Skip to main content

Articles

1641 result(s) for 'natural language processing' within BMC Bioinformatics

Page 3 of 33

  1. In this work, we develop methods using mutual information (MI) and its property, the data processing inequality (DPI), to help characterize associations that were generated based on use of natural language processing

    Authors: Xiaoyan Wang, George Hripcsak and Carol Friedman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  2. This article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ as...

    Authors: George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, Yannis Almirantis, John Pavlopoulos, Nicolas Baskiotis, Patrick Gallinari, Thierry Artiéres, Axel-Cyrille Ngonga Ngomo…
    Citation: BMC Bioinformatics 2015 16:138
    Content type: Research Article Published on:

  3. An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there ha...

    Authors: K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder and Lawrence E Hunter
    Citation: BMC Bioinformatics 2010 11:492
    Content type: Research article Published on:

  4. Electronic medical record (EMR) systems have become widely used throughout the world to improve the quality of healthcare and the efficiency of hospital services. A bilingual medical lexicon of Chinese and Eng...

    Authors: Yan Xu, Luoxin Chen, Junsheng Wei, Sophia Ananiadou, Yubo Fan, Yi Qian, Eric I-Chao Chang and Junichi Tsujii
    Citation: BMC Bioinformatics 2015 16:149
    Content type: Research article Published on:

  6. With the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Bioinformatics Tertiary Analysis is a c...

    Authors: Sara Pidò, Pietro Crovari and Franca Garzotto
    Citation: BMC Bioinformatics 2021 22(Suppl 13):452
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  7. The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature t...

    Authors: H.-M. Müller, K. M. Van Auken, Y. Li and P. W. Sternberg
    Citation: BMC Bioinformatics 2018 19:94
    Content type: Software Published on:

  8. Automatic and accurate recognition of various biomedical named entities from literature is an important task of biomedical text mining, which is the foundation of extracting biomedical knowledge from unstructu...

    Authors: Xiangwen Zheng, Haijian Du, Xiaowei Luo, Fan Tong, Wei Song and Dongsheng Zhao
    Citation: BMC Bioinformatics 2022 23:501
    Content type: Research Published on:

  9. Immunotherapy is a promising route towards personalized cancer treatment. A key algorithmic challenge in this process is to decide if a given peptide (neoepitope) binds with the major histocompatibility comple...

    Authors: Johanna Vielhaben, Markus Wenzel, Wojciech Samek and Nils Strodthoff
    Citation: BMC Bioinformatics 2020 21:279
    Content type: Software Published on:

  11. Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th...

    Authors: Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman
    Citation: BMC Bioinformatics 2020 21:217
    Content type: Research article Published on:

  13. In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature ...

    Authors: John Boyle, Christopher Cavnor, Sarah Killcoyne and Ilya Shmulevich
    Citation: BMC Bioinformatics 2008 9:295
    Content type: Methodology article Published on:

  14. The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic ass...

    Authors: Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson and Matteo Fumagalli
    Citation: BMC Bioinformatics 2019 20(Suppl 9):337
    Content type: Software Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  15. The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising ...

    Authors: Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini and David Manset
    Citation: BMC Bioinformatics 2009 10(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 12

  16. In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical re...

    Authors: Richárd Farkas and György Szarvas
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 3

  17. In order to detect threats to public health and to be well-prepared for endemic and pandemic illness outbreaks, countries usually rely on event-based surveillance (EBS) and indicator-based surveillance systems. E...

    Authors: Antonella Dellanzo, Viviana Cotik, Daniel Yunior Lozano Barriga, Jonathan Jimmy Mollapaza Apaza, Daniel Palomino, Fernando Schiaffino, Alexander Yanque Aliaga and José Ochoa-Luna
    Citation: BMC Bioinformatics 2022 23:558
    Content type: Research Published on:

  18. The Living Evidence Map Project at the Norwegian Institute of Public Health (NIPH) gives an updated overview of research results and publications. As part of NIPH’s mandate to inform evidence-based infection p...

    Authors: Thomas B. Røst, Laura Slaughter, Øystein Nytrø, Ashley E. Muller and Gunn E. Vist
    Citation: BMC Bioinformatics 2021 22(Suppl 11):496
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  20. RNA secondary structure is very important for deciphering cell’s activity and disease occurrence. The first method which was used by the academics to predict this structure is biological experiment, But this meth...

    Authors: Yinchao Fei, Hao Zhang, Yili Wang, Zhen Liu and Yuanning Liu
    Citation: BMC Bioinformatics 2022 23:354
    Content type: Research Published on:

  21. Huge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, whi...

    Authors: Xiao Liu, Antoine Bordes and Yves Grandvalet
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  24. The goal of the first BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) was to provide a set of common evaluation tasks to assess the state of the art for text mining applied to ...

