Skip to content

Advertisement

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.

Page 1 of 4

  1. Content type: Methodology article

    Set enrichment methods are commonly used to analyze high-dimensional molecular data and gain biological insight into molecular or clinical phenotypes. One important category of analysis methods employs an enri...

    Authors: Joanna Roder, Benjamin Linstid and Carlos Oliveira

    Citation: BMC Bioinformatics 2019 20:257

    Published on:

  2. Content type: Software

    With advancements in high-throughput technologies, the cost of obtaining expression profiles of both mRNA and microRNA in the same individual has substantially decreased. Integrated analysis of these profiles ...

    Authors: Ti-Tai Wang, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang

    Citation: BMC Bioinformatics 2019 20:239

    Published on:

  3. Content type: Research article

    Neural network based embedding models are receiving significant attention in the field of natural language processing due to their capability to effectively capture semantic information representing words, sen...

    Authors: Kathrin Blagec, Hong Xu, Asan Agibetov and Matthias Samwald

    Citation: BMC Bioinformatics 2019 20:178

    Published on:

  4. Content type: Methodology article

    For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential ...

    Authors: Wei Gu, Reha Yildirimman, Emmanuel Van der Stuyft, Denny Verbeeck, Sascha Herzinger, Venkata Satagopam, Adriano Barbosa-Silva, Reinhard Schneider, Bodo Lange, Hans Lehrach, Yike Guo, David Henderson and Anthony Rowe

    Citation: BMC Bioinformatics 2019 20:164

    Published on:

  5. Content type: Software

    Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data access...

    Authors: Daniel Perez-Gil, Francisco J. Lopez, Joaquin Dopazo, Pablo Marin-Garcia, Augusto Rendon and Ignacio Medina

    Citation: BMC Bioinformatics 2019 20:159

    Published on:

  6. Content type: Software

    Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...

    Authors: Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki and Dario Greco

    Citation: BMC Bioinformatics 2019 20:79

    Published on:

  7. Content type: Methodology article

    Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...

    Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf and Dirar Homouz

    Citation: BMC Bioinformatics 2019 20:70

    Published on:

  8. Content type: Software

    Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In ...

    Authors: Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos and Robert Hoehndorf

    Citation: BMC Bioinformatics 2019 20:65

    Published on:

  9. Content type: Research article

    Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and de...

    Authors: Xiaozheng Li, Huazhen Wang, Huixin He, Jixiang Du, Jian Chen and Jinzhun Wu

    Citation: BMC Bioinformatics 2019 20:62

    Published on:

  10. Content type: Research article

    Accurate prediction of anticancer drug responses in cell lines is a crucial step to accomplish the precision medicine in oncology. Although many popular computational models have been proposed towards this non...

    Authors: Dong Wei, Chuanying Liu, Xiaoqi Zheng and Yushuang Li

    Citation: BMC Bioinformatics 2019 20:44

    Published on:

  11. 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

    Published on:

  12. 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

    Published on:

  13. 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

    Published on:

  14. 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

    Published on:

  15. 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

    Published on:

  16. 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

    Published on:

  17. 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

    Published on:

  18. 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

    Published on:

  19. 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

    Published on:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

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

  24. 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

    Published on:

  25. 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

    Published on:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

    Published on:

  33. 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

    Published on:

  34. 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

    Published on:

  35. 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

    Published on:

  36. 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

    Published on:

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

Advertisement