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Displaying 1-26 out of 26 total
Guest Editorial for Special Section on BIOKDD
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Tamer Kahveci,Saeed Salem,Mehmet Koyuturk
Issue Date:September 2013
pp. 1199-1200
The International Workshop on Data Mining in Bioinformatics (BIOKDD), held in conjunction with the ACM Conference on Knowledge Discovery and Data Mining (KDD) for 11 years, has successfully established a tradition of providing a platform for the presentati...
 
Guest Editorial for ACM BCB
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Tamer Kahveci,Mona Singh
Issue Date:September 2013
pp. 1089-1090
The special section includes nine papers, which were invited from the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB) in 2012. ACM BCB is the flagship conference of the ACM SIG on Bioinformatics, Computational Biology and ...
 
SiS: Significant subnetworks in massive number of network topologies
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Md Mahmudul Hasan,Yusuf Kavurucu,Tamer Kahveci
Issue Date:October 2012
pp. 1-6
Availability of abundant biological network data and its noisy nature necessitates extracting reliable subnetworks hidden in it. One key step towards that goal is to discover the subnetworks that appear frequently in a collection of networks. This paper pr...
 
Surrogate ranking for very expensive similarity queries
Found in: Data Engineering, International Conference on
By Fei Xu, Ravi Jampani, Mingxi Wu, Chris Jermaine, Tamer Kahveci
Issue Date:March 2010
pp. 848-859
We consider the problem of similarity search in applications where the cost of computing the similarity between two records is very expensive, and the similarity measure is not a metric. In such applications, comparing even a tiny fraction of the database ...
 
Highly Scalable and Accurate Seeds for Subsequence Alignment
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Abhijit Pol, Tamer Kahveci
Issue Date:October 2005
pp. 27-31
We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic index to store the fingerprints of k-grams and a highly scalable and accurate (...
 
Approximate Global Alignment of Sequences
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Tamer Kahveci, Venkatakrishnan Ramaswamy, Han Tao, Tao Li
Issue Date:October 2005
pp. 81-88
We propose two novel dynamic programming (DP) methods that solve the the approximate bounded and unbounded global alignment problems for biological sequences. Our first method solves the bounded alignment problem. It computes the distribution of the edit d...
 
Workload Characterization of Bioinformatics Applications
Found in: Modeling, Analysis, and Simulation of Computer Systems, International Symposium on
By Yue Li, Tao Li, Tamer Kahveci, José Fortes
Issue Date:September 2005
pp. 15-22
<p>The exponential growth in the amount of genomic information has spurred growing interest in large scale analysis of genetic data. Bioinformatics applications represent the increasingly important workloads. However, very few results on the behavior...
 
Towards Index-based Similarity Search for Protein Structure Databases
Found in: Computational Systems Bioinformatics Conference, International IEEE Computer Society
By Orhan Çamoglu, Tamer Kahveci, Ambuj K. Singh
Issue Date:August 2003
pp. 148
We propose two methods for finding similarities in protein structure databases. Our techniques extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. These feature vectors are then indexed using a multidimensional index str...
 
Fast alignment of large genome databases: A Demonstration
Found in: Data Engineering, International Conference on
By Tamer Kahveci, Ambuj K. Singh
Issue Date:March 2003
pp. 768
No summary available.
 
Joining Massive High-Dimensional Datasets
Found in: Data Engineering, International Conference on
By Tamer Kahveci, Christian A. Lang, Ambuj K. Singh
Issue Date:March 2003
pp. 265
We consider the problem of joining massive datasets. We propose two techniques for minimizing disk I/O cost of join operations for both spatial and sequence data. Our techniques optimize the available buffer space using a global view of the datasets. We bu...
 
Characterizing the Topology of Probabilistic Biological Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Andrei Todor,Alin Dobra,Tamer Kahveci
Issue Date:July 2013
pp. 970-983
Biological interactions are often uncertain events, that may or may not take place with some probability. This uncertainty leads to a massive number of alternative interaction topologies for each such network. The existing studies analyze the degree distri...
 
Uncertain interactions affect degree distribution of biological networks
Found in: 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
By Andrei Todor,Alin Dobra,Tamer Kahveci
Issue Date:October 2012
pp. 1-5
Biological interactions are often uncertain events, that may or may not take place under different scenarios. Existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumsta...
 
Manipulating the Steady State of Metabolic Pathways
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Bin Song, İ. Esra Büyüktahtakin, Sanjay Ranka, Tamer Kahveci
Issue Date:May 2011
pp. 732-747
Metabolic pathways show the complex interactions among enzymes that transform chemical compounds. The state of a metabolic pathway can be expressed as a vector, which denotes the yield of the compounds or the flux in that pathway at a given time. The stead...
 
