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Systems Engineering Approaches for Bioinformatics, Genomics, and Computational Biology

The aim of this special issue is to present the latest advances in the development and application of systems engineering methods in bioinformatics, genomics, and computational biology, in commemoration of the establishment of the Center for Bioinformatics and Genomics Systems Engineering (CBGSE) - a joint center of the Texas A&M Engineering Experiment Station (TEES) and Texas A&M AgriLife Research.

Edited by: Ulisses Braga-Neto, Xiaoning Qian,  Xiaodong Wang and Byung-Jun Yoon

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Research

    Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms

    The inference of gene regulatory networks is a core problem in systems biology. Many inference algorithms have been proposed and all suffer from false positives. In this paper, we use the minimum description l...

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

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:13

    Published on: 3 July 2014

  7. Research

    A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty

    Perfect knowledge of the underlying state transition probabilities is necessary for designing an optimal intervention strategy for a given Markovian genetic regulatory network. However, in many practical situa...

    Mohammadmahdi R Yousefi and Edward R Dougherty

    EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:6

    Published on: 3 April 2014