure to download the OpenOffice.org if you want to edit my presentations: .
OpenOffice exports to almost all formats (including PowerPoint) and is entirely open source.

• Introduction to Boosting and Alternating Decision Trees [PDF], [ODP],
• RepeatMap: Highly Specific Hybridization Probes [PDF], [ODP],

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

Links

Here are some links to other parts of the site.

• Papers on Boosting
• Shell One-Liners
• Wedding Information

Here are some links which I use on a daily basis and don't want to have to deal with bookmarks.