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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: 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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  2. 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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  3. 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

  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. Content type: Research article

    Drug-drug interactions (DDIs) are one of the major concerns in drug discovery. Accurate prediction of potential DDIs can help to reduce unexpected interactions in the entire lifecycle of drugs, and are importa...

    Authors: Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian and Xiaohong Li

    Citation: BMC Bioinformatics 2017 18:18

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  11. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2016 17:544

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  12. Content type: Methodology Article

    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...

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

    Citation: BMC Bioinformatics 2016 17:542

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  13. Content type: Research Article

    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...

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

    Citation: BMC Bioinformatics 2016 17:527

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  14. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2016 17:494

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  15. Content type: Methodology article

    Gene network inference (GNI) algorithms can be used to identify sets of coordinately expressed genes, termed network modules from whole transcriptome gene expression data. The identification of such modules ha...

    Authors: Casey P. Shannon, Virginia Chen, Mandeep Takhar, Zsuzsanna Hollander, Robert Balshaw, Bruce M. McManus, Scott J. Tebbutt, Don D. Sin and Raymond T. Ng

    Citation: BMC Bioinformatics 2016 17:460

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  16. Content type: Research Article

    Accurately prioritizing candidate disease genes is an important and challenging problem. Various network-based methods have been developed to predict potential disease genes by utilizing the disease similarity...

    Authors: Jingchao Ni, Mehmet Koyuturk, Hanghang Tong, Jonathan Haines, Rong Xu and Xiang Zhang

    Citation: BMC Bioinformatics 2016 17:453

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  17. Content type: Research Article

    Biological networks provide great potential to understand how cells function. Network motifs, frequent topological patterns, are key structures through which biological networks operate. Finding motifs in biol...

    Authors: Rasha Elhesha and Tamer Kahveci

    Citation: BMC Bioinformatics 2016 17:408

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  18. Content type: Methodology article

    Prior knowledge networks (PKNs) provide a framework for the development of computational biological models, including Boolean models of regulatory networks which are the focus of this work. PKNs are created by...

    Authors: Julien Dorier, Isaac Crespo, Anne Niknejad, Robin Liechti, Martin Ebeling and Ioannis Xenarios

    Citation: BMC Bioinformatics 2016 17:410

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  19. Content type: Research Article

    Several recent studies have used the Minimum Dominating Set (MDS) model to identify driver nodes, which provide the control of the underlying networks, in protein interaction networks. There may exist multiple...

    Authors: Xiao-Fei Zhang, Le Ou-Yang, Dao-Qing Dai, Meng-Yun Wu, Yuan Zhu and Hong Yan

    Citation: BMC Bioinformatics 2016 17:358

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  20. Content type: Methodology article

    Rapid technological innovation for the generation of single-cell genomics data presents new challenges and opportunities for bioinformatics analysis. One such area lies in the development of new ways to train ...

    Authors: Chee Yee Lim, Huange Wang, Steven Woodhouse, Nir Piterman, Lorenz Wernisch, Jasmin Fisher and Berthold Göttgens

    Citation: BMC Bioinformatics 2016 17:355

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  21. Content type: Methodology Article

    Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for ne...

    Authors: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit

    Citation: BMC Bioinformatics 2016 17:352

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  22. Content type: Software

    The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA—the backbone of microbiome analyses—allows ...

    Authors: Helena Mendes-Soares, Michael Mundy, Luis Mendes Soares and Nicholas Chia

    Citation: BMC Bioinformatics 2016 17:343

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  23. Content type: Methodology article

    Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy, an...

    Authors: Xue Zhang, Wangxin Xiao, Marcio Luis Acencio, Ney Lemke and Xujing Wang

    Citation: BMC Bioinformatics 2016 17:322

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  24. Content type: Research Article

    Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks...

    Authors: Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek and Kourosh Zarringhalam

    Citation: BMC Bioinformatics 2016 17:318

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  25. Content type: Methodology Article

    Sparse Gaussian graphical models are popular for inferring biological networks, such as gene regulatory networks. In this paper, we investigate the consistency of these models across different data platforms, ...

    Authors: Veronica Vinciotti, Ernst C. Wit, Rick Jansen, Eco J. C. N. de Geus, Brenda W. J. H. Penninx, Dorret I. Boomsma and Peter A. C. ’t Hoen

    Citation: BMC Bioinformatics 2016 17:254

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  26. Content type: Software

    Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth...

    Authors: Luciano Fernandez-Ricaud, Olga Kourtchenko, Martin Zackrisson, Jonas Warringer and Anders Blomberg

    Citation: BMC Bioinformatics 2016 17:249

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  27. Content type: Research article

    The targeting of disease-related proteins is important for drug discovery, and yet target-based discovery has not been fruitful. Contextualizing overall biological processes is critical to formulating successf...

    Authors: Naiem T. Issa, Jordan Kruger, Henri Wathieu, Rajarajan Raja, Stephen W. Byers and Sivanesan Dakshanamurthy

    Citation: BMC Bioinformatics 2016 17:202

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  28. Content type: Research article

    Recently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology a...

    Authors: Yijia Zhang, Hongfei Lin, Zhihao Yang and Jian Wang

    Citation: BMC Bioinformatics 2016 17:186

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  29. Content type: Software

    We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG). The language captures in broad terms the effect of the changing...

    Authors: Adam Spiro and Ehud Shapiro

    Citation: BMC Bioinformatics 2016 17:187

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:303

  30. Content type: Software

    Biological research increasingly relies on network models to study complex phenomena. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from ...

    Authors: Gianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna and Stefano Di Carlo

    Citation: BMC Bioinformatics 2016 17:157

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  31. Content type: Software

    Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed...

    Authors: Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gael Jalowicki, Martina Kutmon, Kedar N. Natarajan, David Tolnay, Melanie I. Stefan, Chris T. Evelo and Nicolas Le Novère

    Citation: BMC Bioinformatics 2016 17:154

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  32. Content type: Research Article

    It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein ...

    Authors: Shailesh Tripathi, Salissou Moutari, Matthias Dehmer and Frank Emmert-Streib

    Citation: BMC Bioinformatics 2016 17:129

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  33. Content type: Methodology article

    Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available...

    Authors: Sapna Kumari, Wenping Deng, Chathura Gunasekara, Vincent Chiang, Huann-sheng Chen, Hao Ma, Xin Davis and Hairong Wei

    Citation: BMC Bioinformatics 2016 17:132

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  34. Content type: Methodology Article

    Networks or graphs play an important role in the biological sciences. Protein interaction networks and metabolic networks support the understanding of basic cellular mechanisms. In the human brain, networks of...

    Authors: Klaus Hahn, Peter R. Massopust and Sergei Prigarin

    Citation: BMC Bioinformatics 2016 17:87

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  35. Content type: Methodology article

    Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. A key but inadequately addressed issue is how to test possible differences of the n...

    Authors: Jiadong Ji, Zhongshang Yuan, Xiaoshuai Zhang and Fuzhong Xue

    Citation: BMC Bioinformatics 2016 17:86

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  36. Content type: Software

    Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and ...

    Authors: Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri and Marco Antoniotti

    Citation: BMC Bioinformatics 2016 17:64

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  37. Content type: Research Article

    Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn’s disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray ...

    Authors: Daniele Muraro and Alison Simmons

    Citation: BMC Bioinformatics 2016 17:42

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  38. Content type: Research Article

    Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless,...

    Authors: Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel and Alejandro Maass

    Citation: BMC Bioinformatics 2016 17:35

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


    Social Media Impact
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