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BMC Bioinformatics

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. Content type: Research Article

    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 ...

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

    Citation: BMC Bioinformatics 2017 18:246

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  2. Content type: Software

    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...

    Authors: 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

    Citation: BMC Bioinformatics 2017 18:205

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

  3. Content type: Research article

    Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome s...

    Authors: J. Harry Caufield, Christopher Wimble, Semarjit Shary, Stefan Wuchty and Peter Uetz

    Citation: BMC Bioinformatics 2017 18:171

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  4. Content type: Research article

    With the advancement of high-throughput technologies and enrichment of popular public databases, more and more research focuses of bioinformatics research have been on computational integration of network and ...

    Authors: Hao He, Dongdong Lin, Jigang Zhang, Yu-ping Wang and Hong-wen Deng

    Citation: BMC Bioinformatics 2017 18:149

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  5. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:142

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  6. Content type: Methodology Article

    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....

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

    Citation: BMC Bioinformatics 2017 18:99

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  7. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:94

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

  8. Content type: Methodology Article

    Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can ...

    Authors: Govind Nair, Christian Jungreuthmayer and Jürgen Zanghellini

    Citation: BMC Bioinformatics 2017 18:78

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  9. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:72

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  10. Content type: Methodology Article

    Gene regulatory interactions are of fundamental importance to various biological functions and processes. However, only a few previous computational studies have claimed success in revealing genome-wide regula...

    Authors: Shupeng Gui, Andrew P. Rice, Rui Chen, Liang Wu, Ji Liu and Hongyu Miao

    Citation: BMC Bioinformatics 2017 18:74

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  11. Content type: Research article

    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...

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

    Citation: BMC Bioinformatics 2017 18:57

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  12. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2017 18:52

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  13. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:41

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

    Social Media Impact
    816 mentions