Finding Dynamic Modules of Biological Regulatory Networks
Found in: Bioinformatic and Bioengineering, IEEE International Symposium on
By Ferhat Ay, Thang N. Dinh, My T. Thai, Tamer Kahveci
Issue Date:June 2010
pp. 136-143
Often groups of genes in regulatory networks, also called modules, work collaboratively on similar functions. Mathematically, the modules in a regulatory network has often been thought as a group of genes that interact with each other significantly more th...
 
TRIAL: A Tool for Finding Distant Structural Similarities
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Jayendra Gnanaskandan Venkateswaran, Bin Song, Tamer Kahveci, Christopher Jermaine
Issue Date:May 2011
pp. 819-831
Finding structural similarities in distantly related proteins can reveal functional relationships that can not be identified using sequence comparison. Given two proteins A and B and threshold \epsilon Å, we develop an algorithm, TRiplet-based Iterative AL...
 
Optimizing Similarity Search for Arbitrary Length Time Series Queries
Found in: IEEE Transactions on Knowledge and Data Engineering
By Tamer Kahveci, Ambuj K. Singh
Issue Date:April 2004
pp. 418-433
<p><b>Abstract</b>—We consider the problem of finding similar patterns in a time sequence. Typical applications of this problem involve large databases consisting of long time sequences of different lengths. Current time sequence search t...
 
Similarity Searching for Multi-Attribute Sequences
Found in: Scientific and Statistical Database Management, International Conference on
By Tamer Kahveci, Ambuj Singh, Aliekber Gürel
Issue Date:July 2002
pp. 175
We investigate the problem of searching similar multi-attribute time sequences. Such sequences arise naturally in a number of medical, financial, video, weather forecast, and stock market databases where more than one attribute is of interest at a time ins...
 
Variable Length Queries for Time Series Data
Found in: Data Engineering, International Conference on
By Tamer Kahveci, Ambuj Singh
Issue Date:April 2001
pp. 0273
Abstract: Finding similar patterns in a time sequence is a well-studied problem. Most of the current techniques work well for queries of a prespecified length, but not for variable length queries. We propose a new indexing technique that works well for var...
 
Reachability analysis in probabilistic biological networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Haitham Gabr,Andrei Todor,Alin Dobra,Tamer Kahveci
Issue Date:August 2014
pp. 1
Extra-cellular molecules trigger a response inside the cell by initiating a signal at special membrane receptors (i.e., sources), which is then transmitted to reporters (i.e., targets) through various chains of interactions among proteins. Understanding wh...
 
Genome on Demand: Interactive Substring Searching
Found in: Computational Systems Bioinformatics Conference, International IEEE Computer Society
By Tamer Kahveci, Ambuj K. Singh
Issue Date:August 2003
pp. 551
No summary available.
   
Guest Editorial for ACM BCB
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Mona Singh, Tamer Kahveci
Issue Date:September 2013
pp. 1089-1090
For clinical applications, the biological functions of DNA-binding proteins require that they interact with their target binding site with high affinity and specificity. Advances in randomized production and target-oriented selection of engineered artifici...
     
Characterizing the Topology of Probabilistic Biological Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Alin Dobra, Andrei Todor, Tamer Kahveci
Issue Date:July 2013
pp. 970-983
Biological interactions are often uncertain events, that may or may not take place with some probability. This uncertainty leads to a massive number of alternative interaction topologies for each such network. The existing studies analyze the degree distri...
     
Probabilistic Biological Network Alignment
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Alin Dobra, Andrei Todor, Tamer Kahveci
Issue Date:January 2013
pp. 109-121
Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the pr...
     
Large-Scale Signaling Network Reconstruction
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Eyup Serdar Ayaz, Seyedsasan Hashemikhabir, Tamer Kahveci, Tolga Can, Yusuf Kavurucu
Issue Date:November 2012
pp. 1696-1708
Reconstructing the topology of a signaling network by means of RNA interference (RNAi) technology is an underdetermined problem especially when a single gene in the network is knocked down or observed. In addition, the exponential search space limits the e...
     
TRIAL: A Tool for Finding Distant Structural Similarities
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Bin Song, Chris Jermaine, Jayendra Venkateswaran, Tamer Kahveci
Issue Date:May 2011
pp. 819-831
Finding structural similarities in distantly related proteins can reveal functional relationships that can not be identified using sequence comparison. Given two proteins A and B and threshold \epsilon Å, we develop an algorithm, TRiplet-based Iterati...
     
Manipulating the Steady State of Metabolic Pathways
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Bin Song, I. Esra Buyuktahtakin, Sanjay Ranka, Tamer Kahveci
Issue Date:May 2011
pp. 732-747
Metabolic pathways show the complex interactions among enzymes that transform chemical compounds. The state of a metabolic pathway can be expressed as a vector, which denotes the yield of the compounds or the flux in that pathway at a given time. The stead...
     
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