Electrical Engineering and Computer Science Scholarly Works: Recent submissions
Now showing items 161-180 of 309
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Link adaptation for energy-efficient uplink coordinated multi-point receptions
(Springer, 2011-11-23)We investigate link adaptation methods for energy-efficient uplink coordinated multi-point receptions. A system model for practical cellular networks is introduced, in which only a subset of base stations participates in ... -
Optimal External Memory Interval Management
(Society for Industrial and Applied Mathematics, 2003)In this paper we present the external interval tree, an optimal external memory data structure for answering stabbing queries on a set of dynamically maintained intervals. The external interval tree can be usedin an optimal ... -
Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity
(BioMed Central, 2009-01-30)Background: Automatic identification of structure fingerprints from a group of diverse protein structures is challenging, especially for proteins whose divergent amino acid sequences may fall into the "twilight-" or ... -
A Markov blanket-based method for detecting causal SNPs in GWAS
(Department of Electrical Engineering and Computer Science, 2010-04-29)Background Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies ... -
Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
(Oxford University Press, 2009-08-10)Motivation: Protein-protein interactions (PPIs), though extremely valuable towards a better understanding of protein functions and cellular processes, do not provide any direct information about the regions/domains within ... -
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs
(American Medical Informatics Association, 2012-06-19)Abstract Objective Adverse drug reaction (ADR) is one of the major causes of failure in drug development. Severe ADRs that go undetected until the post-marketing phase of a drug often lead to patient morbidity. Accurate ... -
Machine Learning and Its Applications to Biology
(Public Library of Science, 2007-06-29) -
Spatial Anisotropies and Temporal Fluctuations in Extracellular Matrix Network Texture during Early Embryogenesis
(Public Library of Science, 2012-05-31)Early stages of vertebrate embryogenesis are characterized by a remarkable series of shape changes. The resulting morphological complexity is driven by molecular, cellular, and tissue-scale biophysical alterations. Operating ... -
Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions
(Public Library of Science, 2008-02-06)Background As we move into the post genome-sequencing era, an immediate challenge is how to make best use of the large amount of high-throughput experimental data to assign functions to currently uncharacterized proteins. ... -
Finding minimum gene subsets with heuristic breadth-first search algorithm for robust tumor classification
(BioMed Central, 2012-07-25)Background: Previous studies on tumor classification based on gene expression profiles suggest that gene selection plays a key role in improving the classification performance. Moreover, finding important tumor-related ... -
Application of kernel functions for accurate similarity search in large chemical databases
(BioMed Central, 2010-04-29)Background: Similaritysearch in chemical structure databases is an important problem with many applications in chemical genomics, drug design, and efficient chemical probe screening among others. It is widely believed that ... -
Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template
(BioMed Central, 2013-05-09)Motivation: Complex diseases induce perturbations to interaction and regulation networks in living systems, resulting in dynamic equilibrium states that differ for different diseases and also normal states. Thus identifying ... -
Gene conversion in the rice genome
(BioMed Central, 2008-02-25)Background: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene ... -
Identification and characterization of insect-specific proteins by genome data analysis
(BioMed Central, 2007-04-04)Background: Insects constitute the vast majority of known species with their importance including biodiversity, agricultural, and human health concerns. It is likely that the successful adaptation of the Insecta clade ... -
Predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using short polypeptide clusters
(BioMed Central, 2012-06-21)Background: Protein synthetic lethal genetic interactions are useful to define functional relationships between proteins and pathways. However, the molecular mechanism of synthetic lethal genetic interactions remains ... -
Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism
(BioMed Central, 2010-10-07)Background: Dynamic Bayesian Networks (DBNs) are widely used in regulatory network structure inference with gene expression data. Current methods assumed that the underlying stochastic processes that generate the gene ... -
A Markov Blanket-Based Method for Detecting Causal SNPs in GWAS
(BioMed Central, 2010-04-29)Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies (GWAS), designing ... -
Genetic Studies of Complex Human Diseases: Characterizing SNP-Disease Associations Using Bayesian Networks
(BioMed Central, 2012-12-17)Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis, and treatment of complex human diseases. Applying machine learning or statistical methods to epistatic interaction ... -
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms
(BioMed Central, 2009-04-29)Background: Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-scale ... -
New Threats to Health Data Privacy
(BioMed Central, 2011-11-24)Background: Along with the rapid digitalization of health data (e.g. Electronic Health Records), there is an increasing concern on maintaining data privacy while garnering the benefits, especially when the data are required ...