IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB

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From the July/August 2018 Issue

A Model-Based Tool for the Analysis and Design of Gene Regulatory Networks

By Liliana Ironi and Ettore Lanzarone

Featured article thumbnail image Computational and mathematical models have significantly contributed to the rapid progress in the study of gene regulatory networks (GRN), but researchers still lack a reliable model-based framework for computer-aided analysis and design. Such tool should both reveal the relation between network structure and dynamics and find parameter values and/or constraints that enable the simulated dynamics to reproduce specific behaviors. This paper addresses these issues and proposes a computational framework that facilitates network analysis or design. It follows a modeling cycle that alternates phases of hypothesis testing with parameter space refinement to ultimately propose a network that exhibits specified behaviors with the highest probability. Hypothesis testing is performed via qualitative simulation of GRNs modeled by a class of nonlinear and temporal multiscale ODEs, where regulation functions are expressed by steep sigmoid functions and incompletely known parameter values by order relations only. Parameter space refinement, grounded on a method that considers the intrinsic stochasticity of regulation by expressing network uncertainty with fluctuations in parameter values only, optimizes parameter stochastic values initialized by probability distributions with large variances. The power and ease of our framework is demonstrated by working out a benchmark synthetic network to get a synthetic oscillator.

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Editorials and Announcements


  • We are pleased to announce that Aidong Zhang, the SUNY Distinguished Professor in the Department of Computer Science and Engineering at the University at Buffalo, The State University of New York, has been named the new Editor-in-Chief of the IEEE/ACM Transactions on Computational Biology and Bioinformatics starting in 2017.
  • TCBB now offers authors access to Code Ocean. Code Ocean is a cloud-based executable research platform that allows authors to share their algorithms in an effort to make the world’s scientific code more open and reproducible. Learn more or sign up for free.


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TCBB is a joint publication of the IEEE Computer Society and the Association for Computing Machinery.

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Published in cooperation with: IEEE Control Systems Society and IEEE Engineering in Medicine and Biology Society

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