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. 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

  2. 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

  3. 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

  4. 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. Shelbourne and Marina Vannucci

    BMC Bioinformatics 2017 18:94

    Published on: 8 February 2017

  5. 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

  6. 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

  7. 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

  8. Software

    SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information

    The molecular assays that test gene expression, transcriptional, and epigenetic regulation are increasingly diverse and numerous. The information generated by each type of assay individually gives an insight i...

    N. Ari Wijetunga, Andrew D. Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim and John M. Greally

    BMC Bioinformatics 2017 18:41

    Published on: 18 January 2017

  9. Methodology Article

    Block network mapping approach to quantitative trait locus analysis

    Advances in experimental biology have enabled the collection of enormous troves of data on genomic variation in living organisms. The interpretation of this data to extract actionable information is one of the...

    Zeina Z. Shreif, Daniel M. Gatti and Vipul Periwal

    BMC Bioinformatics 2016 17:544

    Published on: 22 December 2016

  10. Methodology Article

    Efficient randomization of biological networks while preserving functional characterization of individual nodes

    Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and...

    Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman and Julio Saez-Rodriguez

    BMC Bioinformatics 2016 17:542

    Published on: 20 December 2016

  11. Research Article

    PROPER: global protein interaction network alignment through percolation matching

    The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can...

    Ehsan Kazemi, Hamed Hassani, Matthias Grossglauser and Hassan Pezeshgi Modarres

    BMC Bioinformatics 2016 17:527

    Published on: 12 December 2016

  12. Software

    STON: exploring biological pathways using the SBGN standard and graph databases

    When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient sto...

    Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet and Charles Auffray

    BMC Bioinformatics 2016 17:494

    Published on: 5 December 2016

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