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CIBCB
2007
IEEE
11 years 7 months ago
Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms
—In metabolic engineering it is difficult to identify which set of genetic manipulations will result in a microbial strain that achieves a desired production goal, due to the co...
Miguel Rocha, José P. Pinto, Isabel Rocha, ...
CIBCB
2007
IEEE
11 years 9 months ago
Hybrid Architecture for Accelerating DNA Codeword Library Searching
-- A large and reliable DNA codeword library is the key to the success of DNA based computing. Searching for the set of reliable DNA codewords is an NP-hard problem, which can take...
Qinru Qiu, Daniel J. Burns, Qing Wu, Prakash Mukre
CIBCB
2007
IEEE
11 years 9 months ago
Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks
The accurate prediction of enzyme catalytic sites remains an open problem in bioinformatics. Recently, several structure-based methods have become popular; however, few robust seq...
Swati Pande, Amar Raheja, Dennis R. Livesay
CIBCB
2007
IEEE
11 years 9 months ago
Genetic Regulatory Network Modeling Using Network Component Analysis and Fuzzy Clustering
Gene regulatory network model is the most widely used mechanism to model and predict the behavior of living organisms. Network Component Analysis (NCA) as an emerging issue for unc...
Fatemeh Bakouie, Mohammad Hassan Moradi
CIBCB
2007
IEEE
11 years 9 months ago
Associative Artificial Neural Network for Discovery of Highly Correlated Gene Groups Based on Gene Ontology and Gene Expression
Abstract-- The advance of high-throughput experimental technologies poses continuous challenges to computational data analysis in functional and comparative genomics studies. Gene ...
Ji He, Xinbin Dai, Xuechun Zhao
CIBCB
2007
IEEE
11 years 11 months ago
A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins
Abstract— We applied Support Vector Machines to the prediction of the subcellular localization of transmembrane proteins, and compared the performance of different sequence kerne...
Stefan Maetschke, Marcus Gallagher, Mikael Bod&eac...
CIBCB
2007
IEEE
11 years 11 months ago
Overestimation for Multiple Sequence Alignment
Abstract— Multiple sequence alignment is an important problem in computational biology. A-star is an algorithm that can be used to find exact alignments. We present a simple mod...
Tristan Cazenave
CIBCB
2007
IEEE
11 years 11 months ago
Evolving Extremal Epidemic Networks
The susceptible, infected, removed model for epidemics assumes that the population in which the epidemic takes place is well mixed. This strong assumption can be relaxed by permit...
Dan Ashlock, Fatemeh Jafargholi
CIBCB
2007
IEEE
11 years 11 months ago
Multiple Sequence Alignment using Fuzzy Logic
—DNA matching is a crucial step in sequence alignment. Since sequence alignment is an approximate matching process there is a need for good approximate algorithms. The process of...
Sara Nasser, Gregory Vert, Monica N. Nicolescu, Al...
CIBCB
2007
IEEE
11 years 11 months ago
Modeling protein-DNA binding time in Stochastic Discrete Event Simulation of Biological Processes
Abstract— This paper presents a parametric model to estimate the DNA-protein binding time using the DNA and protein structures and details of the binding site. To understand the ...
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. ...
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