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1632 result(s) for 'natural language processing' within BMC Bioinformatics

Page 4 of 33

  1. 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
  2. With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study is ...

    Authors: Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham and Cui Tao
    Citation: BMC Bioinformatics 2023 24(Suppl 3):477

    This article is part of a Supplement: Volume 24 Supplement 3

  3. 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

  4. Despite the many progresses with alignment algorithms, aligning divergent protein sequences with less than 20–35% pairwise identity (so called "twilight zone") remains a difficult problem. Many alignment algor...

    Authors: Benjamin Giovanni Iovino and Yuzhen Ye
    Citation: BMC Bioinformatics 2024 25:85
  5. 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

  6. Twitter is a popular social networking site where short messages or “tweets” of users have been used extensively for research purposes. However, not much research has been done in mining the medical profession...

    Authors: Kazi Zainab, Gautam Srivastava and Vijay Mago
    Citation: BMC Bioinformatics 2022 22(Suppl 10):630

    This article is part of a Supplement: Volume 22 Supplement 10

  7. The accelerating pace of biomedical publication has made it impractical to manually, systematically identify papers containing specific information and extract this information. This is especially challenging ...

    Authors: Adam J. H. Newton, David Chartash, Steven H. Kleinstein and Robert A. McDougal
    Citation: BMC Bioinformatics 2023 24:292
  8. 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
  9. 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
  10. 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
  11. Model card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document is of interest to the National Institutes of Health’s Bridge2AI initia...

    Authors: Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):281

    This article is part of a Supplement: Volume 23 Supplement 6

  12. 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
  13. All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being des...

    Authors: Roman Lukyanenko, Veda C. Storey and Oscar Pastor
    Citation: BMC Bioinformatics 2023 23(Suppl 11):574

    This article is part of a Supplement: Volume 23 Supplement 11

  14. 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

  15. 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
  16. 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
  17. 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

  18. 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

  19. 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
  20. 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

  21. 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

  22. Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scienti...

    Authors: Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen and Tapio Salakoski
    Citation: BMC Bioinformatics 2007 8:50
  23. Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools...

    Authors: Thomas Kuhn, Egon L Willighagen, Achim Zielesny and Christoph Steinbeck
    Citation: BMC Bioinformatics 2010 11:159
  24. 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

  25. The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development suppo...

    Authors: Anna-Lena Lamprecht, Tiziana Margaria and Bernhard Steffen
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S8

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

  26. In this work we describe an approach that facilitates the automatic recognition of eight relationships defined between medical problems, treatments and tests. Unlike the traditional bag-of-words representation, i...

    Authors: Rezarta Islamaj Doğan, Aurélie Névéol and Zhiyong Lu
    Citation: BMC Bioinformatics 2011 12(Suppl 3):S3

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

  27. 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
  28. A fundamental goal of the U.S. National Institute of Health (NIH) "Roadmap" is to strengthen Translational Research, defined as the movement of discoveries in basic research to application at the clinical level. ...

    Authors: Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens…
    Citation: BMC Bioinformatics 2007 8(Suppl 3):S2

    This article is part of a Supplement: Volume 8 Supplement 3

  29. Biological contextual information helps understand various phenomena occurring in the biological systems consisting of complex molecular relations. The construction of context-specific relational resources vas...

    Authors: Jaehyun Lee, Doheon Lee and Kwang Hyung Lee
    Citation: BMC Bioinformatics 2020 21(Suppl 5):250

    This article is part of a Supplement: Volume 21 Supplement 5

  30. With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation ...

    Authors: Swapna Vidhur Daulatabad, Rajneesh Srivastava and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2021 22:279
  31. The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...

    Authors: Angus Roberts, Robert Gaizauskas, Mark Hepple and Yikun Guo
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S3

    This article is part of a Supplement: Volume 9 Supplement 11

  32. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang
    Citation: BMC Bioinformatics 2020 21:544
  33. As Twitter has become an active data source for health surveillance research, it is important that efficient and effective methods are developed to identify tweets related to personal health experience. Conven...

    Authors: Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta and Gordon R. Bernard
    Citation: BMC Bioinformatics 2018 19(Suppl 8):210

    This article is part of a Supplement: Volume 19 Supplement 8

  34. Making accurate patient care decision, as early as possible, is a constant challenge, especially for physicians in the emergency department. The increasing volumes of electronic medical records (EMRs) open new...

    Authors: Huaixiao Tou, Lu Yao, Zhongyu Wei, Xiahai Zhuang and Bo Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 5):117

    This article is part of a Supplement: Volume 19 Supplement 5

  35. Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these framewo...

    Authors: Giulio Caravagna, Luca De Sano and Marco Antoniotti
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S8

    This article is part of a Supplement: Volume 16 Supplement 9

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