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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.

Page 1 of 8

  1. Content type: Software

    Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exi...

    Authors: Deisy Morselli Gysi, Andre Voigt, Tiago de Miranda Fragoso, Eivind Almaas and Katja Nowick

    Citation: BMC Bioinformatics 2018 19:392

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  2. Content type: Research article

    Protein complexes are one of the keys to deciphering the behavior of a cell system. During the past decade, most computational approaches used to identify protein complexes have been based on discovering dense...

    Authors: Xiaoxia Liu, Zhihao Yang, Shengtian Sang, Ziwei Zhou, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang and Bo Xu

    Citation: BMC Bioinformatics 2018 19:332

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  3. Content type: Research article

    Constraint-based metabolic flux analysis of knockout strategies is an efficient method to simulate the production of useful metabolites in microbes. Owing to the recent development of technologies for artifici...

    Authors: Takeyuki Tamura

    Citation: BMC Bioinformatics 2018 19:325

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  4. Content type: Software

    Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often (“motifs”). A societal example of a motif might be a household. Replacing such motifs by named supernode...

    Authors: Danilo Dessì, Jacopo Cirrone, Diego Reforgiato Recupero and Dennis Shasha

    Citation: BMC Bioinformatics 2018 19:318

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  5. Content type: Research article

    Target identification is necessary for the comprehensive inference of the mechanism of action of a compound. The application of computational methods to predict the targets of bioactive compounds saves cost an...

    Authors: Hao Sun, Yiting Shen, Guangwen Luo, Yuepiao Cai and Zheng Xiang

    Citation: BMC Bioinformatics 2018 19:315

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  6. Content type: Software

    Genetic epistasis is an often-overlooked area in the study of the genomics of complex traits. Genome-wide association studies are a useful tool for revealing potential causal genetic variants, but in this cont...

    Authors: Victor A. O. Carmelo, Lisette J. A. Kogelman, Majbritt Busk Madsen and Haja N. Kadarmideen

    Citation: BMC Bioinformatics 2018 19:277

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  7. Content type: Research article

    There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predic...

    Authors: Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin

    Citation: BMC Bioinformatics 2018 19:264

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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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

  32. 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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  33. 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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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)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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