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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

    The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genot...

    Authors: Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts and Karen E. Nelson

    Citation: BMC Bioinformatics 2019 20:8

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  2. Content type: Research article

    Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific res...

    Authors: Andre Lamurias, Diana Sousa, Luka A. Clarke and Francisco M. Couto

    Citation: BMC Bioinformatics 2019 20:10

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  3. Content type: Research article

    Biomedical knowledge grows in complexity, and becomes encoded in network-based repositories, which include focused, expert-drawn diagrams, networks of evidence-based associations and established ontologies. Co...

    Authors: Marek Ostaszewski, Emmanuel Kieffer, Grégoire Danoy, Reinhard Schneider and Pascal Bouvry

    Citation: BMC Bioinformatics 2018 19:308

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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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

  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. Content type: Methodology article

    Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional re...

    Authors: Miguel Ángel Rodríguez-García and Robert Hoehndorf

    Citation: BMC Bioinformatics 2018 19:7

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  21. Content type: Methodology Article

    Prediction in high dimensional settings is difficult due to the large number of variables relative to the sample size. We demonstrate how auxiliary ‘co-data’ can be used to improve the performance of a Random ...

    Authors: Dennis E. te Beest, Steven W. Mes, Saskia M. Wilting, Ruud H. Brakenhoff and Mark A. van de Wiel

    Citation: BMC Bioinformatics 2017 18:584

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  22. Content type: Methodology Article

    In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practic...

    Authors: Bart J. G. Broeckx, Luc Peelman, Jimmy H. Saunders, Dieter Deforce and Lieven Clement

    Citation: BMC Bioinformatics 2017 18:535

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  23. Content type: Methodology Article

    Researchers have previously developed a multitude of methods designed to identify biological pathways associated with specific clinical or experimental conditions of interest, with the aim of facilitating biol...

    Authors: Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist and Jaques Reifman

    Citation: BMC Bioinformatics 2017 18:453

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  24. Content type: Research Article

    The prediction of human gene–abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with ...

    Authors: Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini

    Citation: BMC Bioinformatics 2017 18:449

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  25. Content type: Research Article

    Drug-drug interactions (DDIs) often bring unexpected side effects. The clinical recognition of DDIs is a crucial issue for both patient safety and healthcare cost control. However, although text-mining-based s...

    Authors: Wei Zheng, Hongfei Lin, Ling Luo, Zhehuan Zhao, Zhengguang Li, Yijia Zhang, Zhihao Yang and Jian Wang

    Citation: BMC Bioinformatics 2017 18:445

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  26. Content type: Research Article

    Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling techno...

    Authors: Maria Taboada, Hadriana Rodriguez, Ranga C. Gudivada and Diego Martinez

    Citation: BMC Bioinformatics 2017 18:446

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  27. Content type: Research Article

    The human microbiota is associated with various disease states and holds a great promise for non-invasive diagnostics. However, microbiota data is challenging for traditional diagnostic approaches: It is high-...

    Authors: A. Eck, L. M. Zintgraf, E. F. J. de Groot, T. G. J. de Meij, T. S. Cohen, P. H. M. Savelkoul, M. Welling and A. E. Budding

    Citation: BMC Bioinformatics 2017 18:441

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  28. Content type: Research Article

    Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...

    Authors: K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer and Lawrence E. Hunter

    Citation: BMC Bioinformatics 2017 18:372

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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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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)


    Social Media Impact
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