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Computational methods for biomarker discovery and systems biology research

This special issue consists of recent advances in computational methods, algorithms, and applications in biomarker discovery and systems biology research.

Edited by: Habtom Ressom

  1. Research

    Tracking of time-varying genomic regulatory networks with a LASSO-Kalman smoother

    It is widely accepted that cellular requirements and environmental conditions dictate the architecture of genetic regulatory networks. Nonetheless, the status quo in regulatory network modeling and analysis as...

    Jehandad Khan, Nidhal Bouaynaya and Hassan M Fathallah-Shaykh

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:3

    Published on: 12 February 2014

  2. Research

    Identification of genomic functional hotspots with copy number alteration in liver cancer

    Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic surve...

    Tzu-Hung Hsiao, Hung-I Harry Chen, Stephanie Roessler, Xin Wei Wang and Yidong Chen

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:14

    Published on: 25 October 2013

  3. Research

    Bayesian methods for expression-based integration of various types of genomics data

    We propose methods to integrate data across several genomic platforms using a hierarchical Bayesian analysis framework that incorporates the biological relationships among the platforms to identify genes whose...

    Elizabeth M Jennings, Jeffrey S Morris, Raymond J Carroll, Ganiraju C Manyam and Veerabhadran Baladandayuthapani

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:13

    Published on: 21 September 2013

  4. Research

    Feature ranking based on synergy networks to identify prognostic markers in DPT-1

    Interaction among different risk factors plays an important role in the development and progress of complex disease, such as diabetes. However, traditional epidemiological methods often focus on analyzing indi...

    Amin Ahmadi Adl, Xiaoning Qian, Ping Xu, Kendra Vehik and Jeffrey P Krischer

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:12

    Published on: 19 September 2013

  5. Research

    Integrating multi-platform genomic data using hierarchical Bayesian relevance vector machines

    Recent advances in genome technologies and the subsequent collection of genomic information at various molecular resolutions hold promise to accelerate the discovery of new therapeutic targets. A critical step...

    Sanvesh Srivastava, Wenyi Wang, Ganiraju Manyam, Carlos Ordonez and Veerabhadran Baladandayuthapani

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:9

    Published on: 28 June 2013

  6. Research

    Identification of thresholds for dichotomizing DNA methylation data

    DNA methylation plays an important role in many biological processes by regulating gene expression. It is commonly accepted that turning on the DNA methylation leads to silencing of the expression of the corre...

    Yihua Liu, Yuan Ji and Peng Qiu

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:8

    Published on: 6 June 2013

  7. Research

    Hierarchical Dirichlet process model for gene expression clustering

    Clustering is an important data processing tool for interpreting microarray data and genomic network inference. In this article, we propose a clustering algorithm based on the hierarchical Dirichlet processes ...

    Liming Wang and Xiaodong Wang

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:5

    Published on: 12 April 2013

  8. Research

    Protein network-based Lasso regression model for the construction of disease-miRNA functional interactions

    There is a growing body of evidence associating microRNAs (miRNAs) with human diseases. MiRNAs are new key players in the disease paradigm demonstrating roles in several human diseases. The functional associat...

    Ala Qabaja, Mohammed Alshalalfa, Tarek A Bismar and Reda Alhajj

    EURASIP Journal on Bioinformatics and Systems Biology 2013 2013:3

    Published on: 22 January 2013