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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. 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

    Content type: Research Article

    Published on:

  2. 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

    Content type: Methodology Article

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  3. 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

    Content type: Methodology Article

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  6. 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

    Content type: Research article

    Published on:

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

  7. 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

    Content type: Database

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  8. 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

    Content type: Software

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  9. 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

    Content type: Research Article

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  10. Existing feature selection methods typically do not consider prior knowledge in the form of structural relationships among features. In this study, the features are structured based on prior knowledge into gro...

    Authors: Mohamed F. Ghalwash, Xi Hang Cao, Ivan Stojkovic and Zoran Obradovic

    Citation: BMC Bioinformatics 2016 17:158

    Content type: Methodology Article

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  12. Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is ...

    Authors: Xiaochun Sun and Rita H. Mumm

    Citation: BMC Bioinformatics 2016 17:73

    Content type: Methodology article

    Published on:

  13. All proteins associate with other molecules. These associated molecules are highly predictive of the potential functions of proteins. The association of a protein and a molecule can be determined from their co...

    Authors: Kamal Taha and Paul D. Yoo

    Citation: BMC Bioinformatics 2016 17:34

    Content type: Research article

    Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:105

  14. Natural language processing (NLP) applications are increasingly important in biomedical data analysis, knowledge engineering, and decision support. Concept recognition is an important component task for NLP pi...

    Authors: Eugene Tseytlin, Kevin Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan and Rebecca S. Jacobson

    Citation: BMC Bioinformatics 2016 17:32

    Content type: Software

    Published on:

  15. Precision medicine requires the tight integration of clinical and molecular data. To this end, it is mandatory to define proper technological solutions able to manage the overwhelming amount of high throughput...

    Authors: Matteo Gabetta, Ivan Limongelli, Ettore Rizzo, Alberto Riva, Daniele Segagni and Riccardo Bellazzi

    Citation: BMC Bioinformatics 2015 16:415

    Content type: Software

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  18. Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment of Gene Ontology (GO) annotations to genes ...

    Authors: Pietro Di Lena, Giacomo Domeniconi, Luciano Margara and Gianluca Moro

    Citation: BMC Bioinformatics 2015 16:346

    Content type: Methodology Article

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  19. Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or ...

    Authors: Ashley J. Waardenberg, Samuel D. Bassett, Romaric Bouveret and Richard P. Harvey

    Citation: BMC Bioinformatics 2015 16:275

    Content type: Software

    Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:179

  21. Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisa...

    Authors: Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard and Chris T. Evelo

    Citation: BMC Bioinformatics 2015 16:267

    Content type: Software

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  22. Feature engineering is a time consuming component of predictive modeling. We propose a versatile platform to automatically extract features for risk prediction, based on a pre-defined and extensible entity sch...

    Authors: Truyen Tran, Wei Luo, Dinh Phung, Sunil Gupta, Santu Rana, Richard Lee Kennedy, Ann Larkins and Svetha Venkatesh

    Citation: BMC Bioinformatics 2014 15:425

    Content type: Research article

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  24. Biomedical ontologies are increasingly instrumental in the advancement of biological research primarily through their use to efficiently consolidate large amounts of data into structured, accessible sets. Howe...

    Authors: Joao A Ascensao, Mary E Dolan, David P Hill and Judith A Blake

    Citation: BMC Bioinformatics 2014 15:405

    Content type: Methodology article

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  25. Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ‘omics’ data can be...

    Authors: Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov and Martin Kuiper

    Citation: BMC Bioinformatics 2014 15:386

    Content type: Research article

    Published on:

  26. The invasion of red blood cells (RBCs) by malarial parasites is an essential step in the life cycle of Plasmodium falciparum. Human-parasite surface protein interactions play a critical role in this process. Alth...

    Authors: Xuewu Liu, Yuxiao Huang, Jiao Liang, Shuai Zhang, Yinghui Li, Jun Wang, Yan Shen, Zhikai Xu and Ya Zhao

    Citation: BMC Bioinformatics 2014 15:393

    Content type: Research article

    Published on:

  27. In order to extract meaningful information from electronic medical records, such as signs and symptoms, diagnoses, and treatments, it is important to take into account the contextual properties of the identifi...

    Authors: Zubair Afzal, Ewoud Pons, Ning Kang, Miriam CJM Sturkenboom, Martijn J Schuemie and Jan A Kors

    Citation: BMC Bioinformatics 2014 15:373

    Content type: Research article

    Published on:

  28. Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological proces...

    Authors: Rocío Rodríguez-López, Armando Reyes-Palomares, Francisca Sánchez-Jiménez and Miguel Ángel Medina

    Citation: BMC Bioinformatics 2014 15:375

    Content type: Software

    Published on:

  29. In modern biomedical research of complex diseases, a large number of demographic and clinical variables, herein called phenomic data, are often collected and missing values (MVs) are inevitable in the data col...

