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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: 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. Content type: Research Article

    Colorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through t...

    Authors: Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun and Qingling Zhang

    Citation: BMC Bioinformatics 2017 18:388

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  11. Content type: Research Article

    As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasing...

    Authors: Lisa Katharina Blaß, Christian Weyler and Elmar Heinzle

    Citation: BMC Bioinformatics 2017 18:366

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  12. Content type: Software

    sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA)....

    Authors: Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer and Frank Emmert-Streib

    Citation: BMC Bioinformatics 2017 18:325

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  13. Content type: Research Article

    Colorectal carcinoma evolves through a multitude of molecular events including somatic mutations, epigenetic alterations, and aberrant protein expression, influenced by host immune reactions. One way to interr...

    Authors: Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino and Jukka-Pekka Onnela

    Citation: BMC Bioinformatics 2017 18:304

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  14. Content type: Software

    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...

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

    Citation: BMC Bioinformatics 2017 18:262

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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