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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

    Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associate...

    Authors: Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung and Steven H. Kleinstein

    Citation: BMC Bioinformatics 2018 19:268

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  2. Content type: Database

    For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers...

    Authors: John A. Bachman, Benjamin M. Gyori and Peter K. Sorger

    Citation: BMC Bioinformatics 2018 19:248

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  3. Content type: Methodology article

    Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tool...

    Authors: Rafael V. Veiga, Helio J. C. Barbosa, Heder S. Bernardino, João M. Freitas, Caroline A. Feitosa, Sheila M. A. Matos, Neuza M. Alcântara-Neves and Maurício L. Barreto

    Citation: BMC Bioinformatics 2018 19:245

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  4. Content type: Research article

    Identifying protein functional sites (PFSs) and, particularly, the physicochemical interactions at these sites is critical to understanding protein functions and the biochemical reactions involved. Several kno...

    Authors: Min Han, Yifan Song, Jiaqiang Qian and Dengming Ming

    Citation: BMC Bioinformatics 2018 19:204

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  5. Content type: Research article

    Predicting a list of plant taxa most likely to be observed at a given geographical location and time is useful for many scenarios in biodiversity informatics. Since efficient plant species identification is im...

    Authors: Hans Christian Wittich, Marco Seeland, Jana Wäldchen, Michael Rzanny and Patrick Mäder

    Citation: BMC Bioinformatics 2018 19:190

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  6. Content type: Software

    A quantitative trait locus (QTL) is a genomic region that correlates with a phenotype. Most of the experimental information about QTL mapping studies is described in tables of scientific publications. Traditio...

    Authors: Gurnoor Singh, Arnold Kuzniar, Erik M. van Mulligen, Anand Gavai, Christian W. Bachem, Richard G.F. Visser and Richard Finkers

    Citation: BMC Bioinformatics 2018 19:183

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  7. Content type: Methodology article

    Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most wi...

    Authors: Jiongmin Zhang, Ke Jia, Jinmeng Jia and Ying Qian

    Citation: BMC Bioinformatics 2018 19:161

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  8. Content type: Research article

    Mutations in the FMS-like tyrosine kinase 3 (FLT3) are associated with uncontrolled cellular functions that contribute to the development of acute myeloid leukaemia (AML). We performed computer simulations of ...

    Authors: Antoine Buetti-Dinh and Ran Friedman

    Citation: BMC Bioinformatics 2018 19:155

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  9. Content type: Research article

    Recent cancer genome studies on many human cancer types have relied on multiple molecular high-throughput technologies. Given the vast amount of data that has been generated, there are surprisingly few databas...

    Authors: Rasmus Krempel, Pranav Kulkarni, Annie Yim, Ulrich Lang, Bianca Habermann and Peter Frommolt

    Citation: BMC Bioinformatics 2018 19:156

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  10. Content type: Research article

    Drug repositioning is the process of identifying new targets for known drugs. It can be used to overcome problems associated with traditional drug discovery by adapting existing drugs to treat new discovered d...

    Authors: Makbule Guclin Ozsoy, Tansel Özyer, Faruk Polat and Reda Alhajj

    Citation: BMC Bioinformatics 2018 19:136

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    The Correction to this article has been published in BMC Bioinformatics 2018 19:250

  11. Content type: Research article

    Drug repositioning is the process of identifying new uses for existing drugs. Computational drug repositioning methods can reduce the time, costs and risks of drug development by automating the analysis of the...

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

    Citation: BMC Bioinformatics 2018 19:129

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  12. Content type: Research article

    Patient background (e.g. age, sex, and primary disease) is an important factor to consider when monitoring adverse drug events (ADEs) for the purpose of pharmacovigilance. However, in disproportionality method...

    Authors: Yoshihiro Noguchi, Anri Ueno, Manami Otsubo, Hayato Katsuno, Ikuto Sugita, Yuta Kanematsu, Aki Yoshida, Hiroki Esaki, Tomoya Tachi and Hitomi Teramachi

    Citation: BMC Bioinformatics 2018 19:124

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  13. Content type: Research Article

    Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health inf...

    Authors: Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton and Dina Demner-Fushman

    Citation: BMC Bioinformatics 2018 19:34

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  14. Content type: Research Article

    Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation ...

    Authors: Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su and Chunlei Wu

    Citation: BMC Bioinformatics 2018 19:30

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  15. Content type: Research Article

    Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and ...

    Authors: Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan and Jaewoo Kang

    Citation: BMC Bioinformatics 2018 19:21

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  16. Content type: Research Article

    The subcellular localization of a protein is an important aspect of its function. However, the experimental annotation of locations is not even complete for well-studied model organisms. Text mining might aid ...

    Authors: Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen and Burkhard Rost

    Citation: BMC Bioinformatics 2018 19:15

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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)

    Usage 
    3784657 downloads
    1405 Usage Factor


    Social Media Impact
    816 mentions

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