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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: Research article

    Drug-disease associations provide important information for the drug discovery. Wet experiments that identify drug-disease associations are time-consuming and expensive. However, many drug-disease associations...

    Authors: Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang and Feng Liu

    Citation: BMC Bioinformatics 2018 19:233

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  2. Content type: Research Article

    A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequ...

    Authors: Shuonan Chen and Jessica C. Mar

    Citation: BMC Bioinformatics 2018 19:232

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  3. Content type: Research article

    Part of the missing heritability in Genome Wide Association Studies (GWAS) is expected to be explained by interactions between genetic variants, also called epistasis. Various statistical methods have been dev...

    Authors: Clément Chatelain, Guillermo Durand, Vincent Thuillier and Franck Augé

    Citation: BMC Bioinformatics 2018 19:231

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  4. Content type: Methodology article

    Discovery of mutated driver genes is one of the primary objective for studying tumorigenesis. To discover some relatively low frequently mutated driver genes from somatic mutation data, many existing methods i...

    Authors: Jianing Xi, Minghui Wang and Ao Li

    Citation: BMC Bioinformatics 2018 19:214

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  5. Content type: Research article

    Link prediction in biomedical graphs has several important applications including predicting Drug-Target Interactions (DTI), Protein-Protein Interaction (PPI) prediction and Literature-Based Discovery (LBD). I...

    Authors: Gamal Crichton, Yufan Guo, Sampo Pyysalo and Anna Korhonen

    Citation: BMC Bioinformatics 2018 19:176

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  6. Content type: Research article

    Recently, numerous laboratory studies have indicated that many microRNAs (miRNAs) are involved in and associated with human diseases and can serve as potential biomarkers and drug targets. Therefore, developin...

    Authors: Haochen Zhao, Linai Kuang, Lei Wang, Pengyao Ping, Zhanwei Xuan, Tingrui Pei and Zhelun Wu

    Citation: BMC Bioinformatics 2018 19:141

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  7. Content type: Software

    Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that research...

    Authors: M. Sivade (Dumousseau), D. Alonso-López, M. Ammari, G. Bradley, N. H. Campbell, A. Ceol, G. Cesareni, C. Combe, J. De Las Rivas, N. del-Toro, J. Heimbach, H. Hermjakob, I. Jurisica, M. Koch, L. Licata, R. C. Lovering…

    Citation: BMC Bioinformatics 2018 19:134

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  8. Content type: Software

    A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interc...

    Authors: M. Sivade (Dumousseau), M. Koch, A. Shrivastava, D. Alonso-López, J. De Las Rivas, N. del-Toro, C. W. Combe, B. H. M. Meldal, J. Heimbach, J. Rappsilber, J. Sullivan, Y. Yehudi and S. Orchard

    Citation: BMC Bioinformatics 2018 19:133

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  9. Content type: Methodology Article

    Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our...

    Authors: Yaogong Zhang, Jiahui Liu, Xiaohu Liu, Xin Fan, Yuxiang Hong, Yuan Wang, YaLou Huang and MaoQiang Xie

    Citation: BMC Bioinformatics 2018 19:47

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  10. Content type: Methodology Article

    Alzheimer’s disease (AD) is a chronic neuro-degenerative disruption of the brain which involves in large scale transcriptomic variation. The disease does not impact every regions of the brain at the same time,...

    Authors: Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun and Anirban Mukhopadhyay

    Citation: BMC Bioinformatics 2017 18:579

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  11. Content type: Research Article

    Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is curr...

    Authors: Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek and Kourosh Zarringhalam

    Citation: BMC Bioinformatics 2017 18:565

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  12. Content type: Methodology Article

    Transcription factors (TFs) form a complex regulatory network within the cell that is crucial to cell functioning and human health. While methods to establish where a TF binds to DNA are well established, thes...

    Authors: Maxwell Spadafore, Kayvan Najarian and Alan P. Boyle

    Citation: BMC Bioinformatics 2017 18:530

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  13. Content type: Software

    Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in m...

    Authors: Levi D. Mcclenny, Mahdi Imani and Ulisses M. Braga-Neto

    Citation: BMC Bioinformatics 2017 18:519

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  14. Content type: Software

    ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a...

    Authors: Yomtov Almozlino, Nir Atias, Dana Silverbush and Roded Sharan

    Citation: BMC Bioinformatics 2017 18:495

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  15. Content type: Research Article

    MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, ...

    Authors: Duc-Hau Le, Lieven Verbeke, Le Hoang Son, Dinh-Toi Chu and Van-Huy Pham

    Citation: BMC Bioinformatics 2017 18:479

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  16. Content type: Research Article

    An organism’s protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally...

    Authors: R. Greg Stacey, Michael A. Skinnider, Nichollas E. Scott and Leonard J. Foster

    Citation: BMC Bioinformatics 2017 18:457

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  17. Content type: Research Article

    Computational fusion approaches to drug-target interaction (DTI) prediction, capable of utilizing multiple sources of background knowledge, were reported to achieve superior predictive performance in multiple ...

    Authors: Bence Bolgár and Péter Antal

    Citation: BMC Bioinformatics 2017 18:440

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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