Guest Editors: Jorma Rissanen, Peter Grünwald, Jukka Heikkonen, Petri Myllymäki, Teemu Roos, and Juho Rousu
Information Theoretic Methods for Bioinformatics
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Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:79128
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NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks
Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data....
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:90947 -
Aligning Sequences by Minimum Description Length
This paper presents a new information theoretic framework for aligning sequences in bioinformatics. A transmitter compresses a set of sequences by constructing a regular expression that describes the regions o...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:72936 -
Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information
Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcripti...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:13853 -
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances....
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:14741 -
Compressing Proteomes: The Relevance of Medium Range Correlations
We study the nonrandomness of proteome sequences by analysing the correlations that arise between amino acids at a short and medium range, more specifically, between amino acids located 10 or 100 residues apar...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:60723 -
A Study of Residue Correlation within Protein Sequences and Its Application to Sequence Classification
We investigate methods of estimating residue correlation within protein sequences. We begin by using mutual information (MI) of adjacent residues, and improve our methodology by defining the mutual information ve...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:87356 -
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlatio...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:61374 -
Information-Theoretic Inference of Large Transcriptional Regulatory Networks
The paper presents MRNET, an original method for inferring genetic networks from microarray data. The method is based on maximum relevance/minimum redundancy (MRMR), an effective information-theoretic techniqu...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:79879 -
Splitting the BLOSUM Score into Numbers of Biological Significance
Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum)...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:31450