Skip to main content

Articles

1661 result(s) for 'natural language processing' within BMC Bioinformatics

Page 7 of 34

  1. Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop,...

    Authors: Riccardo Bellazzi, Marco Masseroli, Shawn Murphy, Amnon Shabo and Paolo Romano
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 13 Supplement 14

  2. The roles of antibody and antigen are indispensable in targeted diagnosis, therapy, and biomedical discovery. On top of that, massive numbers of new scientific articles about antibodies and/or antigens are publis...

    Authors: Thuy Trang Dinh, Trang Phuong Vo-Chanh, Chau Nguyen, Viet Quoc Huynh, Nam Vo and Hoang Duc Nguyen
    Citation: BMC Bioinformatics 2022 23:524
    Content type: Research Published on:

  3. With recent advances in microscopy, recordings of cell behaviour can result in terabyte-size datasets. The lattice light sheet microscope (LLSM) images cells at high speed and high 3D resolution, accumulating ...

    Authors: James G. Lefevre, Yvette W. H. Koh, Adam A. Wall, Nicholas D. Condon, Jennifer L. Stow and Nicholas A. Hamilton
    Citation: BMC Bioinformatics 2021 22:410
    Content type: Software Published on:

  4. 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 bo...

    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:

  6. Understanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue or even an organ. Many tools are available for either processing, ana...

    Authors: Xuemin Dong, Shanshan Dong, Shengkai Pan and Xiangjiang Zhan
    Citation: BMC Bioinformatics 2022 23:26
    Content type: Software Published on:

  7. Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological o...

    Authors: Anna Maria Masci, Cecilia N Arighi, Alexander D Diehl, Anne E Lieberman, Chris Mungall, Richard H Scheuermann, Barry Smith and Lindsay G Cowell
    Citation: BMC Bioinformatics 2009 10:70
    Content type: Research article Published on:

  8. Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedic...

    Authors: Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and YiJia Zhang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):380
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  11. A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure suc...

    Authors: Nikolaos Alachiotis, Simon Berger, Tomáš Flouri, Solon P Pissis and Alexandros Stamatakis
    Citation: BMC Bioinformatics 2013 14(Suppl 11):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 14 Supplement 11

  12. Entity normalization is an important information extraction task which has gained renewed attention in the last decade, particularly in the biomedical and life science domains. In these domains, and more gener...

    Authors: Arnaud Ferré, Louise Deléger, Robert Bossy, Pierre Zweigenbaum and Claire Nédellec
    Citation: BMC Bioinformatics 2020 21(Suppl 23):579
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 23

  13. Extraction of adverse drug events from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Existing...

    Authors: Harshit Jain, Nishant Raj and Suyash Mishra
    Citation: BMC Bioinformatics 2021 22(Suppl 11):330
    Content type: Research Published on:

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

  14. The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortu...

    Authors: Leonid L Chepelev, Alexandre Riazanov, Alexandre Kouznetsov, Hong Sang Low, Michel Dumontier and Christopher JO Baker
    Citation: BMC Bioinformatics 2011 12:303
    Content type: Methodology article Published on:

  16. Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology. This new technique uses pooled DNA, thereby reducing costs...

    Authors: Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice LT Yu, Mitchell B Diccianni, Jer-Yuarn Wu, Yuan-Tsong Chen and Cathy SJ Fann
    Citation: BMC Bioinformatics 2008 9:196
    Content type: Software Published on:

  18. Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are intero...

    Authors: Malcolm E. Fisher, Erik Segerdell, Nicolas Matentzoglu, Mardi J. Nenni, Joshua D. Fortriede, Stanley Chu, Troy J. Pells, David Osumi-Sutherland, Praneet Chaturvedi, Christina James-Zorn, Nivitha Sundararaj, Vaneet S. Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov…
    Citation: BMC Bioinformatics 2022 23:99
    Content type: Research Published on:

  19. Time delays are important factors that are often neglected in gene regulatory network (GRN) inference models. Validating time delays from knowledge bases is a challenge since the vast majority of biological da...

    Authors: Wenting Liu, Kui Miao, Guangxia Li, Kuiyu Chang, Jie Zheng and Jagath C Rajapakse
    Citation: BMC Bioinformatics 2014 15(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 2

  20. Histone Mark Modifications (HMs) are crucial actors in gene regulation, as they actively remodel chromatin to modulate transcriptional activity: aberrant combinatorial patterns of HMs have been connected with ...

    Authors: Fabrizio Frasca, Matteo Matteucci, Michele Leone, Marco J. Morelli and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:151
    Content type: Research Published on:

  21. Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generat...

    Authors: Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe and Leonardo Collado-Torres
    Citation: BMC Bioinformatics 2023 24:340
    Content type: Software Published on:

  23. Adverse drug events (ADEs) constitute one of the leading causes of post-therapeutic death and their identification constitutes an important challenge of modern precision medicine. Unfortunately, the onset and ...

    Authors: Ryan Eshleman and Rahul Singh
    Citation: BMC Bioinformatics 2016 17(Suppl 13):335
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 17 Supplement 13

  24. The analysis of gene expression from time series underpins many biological studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) genes from the study and determining which...

    Authors: Alfredo A Kalaitzis and Neil D Lawrence
    Citation: BMC Bioinformatics 2011 12:180
    Content type: Research article Published on:

  25. Automated text classification has many important applications in the clinical setting; however, obtaining labelled data for training machine learning and deep learning models is often difficult and expensive. ...

