Skip to content

Advertisement

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. Content type: Research

    Discovery and validation of protein biomarkers with high specificity is the main challenge of current proteomics studies. Different mass spectrometry models are used as shotgun tools for the discovery of bioma...

    Authors: Esmaeil Atashpaz-Gargari, Ulisses M Braga-Neto and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:17

    Published on:

  2. Content type: Research

    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...

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

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:15

    Published on:

  3. Content type: Research

    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...

    Authors: Noah Berlow, Lara Davis, Charles Keller and Ranadip Pal

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:14

    Published on:

  4. Content type: Research

    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...

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

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:12

    Published on:

  5. Content type: Research

    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...

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

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:10

    Published on:

  6. Content type: Research

    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...

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

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:13

    Published on:

  7. Content type: Research

    Copy number variations (CNVs) are abundant in the human genome. They have been associated with complex traits in genome-wide association studies (GWAS) and expected to continue playing an important role in ide...

    Authors: Alexandros Iliadis, Dimitris Anastassiou and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:7

    Published on:

  8. Content type: Research

    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...

    Authors: Mohammadmahdi R Yousefi and Edward R Dougherty

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:6

    Published on:

  9. Content type: Research

    Parameter estimation in dynamic systems finds applications in various disciplines, including system biology. The well-known expectation-maximization (EM) algorithm is a popular method and has been widely used ...

    Authors: Bin Jia and Xiaodong Wang

    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2014 2014:5

    Published on: