Difference between revisions of "User:Denizkural"

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== Information ==
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== Currently Working on ==
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Understanding E. Coli
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== 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:
 
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.
 
- genomics & next gen sequencing for variation discovery.
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- budding interest in regulatory genomics.
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- Read/Write biology.
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== Publications ==
  
- budding interest in regulatory genomics.
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=== -1- ===
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'''COMIT: identification of noncoding motifs under selection in coding sequences'''
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Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi and Jeffrey H Chuang
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'''Abstract'''
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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.
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http://genomebiology.com/2009/10/11/R133
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(open access)
  
Will try to put a list of annotated publications soon.
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Genome Biology 2009, 10:R133 doi:10.1186/gb-2009-10-11-r133
  
  

Revision as of 12:28, 13 October 2010

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

-1-

COMIT: identification of noncoding motifs under selection in coding sequences Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi and Jeffrey H Chuang

Abstract 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.

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

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


< 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 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>