PICKY: a novel SVD-based NMR spectra peak picking method (2009)
Alipanahi, Babak, Gao, Xin, Karakoc, Emre, Donaldson, Logan, Li, Ming
Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear...
COMPARATIVE QSAR ANALYSIS OF BACTERIAL-, FUNGAL- PLANT- AND HUMAN METABOLITES. (2008)
Emre Karakoc, S. Cenk Sahinalp
Several QSAR models have been developed using a linear optimization approach that enabled distinguishing metabolic substances isolated from human-, bacterial-, plant- and fungal- cells. Seven binary...
Daniel P. Miranker, Willard J. Briggs, Rui Mao, Shulin Ni, Weijia Xu, Arthur Kaufmann, ...
The Bulletin of the Technical Committee on Data Engineering is published quarterly and is distributed to all TC members. Its scope includes the design, implementation, modelling, theory and...
Emre Karakoc, Z. Meral Ozsoyoglu, Murat Tasan, Xiang Zhang, S. Cenk Sahinalp
In many biomolecular database applications involving string/sequence data, it is common to have similarity search in the form of near neighbor queries or nearest neighbor queries. The similarity...
Cagri Aksay, Emre Karakoc, Chi Kin Ho, Peter J. Unrau, S. Cenk
and functional identification via
COMPARATIVE QSAR ANALYSIS OF BACTERIAL-, FUNGAL- PLANT- AND HUMAN METABOLITES. (2008)
Emre Karakoc, S. Cenk Sahinalp
Several QSAR models have been developed using a linear optimization approach that enabled distinguishing metabolic substances isolated from human-, bacterial-, plant- and fungal- cells. Seven binary...
Structural similarity search among small molecules is a standard tool used in molecular classification and in-silico drug discovery. The effectiveness of this general approach depends on how well the...
taveRNA: a web suite for RNA algorithms and applications (2007)
Aksay, Cagri, Salari, Raheleh, Karakoc, Emre, Alkan, Can, Sahinalp, S. Cenk
We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic...
RNA secondary structure prediction via energy density minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alex, Kaizhong Zhang, ...
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety...
RNA Secondary Structure Prediction via Energy Density Minimization (2006)
Can Alkan, Emre Karakoc, S. Cenk Sahinalp, Peter Unrau, H. Alexander Ebhardt, H. Alex, ...
There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding RNAs with a variety of...
Distance Based Algorithms for Small Biomolecule Classification (2006)
And Structural Similarity, Emre Karakoc, Artem Cherkasov, S. Cenk Sahinalp
Structural similarity search among small molecules is a standard tool used in molecular classification and insilico drug discovery. The effectiveness of this general approach depends on how well the...
Comparative QSAR- and Fragments Distribution Analysis of Drugs (2006)
Emre Karakoc, S. Cenk Sahinalp, Artem Cherkasov
A number of binary QSAR models have been developed using methods of artificial neural networks, k-nearest neighbors, linear discriminative analysis, and multiple linear regression and have been...
Karakoc, Emre, Cherkasov, Artem, Sahinalp, S. Cenk
Motivation: Structural similarity search among small molecules is a standard tool used in molecular classification and in-silico drug discovery. The effectiveness of this general approach depends on...
taveRNA: a web suite for RNA algorithms and applications
Aksay, Cagri, Salari, Raheleh, Karakoc, Emre, Alkan, Can, Sahinalp, S. Cenk
We present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic...
smyRNA: A Novel Ab Initio ncRNA Gene Finder
Salari, Raheleh, Aksay, Cagri, Karakoc, Emre, Unrau, Peter J., Hajirasouliha, Iman, Sahinalp, S. Cenk
PICKY: a novel SVD-based NMR spectra peak picking method
Alipanahi, Babak, Gao, Xin, Karakoc, Emre, Donaldson, Logan, Li, Ming
Motivation: Picking peaks from experimental NMR spectra is a key unsolved problem for automated NMR protein structure determination. Such a process is a prerequisite for resonance assignment, nuclear...