    Authors: Kevin De Angeli, Shang Gao, Mohammed Alawad, Hong-Jun Yoon, Noah Schaefferkoetter, Xiao-Cheng Wu, Eric B. Durbin, Jennifer Doherty, Antoinette Stroup, Linda Coyle, Lynne Penberthy and Georgia Tourassi
    Citation: BMC Bioinformatics 2021 22:113
    Content type: Research article Published on:

  26. Numerous publicly available biomedical databases derive data by curating from literatures. The curated data can be useful as training examples for information extraction, but curated data usually lack the exac...

    Authors: Suvir Jain, Kashyap R., Tsung-Ting Kuo, Shitij Bhargava, Gordon Lin and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2016 17(Suppl 1):S1
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:84

  27. The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles ar...

    Authors: Anne-Lise Veuthey, Alan Bridge, Julien Gobeill, Patrick Ruch, Johanna R McEntyre, Lydie Bougueleret and Ioannis Xenarios
    Citation: BMC Bioinformatics 2013 14:104
    Content type: Methodology article Published on:

  28. Genotype–phenotype predictions are of great importance in genetics. These predictions can help to find genetic mutations causing variations in human beings. There are many approaches for finding the associatio...

    Authors: Muhammad Muneeb and Andreas Henschel
    Citation: BMC Bioinformatics 2021 22:198
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:319

  29. When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient sto...

    Authors: Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet and Charles Auffray
    Citation: BMC Bioinformatics 2016 17:494
    Content type: Software Published on:

  30. Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious d...

    Authors: Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez and Víctor Maojo
    Citation: BMC Bioinformatics 2010 11:410
    Content type: Methodology article Published on:

  31. Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge in computational biology. Currently,...

    Authors: Susanna R. Grigson, Jody C. McKerral, James G. Mitchell and Robert A. Edwards
    Citation: BMC Bioinformatics 2022 23:385
    Content type: Research Published on:

  32. The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity...

    Authors: Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2009 10:403
    Content type: Research article Published on:

  33. Metagenomics studies provide valuable insight into the composition and function of microbial populations from diverse environments; however, the data processing pipelines that rely on mapping reads to gene cat...

    Authors: Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski and Lee Ann McCue
    Citation: BMC Bioinformatics 2020 21:257
    Content type: Software Published on:

  34. This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear corresp...

    Authors: Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga-Llavori and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S4
    Content type: Research Published on:

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

  35. The adverse reactions that are caused by drugs are potentially life-threatening problems. Comprehensive knowledge of adverse drug reactions (ADRs) can reduce their detrimental impacts on patients. Detecting AD...

    Authors: Tongxuan Zhang, Hongfei Lin, Yuqi Ren, Liang Yang, Bo Xu, Zhihao Yang, Jian Wang and Yijia Zhang
    Citation: BMC Bioinformatics 2019 20:479
    Content type: Research Article Published on:

  36. Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the comple...

    Authors: Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert Jr, Joseph White, Patricia L Whetzel…
    Citation: BMC Bioinformatics 2006 7:489
    Content type: Commentary Published on:

  37. As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far...

    Authors: Doheon Lee, Sangwoo Kim and Younghoon Kim
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  41. The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such stud...

    Authors: Olivo Miotto, Tin Wee Tan and Vladimir Brusic
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 1

  42. The effectiveness of knowledge-based word sense disambiguation (WSD) approaches depends in part on the information available in the reference knowledge resource. Off the shelf, these resources are not optimize...

    Authors: Antonio Jimeno-Yepes, Bridget T Mclnnes and Alan R Aronson
    Citation: BMC Bioinformatics 2011 12(Suppl 3):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 3

  43. In this work we present a novel method to extract and combine relationships between HIV drugs and mutations in viral genomes. Our extraction method is based on natural language processing (NLP) which produces gra...

    Authors: Quoc-Chinh Bui, Breanndán Ó Nualláin, Charles A Boucher and Peter MA Sloot
    Citation: BMC Bioinformatics 2010 11:101
    Content type: Research article Published on:

  46. Deep learning has become a prevalent method in identifying genomic regulatory sequences such as promoters. In a number of recent papers, the performance of deep learning models has continually been reported as...

    Authors: Raul I. Perez Martell, Alison Ziesel, Hosna Jabbari and Ulrike Stege
    Citation: BMC Bioinformatics 2022 23:118
    Content type: Research Published on:

  49. Ultraconserved elements are nucleotide or protein sequences with 100% identity (no mismatches, insertions, or deletions) in the same organism or between two or more organisms. Studies indicate that these conse...

    Authors: Scott Christley, Neil F Lobo and Greg Madey
    Citation: BMC Bioinformatics 2008 9:15
    Content type: Methodology article Published on:

  50. Pharmacogenomics studies the relationship between genetic variation and the variation in drug response phenotypes. The field is rapidly gaining importance: it promises drugs targeted to particular subpopulatio...

    Authors: Yael Garten and Russ B Altman
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 2

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • Citation Impact 2023
    Journal Impact Factor: 2.9
    5-year Journal Impact Factor: 3.6
    Source Normalized Impact per Paper (SNIP): 0.821
    SCImago Journal Rank (SJR): 1.005

    Speed 2023
    Submission to first editorial decision (median days): 12
    Submission to acceptance (median days): 146

    Usage 2023
    Downloads: 5,987,678
    Altmetric mentions: 4,858

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us