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Genomic Signal Processing 2010

  1. Editorial

    Genomic Signal Processing

    Ulisses Braga-Neto, Rui Kuang, Harri Lähdesmäki, Haris Vikalo and Byung-Jun Yoon

    EURASIP Journal on Advances in Signal Processing 2011 2010:137263

    Published on: 4 January 2011

  2. Research Article

    A Metastate HMM with Application to Gene Structure Identification in Eukaryotes

    We introduce a generalized-clique hidden Markov model (HMM) and apply it to gene finding in eukaryotes (C. elegans). We demonstrate a HMM structure identification platform that is novel and robustly-performing in...

    Stephen Winters-Hilt and Carl Baribault

    EURASIP Journal on Advances in Signal Processing 2010 2010:581373

    Published on: 30 November 2010

  3. Research Article

    Hidden Markov Model with Duration Side Information for Novel HMMD Derivation, with Application to Eukaryotic Gene Finding

    We describe a new method to introduce duration into an HMM using side information that can be put in the form of a martingale series. Our method makes use of ratios of duration cumulant probabilities in a mann...

    S. Winters-Hilt, Z. Jiang and C. Baribault

    EURASIP Journal on Advances in Signal Processing 2010 2010:761360

    Published on: 4 October 2010

  4. Research Article

    Small-Sample Error Estimation for Bagged Classification Rules

    Application of ensemble classification rules in genomics and proteomics has become increasingly common. However, the problem of error estimation for these classification rules, particularly for bagging under t...

    T. T. Vu and U. M. Braga-Neto

    EURASIP Journal on Advances in Signal Processing 2010 2010:548906

    Published on: 30 September 2010

  5. Research Article

    Inferring Parameters of Gene Regulatory Networks via Particle Filtering

    Gene regulatory networks are highly complex dynamical systems comprising biomolecular components which interact with each other and through those interactions determine gene expression levels, that is, determi...

    Xiaohu Shen and Haris Vikalo

    EURASIP Journal on Advances in Signal Processing 2010 2010:204612

    Published on: 30 August 2010

  6. Research Article

    Novel Data Fusion Method and Exploration of Multiple Information Sources for Transcription Factor Target Gene Prediction

    Background. Revealing protein-DNA interactions is a key problem in understanding transcriptional regulation at mechanistic level. Computational methods have an important role in predicting transcription factor ta...

    Xiaofeng Dai, Olli Yli-Harja and Harri Lähdesmäki

    EURASIP Journal on Advances in Signal Processing 2010 2010:235795

    Published on: 17 August 2010

  7. Research Article

    An MCMC Algorithm for Target Estimation in Real-Time DNA Microarrays

    DNA microarrays detect the presence and quantify the amounts of nucleic acid molecules of interest. They rely on a chemical attraction between the target molecules and their Watson-Crick complements, which ser...

    Haris Vikalo and Mahsuni Gokdemir

    EURASIP Journal on Advances in Signal Processing 2010 2010:736301

    Published on: 2 August 2010

  8. Research Article

    Exact Performance of CoD Estimators in Discrete Prediction

    The coefficient of determination (CoD) has significant applications in genomics, for example, in the inference of gene regulatory networks. We study several CoD estimators, based upon the resubstitution, leave...

    Ting Chen and Ulisses Braga-Neto

    EURASIP Journal on Advances in Signal Processing 2010 2010:487893

    Published on: 27 July 2010

  9. Research Article

    Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that m...

    Jia Meng, Jianqiu(Michelle) Zhang, Yuan(Alan) Qi, Yidong Chen and Yufei Huang

    EURASIP Journal on Advances in Signal Processing 2010 2010:538919

    Published on: 13 July 2010

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