Skip to main content

Information Theoretic Methods for Bioinformatics

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

  1. Research Article

    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....

    Petri Kontkanen, Hannes Wettig and Petri Myllymäki

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:90947

    Published on: 20 January 2008

  2. Research Article

    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...

    JohnS Conery

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2007:72936

    Published on: 2 January 2008

  3. Research Article

    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...

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

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:13853

    Published on: 24 December 2007

  4. Research Article

    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....

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

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:14741

    Published on: 5 December 2007

  5. Research Article

    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...

    Dario Benedetto, Emanuele Caglioti and Claudia Chica

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:60723

    Published on: 30 October 2007

  6. Research Article

    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...

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

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:79879

    Published on: 24 June 2007

  7. Research Article

    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)...

    Francesco Fabris, Andrea Sgarro and Alessandro Tossi

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:31450

    Published on: 4 June 2007