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Information Theoretic Methods for Bioinformatics

Guest Editors: Jorma Rissanen, Peter Grünwald, Jukka Heikkonen, Petri Myllymäki, Teemu Roos, and Juho Rousu

  1. Content type: Research Article

    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....

    Authors: Petri Kontkanen, Hannes Wettig and Petri Myllymäki

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:90947

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  2. Content type: Research Article

    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...

    Authors: JohnS Conery

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:72936

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  3. Content type: Research Article

    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...

    Authors: Arvind Rao, Alfred O Hero III, David J States and James Douglas Engel

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:13853

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  4. Content type: Research Article

    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....

    Authors: Hasan Metin Aktulga, Ioannis Kontoyiannis, L Alex Lyznik, Lukasz Szpankowski, Ananth Y Grama and Wojciech Szpankowski

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:14741

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  5. Content type: Research Article

    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...

    Authors: Dario Benedetto, Emanuele Caglioti and Claudia Chica

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:60723

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  6. Content type: Research Article

    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...

    Authors: Chris Hemmerich and Sun Kim

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:87356

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  7. Content type: Research Article

    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...

    Authors: Haruo Suzuki, Rintaro Saito and Masaru Tomita

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:61374

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  8. Content type: Research Article

    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...

    Authors: Patrick E Meyer, Kevin Kontos, Frederic Lafitte and Gianluca Bontempi

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:79879

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  9. Content type: Research Article

    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)...

    Authors: Francesco Fabris, Andrea Sgarro and Alessandro Tossi

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:31450

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