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BMC Bioinformatics

Knowledge-based analysis

Section edited by Hagit Shatkay

This section incorporates all aspects of knowledge-based analysis in biology including but not limited to: methods for the processing of text, ontologies and other computational representations of biological knowledge, as well as applications of knowledge-based systems for gaining insight into biology and biological data.

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  1. Content type: Software

    The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were de...

    Authors: Qing Wei, Ishita K. Khan, Ziyun Ding, Satwica Yerneni and Daisuke Kihara

    Citation: BMC Bioinformatics 2017 18:177

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  2. Content type: Research Article

    Investigating and understanding drug-drug interactions (DDIs) is important in improving the effectiveness of clinical care. DDIs can occur when two or more drugs are administered together. Experimentally based...

    Authors: Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic and Saman Halgamuge

    Citation: BMC Bioinformatics 2017 18:140

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  3. Content type: Research article

    The dominant paradigm in understanding drug action focuses on the intended therapeutic effects and frequent adverse reactions. However, this approach may limit opportunities to grasp unintended drug actions, w...

    Authors: Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park and Youngmi Yoon

    Citation: BMC Bioinformatics 2017 18:131

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  4. Content type: Research article

    The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the lack of ...

    Authors: Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade and Hong Cui

    Citation: BMC Bioinformatics 2016 17:528

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  5. Content type: Research article

    Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set o...

    Authors: Hong Cui, Dongfang Xu, Steven S. Chong, Martin Ramirez, Thomas Rodenhausen, James A. Macklin, Bertram Ludäscher, Robert A. Morris, Eduardo M. Soto and Nicolás Mongiardino Koch

    Citation: BMC Bioinformatics 2016 17:471

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  6. Content type: Research article

    Transcription factors are key proteins in the regulation of gene transcription. An important step in this process is the opening of chromatin in order to make genomic regions available for transcription. Data ...

    Authors: Rezvan Ehsani, Shahram Bahrami and Finn Drabløs

    Citation: BMC Bioinformatics 2016 17:459

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  7. Content type: Methodology Article

    Gene set testing, or pathway analysis, is a bioinformatics technique that performs statistical testing on biologically meaningful sets of genomic variables. Although originally developed for supervised analyse...

    Authors: H. Robert Frost and Christopher I. Amos

    Citation: BMC Bioinformatics 2016 17:442

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  8. Content type: Research article

    The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just sev...

    Authors: Junli Du, Manlin Li, Zhifa Yuan, Mancai Guo, Jiuzhou Song, Xiaozhen Xie and Yulin Chen

    Citation: BMC Bioinformatics 2016 17:407

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  9. Content type: Research article

    Clinical trial registries may allow for producing a global mapping of health research. However, health conditions are not described with standardized taxonomies in registries. Previous work analyzed clinical t...

    Authors: Ignacio Atal, Jean-David Zeitoun, Aurélie Névéol, Philippe Ravaud, Raphaël Porcher and Ludovic Trinquart

    Citation: BMC Bioinformatics 2016 17:392

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  10. Content type: Research Article

    Plants are natural products that humans consume in various ways including food and medicine. They have a long empirical history of treating diseases with relatively few side effects. Based on these strengths, ...

    Authors: Wonjun Choi, Baeksoo Kim, Hyejin Cho, Doheon Lee and Hyunju Lee

    Citation: BMC Bioinformatics 2016 17:386

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  11. Content type: Database

    Burkholderia mallei and B. pseudomallei are the causative agents of glanders and melioidosis, respectively, diseases with high morbidity and mortality rates. B. mallei and B. pseudomal...

    Authors: Vesna Memišević, Kamal Kumar, Nela Zavaljevski, David DeShazer, Anders Wallqvist and Jaques Reifman

    Citation: BMC Bioinformatics 2016 17:387

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  12. Content type: Methodology Article

    Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerge...

    Authors: Jose M González-Calabozo, Francisco J Valverde-Albacete and Carmen Peláez-Moreno

    Citation: BMC Bioinformatics 2016 17:374

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  13. Content type: Methodology Article

    It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit this information when the number of determinan...

    Authors: Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe and Arnoldo Frigessi

    Citation: BMC Bioinformatics 2016 17:344

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  14. Content type: Research article

    Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for larg...

    Authors: Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong and Wen Zou

    Citation: BMC Bioinformatics 2016 17:213

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:301

  15. Content type: Software

    MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation o...

    Authors: Julia Bayer, Carsten Kuenne, Jens Preussner and Mario Looso

    Citation: BMC Bioinformatics 2016 17:210

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  16. Content type: Database

    The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possibl...

    Authors: Christos Karapiperis, Stefan J. Kempf, Roel Quintens, Omid Azimzadeh, Victoria Linares Vidal, Simonetta Pazzaglia, Dimitry Bazyka, Pier G. Mastroberardino, Zacharias G. Scouras, Soile Tapio, Mohammed Abderrafi Benotmane and Christos A. Ouzounis

    Citation: BMC Bioinformatics 2016 17:212

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  17. Content type: Research Article

    Entity coreference is common in biomedical literature and it can affect text understanding systems that rely on accurate identification of named entities, such as relation extraction and automatic summarizatio...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Thomas C. Rindflesch

    Citation: BMC Bioinformatics 2016 17:163

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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