    Authors: Lynette Hirschman, Alexander Yeh, Christian Blaschke and Alfonso Valencia
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 6 Supplement 1

  26. In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest im...

    Authors: Maíra R Rodrigues, Wagner CS Magalhães, Moara Machado and Eduardo Tarazona-Santos
    Citation: BMC Bioinformatics 2012 13:163
    Content type: Methodology article Published on:

  27. Discovery of new medicinal agents from natural sources has largely been an adventitious process based on screening of plant and microbial extracts combined with bioassay-guided identification and natural produ...

    Authors: Michael HT Li, Peter MU Ung, James Zajkowski, Sylvie Garneau-Tsodikova and David H Sherman
    Citation: BMC Bioinformatics 2009 10:185
    Content type: Software Published on:

  29. Bioinformatics tools for automatic processing of biomedical literature are invaluable for both ... Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus ...

    Authors: Richard Tzong-Han Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2007 8:325
    Content type: Research article Published on:

  30. Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual...

    Authors: Mahira Kirmani, Gagandeep Kour, Mudasir Mohd, Nasrullah Sheikh, Dawood Ashraf Khan, Zahid Maqbool, Mohsin Altaf Wani and Abid Hussain Wani
    Citation: BMC Bioinformatics 2024 25:152
    Content type: Research Published on:

  31. Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published lit...

    Authors: Maciej Rybinski, Sarvnaz Karimi, Vincent Nguyen and Cecile Paris
    Citation: BMC Bioinformatics 2020 21(Suppl 19):572
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 19

  32. RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free s...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli
    Citation: BMC Bioinformatics 2019 20(Suppl 4):161
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  33. 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 summarization. ...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Thomas C. Rindflesch
    Citation: BMC Bioinformatics 2016 17:163
    Content type: Research Article Published on:

  35. The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...

    Authors: Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman and Cathy H Wu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  36. The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful prope...

    Authors: Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  37. Long noncoding RNAs (lncRNAs) play an important role in regulating biological activities and their prediction is significant for exploring biological processes. Long short-term memory (LSTM) and convolutional ...

    Authors: Jun Meng, Qiang Kang, Zheng Chang and Yushi Luan
    Citation: BMC Bioinformatics 2021 22(Suppl 3):242
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  38. 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 deep ...

    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:

  39. We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to su...

    Authors: Thomas A Russ, Cartic Ramakrishnan, Eduard H Hovy, Mihail Bota and Gully APC Burns
    Citation: BMC Bioinformatics 2011 12:351
    Content type: Software Published on:

  41. The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, severa...

    Authors: Guillermo de la Calle, Miguel García-Remesal, Stefano Chiesa, Diana de la Iglesia and Victor Maojo
    Citation: BMC Bioinformatics 2009 10:320
    Content type: Methodology article Published on:

  42. There is a considerable interest in characterizing the biological role of specific protein residue substitutions through mutagenesis experiments. Additionally, recent efforts related to the detection of diseas...

    Authors: Martin Krallinger, Jose MG Izarzugaza, Carlos Rodriguez-Penagos and Alfonso Valencia
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 8

  43. Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ra...

    Authors: John Boyle, Hector Rovira, Chris Cavnor, David Burdick, Sarah Killcoyne and Ilya Shmulevich
    Citation: BMC Bioinformatics 2009 10:79
    Content type: Research article Published on:

  45. In the United States and parts of the world, the human papillomavirus vaccine uptake is below the prescribed coverage rate for the population. Some research have noted that dialogue that communicates the risks...

    Authors: Muhammad Amith, Kirk Roberts and Cui Tao
    Citation: BMC Bioinformatics 2019 20(Suppl 21):706
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  46. A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells an...

    Authors: Yoshitaka Kimori, Norio Baba and Nobuhiro Morone
    Citation: BMC Bioinformatics 2010 11:373
    Content type: Methodology article Published on:

  47. We describe the methodology for automatic curation of Biological Association Networks (BANs) derived by a natural language processing technology called Medscan. The curated data is...

    Authors: Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia and Ilya Mazo
    Citation: BMC Bioinformatics 2006 7:171
    Content type: Methodology article Published on:

  48. Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parame...

    Authors: Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik and Somali Chaterji
    Citation: BMC Bioinformatics 2022 23:25
    Content type: Methodology article Published on:

  49. This paper mainly studies feature extraction and classification of m6A methylation sites in a natural language processing way, which manages to organically integrate the...6A sites. One-hot, RNA word embedding, a...

    Authors: Lin Zhang, Gangshen Li, Xiuyu Li, Honglei Wang, Shutao Chen and Hui Liu
    Citation: BMC Bioinformatics 2021 22:288
    Content type: Methodology article Published on:

  50. The Comparative Data Analysis Ontology (CDAO) is an ontology developed, as part of the EvoInfo and EvoIO groups supported by the National Evolutionary Synthesis Center, to provide semantic descriptions of data an...

    Authors: Brandon Chisham, Ben Wright, Trung Le, Tran Cao Son and Enrico Pontelli
    Citation: BMC Bioinformatics 2011 12:98
    Content type: Software Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us