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1435 result(s) for 'natural language processing' within BMC Bioinformatics

Page 3 of 29

  1. 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

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

  2. 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
  3. 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
  4. 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
  5. 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
  6. 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

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

  7. 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

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

  8. 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

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

  9. 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
  10. 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
  11. 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
  12. 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
  13. 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

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

  14. 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

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

  15. 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
  16. 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
  17. 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

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

  18. 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
  19. Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of ...

    Authors: Ji He, Vagner A Benedito, Mingyi Wang, Jeremy D Murray, Patrick X Zhao, Yuhong Tang and Michael K Udvardi
    Citation: BMC Bioinformatics 2009 10:441
  20. Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an ard...

    Authors: Elena Taycher, Andreas Rolfs, Yanhui Hu, Dongmei Zuo, Stephanie E Mohr, Janice Williamson and Joshua LaBaer
    Citation: BMC Bioinformatics 2007 8:198
  21. Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to the...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S8

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

  22. The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational method...

    Authors: Ian Donaldson, Joel Martin, Berry de Bruijn, Cheryl Wolting, Vicki Lay, Brigitte Tuekam, Shudong Zhang, Berivan Baskin, Gary D Bader, Katerina Michalickova, Tony Pawson and Christopher WV Hogue
    Citation: BMC Bioinformatics 2003 4:11
  23. There are millions of public posts to medical message boards by users seeking support and information on a wide range of medical conditions. It has been shown that these posts can be used to gain a greater und...

    Authors: Adrian Benton, Shawndra Hill, Lyle Ungar, Annie Chung, Charles Leonard, Cristin Freeman and John H Holmes
    Citation: BMC Bioinformatics 2011 12(Suppl 3):S2

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

  24. Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for query...

    Authors: Sean R Wilkinson and Jonas S Almeida
    Citation: BMC Bioinformatics 2014 15:176
  25. Alkaline earth metal ions are important protein binding ligands in human body, and it is of great significance to predict their binding residues.

    Authors: Kai Sun, Xiuzhen Hu, Zhenxing Feng, Hongbin Wang, Haotian Lv, Ziyang Wang, Gaimei Zhang, Shuang Xu and Xiaoxiao You
    Citation: BMC Bioinformatics 2022 22(Suppl 12):324

    This article is part of a Supplement: Volume 22 Supplement 12

  26. The manual diagnosis of neurodegenerative disorders such as Alzheimer’s disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic crit...

    Authors: Sylvester O. Orimaye, Jojo S-M. Wong, Karen J. Golden, Chee P. Wong and Ireneous N. Soyiri
    Citation: BMC Bioinformatics 2017 18:34
  27. The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5–6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behavio...

    Authors: Irena Spasić, Warwick B Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G Oliver and Douglas B Kell
    Citation: BMC Bioinformatics 2006 7:281
  28. Most biomedical information extraction focuses on binary relations within single sentences. However, extracting n-ary relations that span multiple sentences is in huge demand. At present, in the cross-sentence...

    Authors: Di Zhao, Jian Wang, Yijia Zhang, Xin Wang, Hongfei Lin and Zhihao Yang
    Citation: BMC Bioinformatics 2020 21:312
  29. In this study, we developed MHCSeqNet, an open-source deep learning model, which not only outperforms state-of-the-art predictors on both MHC binding affinity and MHC ligand peptidome datasets but also exhibits p...

    Authors: Poomarin Phloyphisut, Natapol Pornputtapong, Sira Sriswasdi and Ekapol Chuangsuwanich
    Citation: BMC Bioinformatics 2019 20:270
  30. Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. T...

    Authors: Christopher Brewster, Simon Jupp, Joanne Luciano, David Shotton, Robert D Stevens and Ziqi Zhang
    Citation: BMC Bioinformatics 2009 10(Suppl 5):S1

    This article is part of a Supplement: Volume 10 Supplement 5

  31. Quantitative proteomics holds great promise for identifying proteins that are differentially abundant between populations representing different physiological or disease states. A range of computational tools ...

    Authors: Mi-Youn Brusniak, Bernd Bodenmiller, David Campbell, Kelly Cooke, James Eddes, Andrew Garbutt, Hollis Lau, Simon Letarte, Lukas N Mueller, Vagisha Sharma, Olga Vitek, Ning Zhang, Ruedi Aebersold and Julian D Watts
    Citation: BMC Bioinformatics 2008 9:542
  32. The Internet is a major source of health information but most seekers are not familiar with medical vocabularies. Hence, their searches fail due to bad query formulation. Several methods have been proposed to ...

    Authors: Lina F Soualmia, Elise Prieur-Gaston, Zied Moalla, Thierry Lecroq and Stéfan J Darmoni
    Citation: BMC Bioinformatics 2012 13(Suppl 14):S11

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

  33. Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at a...

    Authors: George Zheng and Athman Bouguettaya
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S6

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

  34. Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in dynamic contrast-enhanced (DCE) magnetic resonance...

    Authors: Charlotte Debus, Ralf Floca, Michael Ingrisch, Ina Kompan, Klaus Maier-Hein, Amir Abdollahi and Marco Nolden
    Citation: BMC Bioinformatics 2019 20:31
  35. In task 1A of the BioCreAtIvE evaluation, systems had to be devised that recognize words and phrases forming gene or protein names in natural language sentences. We approach this problem by building ... Machine, ...

    Authors: Jörg Hakenberg, Steffen Bickel, Conrad Plake, Ulf Brefeld, Hagen Zahn, Lukas Faulstich, Ulf Leser and Tobias Scheffer
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S9

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

  36. The detection and interpretation of CNVs are of clinical importance in genetic testing. Several databases and web services are already being used by clinical geneticists to interpret the medical relevance of i...

    Authors: Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu and Kai Lu
    Citation: BMC Bioinformatics 2018 19(Suppl 19):528

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

  37. It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural ...

    Authors: Erich A Peterson, Michael A Bauer, Shweta S Chavan, Cody Ashby, Niels Weinhold, Christoph J Heuck, Gareth J Morgan and Donald J Johann
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S7

    This article is part of a Supplement: Volume 16 Supplement 13

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