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  1. Research

    Precise periodic components estimation for chronobiological signals through Bayesian Inference with sparsity enforcing prior

    The toxicity and efficacy of more than 30 anticancer agents present very high variations, depending on the dosing time. Therefore, the biologists studying the circadian rhythm require a very precise method for...

    Mircea Dumitru, Ali Mohammad-Djafari and Simona Baghai Sain

    EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:3

    Published on: 20 January 2016

  2. Research

    Bayesian estimation of the discrete coefficient of determination

    The discrete coefficient of determination (CoD) measures the nonlinear interaction between discrete predictor and target variables and has had far-reaching applications in Genomic Signal Processing. Previous w...

    Ting Chen and Ulisses M. Braga-Neto

    EURASIP Journal on Bioinformatics and Systems Biology 2016 2016:1

    Published on: 15 January 2016

  3. Research

    Identification of Th1/Th2 regulatory switch to promote healing response during leishmaniasis: a computational approach

    Leishmania devices its survival strategy by suppressing the host’s immune functions. The antigen molecules produced by Leishmania interferes with the host’s cell signaling cascades and co...

    Piyali Ganguli, Saikat Chowdhury, Shomeek Chowdhury and Ram Rup Sarkar

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:13

    Published on: 1 December 2015

  4. Research

    Network inference through synergistic subnetwork evolution

    Study of signaling networks is important for a better understanding of cell behaviors e.g., growth, differentiation, metabolism, proptosis, and gaining deeper insights into the molecular mechanisms of complex ...

    Lipi Acharya, Robert Reynolds and Dongxiao Zhu

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:12

    Published on: 27 November 2015

  5. Research

    Computing interaction probabilities in signaling networks

    Biological networks inherently have uncertain topologies. This arises from many factors. For instance, interactions between molecules may or may not take place under varying conditions. Genetic or epigenetic m...

    Haitham Gabr, Juan Carlos Rivera-Mulia, David M. Gilbert and Tamer Kahveci

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:10

    Published on: 11 November 2015

  6. Research

    Molecular network control through boolean canalization

    Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensi...

    David Murrugarra and Elena S. Dimitrova

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:9

    Published on: 4 November 2015

  7. Research

    On optimal Bayesian classification and risk estimation under multiple classes

    A recently proposed optimal Bayesian classification paradigm addresses optimal error rate analysis for small-sample discrimination, including optimal classifiers, optimal error estimators, and error estimation...

    Lori A. Dalton and Mohammadmahdi R. Yousefi

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:8

    Published on: 24 October 2015

  8. Review

    The post-genomic era of biological network alignment

    Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological k...

    Fazle E Faisal, Lei Meng, Joseph Crawford and Tijana Milenković

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:3

    Published on: 4 June 2015

  9. Review

    Analysis of miRNA, mRNA, and TF interactions through network-based methods

    Recent findings have elucidated that the regulation of messenger RNA (mRNA) levels is due to the synergistic and antagonist actions of transcription factors (TFs) and microRNAs (miRNAs). Mutual interactions am...

    Pietro H Guzzi, Maria Teresa Di Martino, Pierosandro Tagliaferri, Pierfrancesco Tassone and Mario Cannataro

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:4

    Published on: 4 June 2015

  10. Research

    40-Hz ASSR fusion classification system for observing sleep patterns

    This paper presents a fusion-based neural network (NN) classification algorithm for 40-Hz auditory steady state response (ASSR) ensemble averaged signals which were recorded from eight human subjects for obser...

    Gulzar A Khuwaja, Sahar Javaher Haghighi and Dimitrios Hatzinakos

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:2

    Published on: 5 February 2015

  11. Research

    Optimal cancer prognosis under network uncertainty

    Typically, a vast amount of experience and data is needed to successfully determine cancer prognosis in the face of (1) the inherent stochasticity of cell dynamics, (2) incomplete knowledge of healthy cell reg...

    Mohammadmahdi R Yousefi and Lori A Dalton

    EURASIP Journal on Bioinformatics and Systems Biology 2015 2015:1

    Published on: 27 January 2015

  12. Research

    Discovering irregular pupil light responses to chromatic stimuli using waveform shapes of pupillograms

    The waveforms of the pupillary light reflex (PLR) can be analyzed in a diagnostic test that allows for differentiation between disorders affecting photoreceptors and disorders affecting retinal ganglion cells,...

    Minoru Nakayama, Wioletta Nowak, Hitoshi Ishikawa, Ken Asakawa and Yoshiaki Ichibe

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:18

    Published on: 7 October 2014

  13. Research

    Unbiased bootstrap error estimation for linear discriminant analysis

    Convex bootstrap error estimation is a popular tool for classifier error estimation in gene expression studies. A basic question is how to determine the weight for the convex combination between the basic boot...

    Thang Vu, Chao Sima, Ulisses M Braga-Neto and Edward R Dougherty

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:15

    Published on: 3 October 2014

  14. Research

    Inference of dynamic biological networks based on responses to drug perturbations

    Drugs that target specific proteins are a major paradigm in cancer research. In this article, we extend a modeling framework for drug sensitivity prediction and combination therapy design based on drug perturb...

    Noah Berlow, Lara Davis, Charles Keller and Ranadip Pal

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:14

    Published on: 25 September 2014

  15. Research

    Template-based intervention in Boolean network models of biological systems

    A grand challenge in the modeling of biological systems is the identification of key variables which can act as targets for intervention. Boolean networks are among the simplest of models, yet they have been s...

    Michael P Verdicchio and Seungchan Kim

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:11

    Published on: 19 July 2014

  16. Research

    Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network

    The Dialogue for Reverse Engineering Assessments and Methods (DREAM) project was initiated in 2006 as a community-wide effort for the development of network inference challenges for rigorous assessment of reve...

    Peng Li, Ping Gong, Haoni Li, Edward J Perkins, Nan Wang and Chaoyang Zhang

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:12

    Published on: 16 July 2014

  17. Research

    Learning restricted Boolean network model by time-series data

    Restricted Boolean networks are simplified Boolean networks that are required for either negative or positive regulations between genes. Higa et al. (BMC Proc 5:S5, 2011) proposed a three-rule algorithm to inf...

    Hongjia Ouyang, Jie Fang, Liangzhong Shen, Edward R Dougherty and Wenbin Liu

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:10

    Published on: 15 July 2014

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