I am a PhD student at the Bioinformatics Program at the University of Illinois at Chicago. I started school in Fall 2004, passed my qualifying exam in May 2005. Now I am officially a PhD candidate and preparing for my preliminary exam.
My research interests include machine learning algorithms, immunoinformatics, specifically prediction of MHC class II binders. My research advisor is Dr. Yang Dai. So far I have published one paper and one book chapter with her. You can visit Dr. Dai's website at http://array.bioengr.uic.edu/~yangdai/.
Lei Huang, Oleksiy Karpenko, Naveen Murugan, and Yang Dai, "Building a Meta-predictor for MHC Class II Binding Peptides", Immunoinformatics: predicting Immunogenicity in silico. Methods in Molecular Biology. Flower D.R. (eds) Humana Press, Totawa NJ, In press.
Oleksiy Karpenko, Jianming Shi and Yang Dai, "Prediction of MHC class II binders using the ant colony search strategy", Artificial Intelligence in Medicine, Vol. 35, pp.147-156, 2005. PDF
Besides taking classes I work as a research assistant at Dr. Dai's lab. Overall there are about 10 graduate students doing their research in our lab. Here's a nice photo of our lab members before a lab meeting.
From left to right: Peter Larsen, Hong Hu, Oleksiy Karpenko, Zhengdeng "Arden" Lei, Dr. Yang Dai, Naveen Murugan, Eyad Almasri and Lei Huang. Not on the photo: Guanrao Chen and Yijiang Li.
You can visit our lab website at http://array.bioengr.uic.edu.
The University of Illinois at Chicago is the Chicago campus of the University of Illinois. Our campus is located in the city of Chicago, about 10 minutes from the Loop (downtown Chicago). It is a quite big (around 25,000 students) state school. The other two campuses are at Springfield and Urbana-Champaign (UIUC). UIC is a major research center, especially in medical sciences. The school boasts the world's most powerful Fourier Transform Mass Spectrometer (FTMS). The Bioinformatics Program at UIC is the Illinois only master's and PhD program in Bioinformatics accredited by the Illinois Board of Higher Education.
Unfortunately being a PhD student means a lot of work and little time for leisure. Still I try to play soccer on Saturdays at the field behind the Physical Education Building on Morgan and 14th.
Also I enjoy programming. In fact I have a BS in Computer Science and moved to bioinformatics because it provides a huge amount of data and a lot of room for those who are interested in advanced algorithms. Not a long time ago I decided to implement some of my old ideas in freeware computer programs.
The first one is a tiny utility program called Goospell that helps you run Google queries from a clipboard. That is basically from any Windows application. The point is that the results of the search are also put into clipboard so you can paste them in whatever application you are working. You can download Goospell from its website at http://icarus.uic.edu/~okarpe2/goospell.htm.
I hope to add some more when I have time, including some bioinformatics tools. Meanwhile enjoy Goospell! :)
Oleksiy Karpenko
Deparment of Bioengineering
University of Illinois at Chicago
Clinical Science North
820 S. Wood Rm. W125
Chicago, IL 60612
(312) 413-0191