Networks analysis

Section edited by Jean-Philippe Vert

This section incorporates all aspects of network analysis including but not limited to: methods for predicting, analyzing and visualizing networks, and applications to systems biology.

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  1. Software

    NFPscanner: a webtool for knowledge-based deciphering of biomedical networks

    Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are u...

    Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo and Fei Li

    BMC Bioinformatics 2017 18:262

    Published on: 18 May 2017

  2. Research Article

    LASSIE: simulating large-scale models of biochemical systems on GPUs

    Mathematical modeling and in silico analysis are widely acknowledged as complementary tools to biological laboratory methods, to achieve a thorough understanding of emergent behaviors of cellular processes in ...

    Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri and Paolo Cazzaniga

    BMC Bioinformatics 2017 18:246

    Published on: 10 May 2017

  3. Software

    The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

    Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the...

    Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling and Héctor García Martín

    BMC Bioinformatics 2017 18:205

    Published on: 5 April 2017

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:219

  4. Research Article

    The autophagy interaction network of the aging model Podospora anserina

    Autophagy is a conserved molecular pathway involved in the degradation and recycling of cellular components. It is active either as response to starvation or molecular damage. Evidence is emerging that autopha...

    Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz and Ina Koch

    BMC Bioinformatics 2017 18:196

    Published on: 27 March 2017

  5. Methodology Article

    Enhanced construction of gene regulatory networks using hub gene information

    Gene regulatory networks reveal how genes work together to carry out their biological functions. Reconstructions of gene networks from gene expression data greatly facilitate our understanding of underlying bi...

    Donghyeon Yu, Johan Lim, Xinlei Wang, Faming Liang and Guanghua Xiao

    BMC Bioinformatics 2017 18:186

    Published on: 23 March 2017

  6. Methodology Article

    Preservation affinity in consensus modules among stages of HIV-1 progression

    Analysis of gene expression data provides valuable insights into disease mechanism. Investigating relationship among co-expression modules of different stages is a meaningful tool to understand the way in whic...

    Sk Md Mosaddek Hossain, Sumanta Ray and Anirban Mukhopadhyay

    BMC Bioinformatics 2017 18:181

    Published on: 20 March 2017

  7. Software

    Reactome pathway analysis: a high-performance in-memory approach

    Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway a...

    Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner, Pablo Marin-Garcia, Vicente Arnau, Peter D’Eustachio, Lincoln Stein and Henning Hermjakob

    BMC Bioinformatics 2017 18:142

    Published on: 2 March 2017

  8. Methodology Article

    Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO

    Conventional differential gene expression analysis by methods such as student’s t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them....

    Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li and Habtom W. Ressom

    BMC Bioinformatics 2017 18:99

    Published on: 10 February 2017

  9. Methodology Article

    An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data

    The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer...

    W. Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A. Shelburne and Marina Vannucci

    BMC Bioinformatics 2017 18:94

    Published on: 8 February 2017

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:185

  10. Methodology Article

    Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data

    With the increase in the amount of DNA methylation and gene expression data, the epigenetic mechanisms of cancers can be extensively investigate. Available methods integrate the DNA methylation and gene expres...

    Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang and Wanxin Tang

    BMC Bioinformatics 2017 18:72

    Published on: 31 January 2017

  11. Research article

    Dynamic substrate preferences predict metabolic properties of a simple microbial consortium

    Mixed cultures of different microbial species are increasingly being used to carry out a specific biochemical function in lieu of engineering a single microbe to do the same task. However, knowing how differen...

    Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau and Trent R. Northen

    BMC Bioinformatics 2017 18:57

    Published on: 23 January 2017

  12. Methodology Article

    Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

    The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic mod...

    David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo and Julio R. Banga

    BMC Bioinformatics 2017 18:52

    Published on: 21 January 2017

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