User:Denizkural

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Currently Working on

Understanding E. Coli

Interests

Currently a graduate student at Boston College in Computational Biology. Still interested in a lot of the stuff below, but some focuses in Biology:

- genomics & next gen sequencing for variation discovery. - budding interest in regulatory genomics. - Read/Write biology.

Publications

COMIT: identification of noncoding motifs under selection in coding sequences

Coding nucleotide sequences contain myriad functions independent of their encoded protein sequences. We present the COMIT algorithm to detect functional noncoding motifs in coding regions using sequence conservation, explicitly separating nucleotide from amino acid effects. COMIT concurs with diverse experimental datasets, including splicing enhancers, silencers, replication motifs, and microRNA targets, and predicts many novel functional motifs. Intriguingly, COMIT scores are well-correlated to scores uncalibrated for amino acids, suggesting that nucleotide motifs often override peptide-level constraints.

Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi and Jeffrey H Chuang

http://genomebiology.com/2009/10/11/R133 (open access)

Genome Biology 2009, 10:R133, doi:10.1186/gb-2009-10-11-r133, Published: 20 November 2009

< 2007

About

I am a senior at Harvard College, concentrating in mathematics. I am interested in databases, and things like creative commons, open access, open source and so on. I am interested in the intersections of mathematics with biology, and to see if we can make more precise statements beyond "We have observed that protein X was expressed at higher levels". I am also interested in things like Web 2.0, the semantic wiki, machine-readability, data visualization and such as well.

Useful Thing

How to install the latest Biopython on Ubuntu This is probably terribly outdated.

Assignments (2007 Harvard Biophysics 101)

Follow the links to the corresponding assignment

<calendar> name=Harvard:Biophysics_101/2007/Notebook:Denizkural date=2007/03/01 view=threemonths format=%name/%year-%month-%day weekstart=0 </calendar> <calendar> name=Harvard:Biophysics_101/2007/Notebook:Denizkural date=2007/05/01 view=month format=%name/%year-%month-%day weekstart=0 </calendar>