Guest Editors: Erchin Serpedin, Ulisses Braga-Neto, Javier Garcia-Frias and Yufei Huang
Applications of Signal Processing Techniques to Bioinformatics, Genomics, and Proteomics
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Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:250306
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Clustering of Gene Expression Data Based on Shape Similarity
A method for gene clustering from expression profiles using shape information is presented. The conventional clustering approaches such as K-means assume that genes with similar functions have similar expressi...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:195712 -
Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge
Based on time series gene expressions, cyclic genes can be recognized via spectral analysis and statistical periodicity detection tests. These cyclic genes are usually associated with cyclic biological process...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:683463 -
A Hybrid Technique for the Periodicity Characterization of Genomic Sequence Data
Many studies of biological sequence data have examined sequence structure in terms of periodicity, and various methods for measuring periodicity have been suggested for this purpose. This paper compares two su...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:924601 -
Spectral Preprocessing for Clustering Time-Series Gene Expressions
Based on gene expression profiles, genes can be partitioned into clusters, which might be associated with biological processes or functions, for example, cell cycle, circadian rhythm, and so forth. This paper ...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:713248 -
Is Bagging Effective in the Classification of Small-Sample Genomic and Proteomic Data?
There has been considerable interest recently in the application of bagging in the classification of both gene-expression data and protein-abundance mass spectrometry data. The approach is often justified by t...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:158368 -
Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints
When aligning RNAs, it is important to consider both the secondary structure similarity and primary sequence similarity to find an accurate alignment. However, algorithms that can handle RNA secondary structur...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:491074 -
Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited
An approximate representation for the state space of a context-sensitive probabilistic Boolean network has previously been proposed and utilized to devise therapeutic intervention strategies. Whereas the full ...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:360864 -
How to Improve Postgenomic Knowledge Discovery Using Imputation
While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignor...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:717136 -
Compressive Sensing DNA Microarrays
Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor ...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:162824