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1652 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

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

  2. 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
  3. 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

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

  4. 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

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

  5. 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

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

  6. 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
  7. 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
  8. 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

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

  9. 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
  10. 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

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

  11. 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
  12. 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
  13. 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
  14. 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

    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

  15. 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

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

  16. 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
  17. 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

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

  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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

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

  26. 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
  27. 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

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

  28. 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

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

  29. 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

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

  30. 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
  31. 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
  32. 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
  33. 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

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

  34. Protein-amide proton hydrogen-deuterium exchange (HDX) is used to investigate protein conformation, conformational changes and surface binding sites for other molecules. To our knowledge, software tools to aut...

    Authors: Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter and Paul D Gershon
    Citation: BMC Bioinformatics 2008 9:387
  35. Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to an...

    Authors: Abiel Roche-Lima, Michael Domaratzki and Brian Fristensky
    Citation: BMC Bioinformatics 2014 15:318

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