    Authors: Serena G Liao, Yan Lin, Dongwan D Kang, Divay Chandra, Jessica Bon, Naftali Kaminski, Frank C Sciurba and George C Tseng

    Citation: BMC Bioinformatics 2014 15:346

    Content type: Research article

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  32. Text mining is increasingly used in the biomedical domain because of its ability to automatically gather information from large amount of scientific articles. One important task in biomedical text mining is re...

    Authors: Yifan Peng, Manabu Torii, Cathy H Wu and K Vijay-Shanker

    Citation: BMC Bioinformatics 2014 15:285

    Content type: Research article

    Published on:

  34. Natural Language Processing (NLP) has been shown effective to analyze the content of radiology reports and identify diagnosis or patient characteristics. We evaluate the combination of NLP and machine learning...

    Authors: Anne-Dominique Pham, Aurélie Névéol, Thomas Lavergne, Daisuke Yasunaga, Olivier Clément, Guy Meyer, Rémy Morello and Anita Burgun

    Citation: BMC Bioinformatics 2014 15:266

    Content type: Research article

    Published on:

  35. With the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or s...

    Authors: Dany Morisset, Petra Kralj Novak, Darko Zupanič, Kristina Gruden, Nada Lavrač and Jana Žel

    Citation: BMC Bioinformatics 2014 15:258

    Content type: Software

    Published on:

  36. Recent years have brought great progress in efforts to digitize the world’s biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web...

    Authors: Brian J Stucky, John Deck, Tom Conlin, Lukasz Ziemba, Nico Cellinese and Robert Guralnick

    Citation: BMC Bioinformatics 2014 15:257

    Content type: Software

    Published on:

  37. Bacterial pathogenicity represents a major public health concern worldwide. Secretion systems are a key component of bacterial pathogenicity, as they provide the means for bacterial proteins to penetrate host-...

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

    Citation: BMC Bioinformatics 2014 15:244

    Content type: Database

    Published on:

  38. Pulmonary acoustic parameters extracted from recorded respiratory sounds provide valuable information for the detection of respiratory pathologies. The automated analysis of pulmonary acoustic signals can serv...

    Authors: Rajkumar Palaniappan, Kenneth Sundaraj and Sebastian Sundaraj

    Citation: BMC Bioinformatics 2014 15:223

    Content type: Research article

    Published on:

  40. The life-science community faces a major challenge in handling “big data”, highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, a...

    Authors: Daniel Arend, Matthias Lange, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht and Uwe Scholz

    Citation: BMC Bioinformatics 2014 15:214

    Content type: Software

    Published on:

  41. Despite increased investment in pharmaceutical research and development, fewer and fewer new drugs are entering the marketplace. This has prompted studies in repurposing existing drugs for use against diseases...

    Authors: Ruifeng Liu, Narender Singh, Gregory J Tawa, Anders Wallqvist and Jaques Reifman

    Citation: BMC Bioinformatics 2014 15:210

    Content type: Methodology article

    Published on:

  43. Erroneous patient birthdates are common in health databases. Detection of these errors usually involves manual verification, which can be resource intensive and impractical. By identifying a frequent manifesta...

    Authors: Wei Luo, Marcus Gallagher, Bill Loveday, Susan Ballantyne, Jason P Connor and Janet Wiles

    Citation: BMC Bioinformatics 2014 15:185

    Content type: Research article

    Published on:

  44. Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. The amount of disease-related literature...

    Authors: Toshihide Ono and Satoru Kuhara

    Citation: BMC Bioinformatics 2014 15:179

    Content type: Research article

    Published on:

  47. The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational ...

    Authors: Rachael P Huntley, Midori A Harris, Yasmin Alam-Faruque, Judith A Blake, Seth Carbon, Heiko Dietze, Emily C Dimmer, Rebecca E Foulger, David P Hill, Varsha K Khodiyar, Antonia Lock, Jane Lomax, Ruth C Lovering, Prudence Mutowo-Meullenet, Tony Sawford, Kimberly Van Auken…

    Citation: BMC Bioinformatics 2014 15:155

    Content type: Methodology article

    Published on:

  48. A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a d...

    Authors: Barbara Mirel and Carsten Görg

    Citation: BMC Bioinformatics 2014 15:117

    Content type: Commentary

    Published on:

  50. It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally r...

    Authors: Diego H Milone, Georgina Stegmayer, Mariana López, Laura Kamenetzky and Fernando Carrari

    Citation: BMC Bioinformatics 2014 15:101

    Content type: Research article

    Published on:

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