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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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  2. Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of differ...

    Authors: Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöery, Richard I. Kuo and Robert H. S. Kraus

    Citation: BMC Bioinformatics 2020 21:502

    Content type: Database

    Published on:

  3. Data obtained from flow cytometry present pronounced variability due to biological and technical reasons. Biological variability is a well-known phenomenon produced by measurements on different individuals, wi...

    Authors: Eustasio del Barrio, Hristo Inouzhe, Jean-Michel Loubes, Carlos Matrán and Agustín Mayo-Íscar

    Citation: BMC Bioinformatics 2020 21:479

    Content type: Methodology article

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  5. The amount of published full-text articles has increased dramatically. Text mining tools configure an essential approach to building biological networks, updating databases and providing annotation for new pat...

    Authors: Bruna Piereck, Marx Oliveira-Lima, Ana Maria Benko-Iseppon, Sarah Diehl, Reinhard Schneider, Ana Christina Brasileiro-Vidal and Adriano Barbosa-Silva

    Citation: BMC Bioinformatics 2020 21:365

    Content type: Software

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  6. Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole...

    Authors: Vincent Henry, Fatiha Saïs, Olivier Inizan, Elodie Marchadier, Juliette Dibie, Anne Goelzer and Vincent Fromion

    Citation: BMC Bioinformatics 2020 21:327

    Content type: Methodology article

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  7. Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermo...

    Authors: Zhi-Hui Luo, Meng-Wei Shi, Zhuang Yang, Hong-Yu Zhang and Zhen-Xia Chen

    Citation: BMC Bioinformatics 2020 21:252

    Content type: Software

    Published on:

  8. During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research field. While numerous existing methods focus on the in...

    Authors: Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt and Martin Hofmann-Apitius

    Citation: BMC Bioinformatics 2020 21:231

    Content type: Methodology article

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  9. In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we pres...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Dongwook Shin

    Citation: BMC Bioinformatics 2020 21:188

    Content type: Software

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  12. Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...

    Authors: Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun and Hongfei Lin

    Citation: BMC Bioinformatics 2020 21:125

    Content type: Methodology article

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  15. Current approaches to identifying drug-drug interactions (DDIs), include safety studies during drug development and post-marketing surveillance after approval, offer important opportunities to identify potenti...

    Authors: Remzi Celebi, Huseyin Uyar, Erkan Yasar, Ozgur Gumus, Oguz Dikenelli and Michel Dumontier

    Citation: BMC Bioinformatics 2019 20:726

    Content type: Research Article

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  18. In this study, we compared four models for predicting rice blast disease, two operational process-based models (Yoshino and Water Accounting Rice Model (WARM)) and two approaches based on machine learning algo...

    Authors: David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa Sarafijanovic-Djukic, Pau Puigdollers and Roberto Confalonieri

    Citation: BMC Bioinformatics 2019 20:514

    Content type: Research article

    Published on:

  19. Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting li...

    Authors: Alex Sánchez-Pla, Miquel Salicrú and Jordi Ocaña

    Citation: BMC Bioinformatics 2019 20:441

    Content type: Methodology article

    Published on:

  20. Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human...

    Authors: Yipei Wang, Xingyu Fan, Luoxin Chen, Eric I-Chao Chang, Sophia Ananiadou, Junichi Tsujii and Yan Xu

    Citation: BMC Bioinformatics 2019 20:430

    Content type: Methodology article

    Published on:

  21. Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the ass...

    Authors: Jurica Ševa, David Luis Wiegandt, Julian Götze, Mario Lamping, Damian Rieke, Reinhold Schäfer, Patrick Jähnichen, Madeleine Kittner, Steffen Pallarz, Johannes Starlinger, Ulrich Keilholz and Ulf Leser

    Citation: BMC Bioinformatics 2019 20:429

    Content type: Research article

    Published on:

  24. RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particu...

    Authors: Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan and Teresa Wu

    Citation: BMC Bioinformatics 2019 20:373

    Content type: Research article

    Published on:

  27. In the era of precision oncology and publicly available datasets, the amount of information available for each patient case has dramatically increased. From clinical variables and PET-CT radiomics measures to ...

    Authors: Michael C. Rendleman, John M. Buatti, Terry A. Braun, Brian J. Smith, Chibuzo Nwakama, Reinhard R. Beichel, Bart Brown and Thomas L. Casavant

    Citation: BMC Bioinformatics 2019 20:339

    Content type: Research article

    Published on:

  28. Ontology has attracted substantial attention from both academia and industry. Handling uncertainty reasoning is important in researching ontology. For example, when a patient is suffering from cirrhosis, the a...

    Authors: Ying Shen, Yaliang Li, Hai-Tao Zheng, Buzhou Tang and Min Yang

    Citation: BMC Bioinformatics 2019 20:330

    Content type: Research article

    Published on:

  29. The retrieval of plant-related information is a challenging task due to variations in species name mentions as well as spelling or typographical errors across data sources. Scalable solutions are needed for id...

    Authors: Vivekanand Sharma, Maria Isabel Restrepo and Indra Neil Sarkar

    Citation: BMC Bioinformatics 2019 20:263

    Content type: Software

    Published on:

  30. 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

    Content type: Methodology article

    Published on:

  31. 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

    Content type: Software

    Published on:

  33. 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

    Content type: Research article

    Published on:

  34. 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

    Content type: Methodology article

    Published on:

  35. 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

    Content type: Software

    Published on:

  38. 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

    Content type: Software

    Published on:

  40. 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

    Content type: Methodology article

    Published on:

  42. 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

    Content type: Software

    Published on:

  43. 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

    Content type: Research article

    Published on:

  44. 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

    Content type: Research article

    Published on:

  45. 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

    Content type: Research article

    Published on:

  46. 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

    Content type: Software

    Published on:

  50. 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

    Content type: Research article

    Published on:

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