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

Page 8 of 33

  1. A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for th...

    Authors: Karen Sutherland, Kenneth McLeod, Gus Ferguson and Albert Burger
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S12

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

  2. Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a col...

    Authors: Anup Kumar, Björn Grüning and Rolf Backofen
    Citation: BMC Bioinformatics 2023 24:446
  3. Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their...

    Authors: Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari and Abdollah Allahvardi
    Citation: BMC Bioinformatics 2023 24:449
  4. For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encode...

    Authors: Amber L Hartman, Sean Riddle, Timothy McPhillips, Bertram Ludäscher and Jonathan A Eisen
    Citation: BMC Bioinformatics 2010 11:317
  5. 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
  6. The increasing availability of Electronic Health Record (EHR) data and specifically free-text patient notes presents opportunities for phenotype extraction. Text-mining methods in particular can help disease m...

    Authors: Raphael Cohen, Michael Elhadad and Noémie Elhadad
    Citation: BMC Bioinformatics 2013 14:10
  7. Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understandin...

    Authors: Anna Bauer-Mehren, Laura I Furlong, Michael Rautschka and Ferran Sanz
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S6

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

  8. We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and do...

    Authors: Jay Urbain, Ophir Frieder and Nazli Goharian
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S3

    This article is part of a Supplement: Volume 10 Supplement 3

  9. A better understanding of the mechanisms of an enzyme's functionality and stability, as well as knowledge and impact of mutations is crucial for researchers working with enzymes. Though, several of the enzymes...

    Authors: Süveyda Yeniterzi and Uğur Sezerman
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S2

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

  10. The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMe...

    Authors: Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Nikita V. Ivanisenko, Alexander N. Savostianov and Vladimir A. Ivanisenko
    Citation: BMC Bioinformatics 2020 21(Suppl 11):228

    This article is part of a Supplement: Volume 21 Supplement 11

  11. Metabolomics experiments often comprise large numbers of biological samples resulting in huge amounts of data. This data needs to be inspected for plausibility before data evaluation to detect putative sources...

    Authors: Alexandra Maria Simader, Bernhard Kluger, Nora Katharina Nicole Neumann, Christoph Bueschl, Marc Lemmens, Gerald Lirk, Rudolf Krska and Rainer Schuhmacher
    Citation: BMC Bioinformatics 2015 16:341
  12. The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools th...

    Authors: Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess and Martin Romacker
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S3

    This article is part of a Supplement: Volume 7 Supplement 3

  13. The commercial adoption of BCI technologies for both clinical and non-clinical applications is drawing scientists to the creation of wearable devices for daily living. Emotions are essential to human existence...

    Authors: Awwab Mohammad, Farheen Siddiqui, M. Afshar Alam and Sheikh Mohammad Idrees
    Citation: BMC Bioinformatics 2023 24:406
  14. The 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for dise...

    Authors: Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang and Yongqun He
    Citation: BMC Bioinformatics 2021 22(Suppl 6):508

    This article is part of a Supplement: Volume 22 Supplement 6

  15. Biomedical named entity recognition is one of the most essential tasks in biomedical information extraction. Previous studies suffer from inadequate annotated datasets, especially the limited knowledge contain...

    Authors: Huiwei Zhou, Zhe Liu, Chengkun Lang, Yibin Xu, Yingyu Lin and Junjie Hou
    Citation: BMC Bioinformatics 2021 22:295
  16. Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest futur...

    Authors: Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch and Pawel Wojciechowski
    Citation: BMC Bioinformatics 2011 12:181
  17. The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrati...

    Authors: Jamie P McCusker, Joshua A Phillips, Alejandra González Beltrán, Anthony Finkelstein and Michael Krauthammer
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S2

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

  18. The liquid–liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cel...

    Authors: Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai and Jianfeng Pei
    Citation: BMC Bioinformatics 2022 23:72
  19. In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and r...

    Authors: Christopher W Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts and William C Ray
    Citation: BMC Bioinformatics 2012 13(Suppl 8):S8

    This article is part of a Supplement: Volume 13 Supplement 8

  20. Drug-drug interaction extraction (DDI) needs assistance from automated methods to address the explosively increasing biomedical texts. In recent years, deep neural network based models have been developed to a...

    Authors: Wei Wang, Xi Yang, Canqun Yang, Xiaowei Guo, Xiang Zhang and Chengkun Wu
    Citation: BMC Bioinformatics 2017 18(Suppl 16):578

    This article is part of a Supplement: Volume 18 Supplement 16

  21. Drug-target interactions (DTIs) are critical for drug repurposing and elucidation of drug mechanisms, and are manually curated by large databases, such as ChEMBL, BindingDB, DrugBank and DrugTargetCommons. How...

    Authors: Jehad Aldahdooh, Markus Vähä-Koskela, Jing Tang and Ziaurrehman Tanoli
    Citation: BMC Bioinformatics 2022 23:245
  22. Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Pre...

    Authors: Mark Stevenson, Yikun Guo, Robert Gaizauskas and David Martinez
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S7

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

  23. Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to...

    Authors: Aurélie Névéol, Sonya E Shooshan and Vincent Claveau
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S11

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

  24. Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be...

    Authors: Meng Liao, Jian-ping Zhao, Jing Tian and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2022 23:480
  25. To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...

    Authors: Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):407

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

  26. In recent years, biological event extraction has emerged as a key natural language processing task, aiming to address the information overload...generalization and a wider range of text types, event types, and su...

    Authors: Halil Kilicoglu and Sabine Bergler
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S7

    This article is part of a Supplement: Volume 13 Supplement 11

  27. Techniques for reconstruction of biological networks which are based on perturbation experiments often predict direct interactions between nodes that do not exist. Transitive reduction removes such relations i...

    Authors: Dragan Bošnački, Maximilian R Odenbrett, Anton Wijs, Willem Ligtenberg and Peter Hilbers
    Citation: BMC Bioinformatics 2012 13:281
  28. BioProspecting is a novel approach that enabled our team to mine data related to genetic markers from the New England Journal of Medicine (NEJM) utilizing SNOMED CT and the Human Gene Onotology (HUGO). The Biomed...

    Authors: Peter L Elkin, Mark S Tuttle, Brett E Trusko and Steven H Brown
    Citation: BMC Bioinformatics 2009 10(Suppl 2):S9

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

  29. Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific olig...

    Authors: Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W Davis and Nader Pourmand
    Citation: BMC Bioinformatics 2006 7:500
  30. Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth...

    Authors: Luciano Fernandez-Ricaud, Olga Kourtchenko, Martin Zackrisson, Jonas Warringer and Anders Blomberg
    Citation: BMC Bioinformatics 2016 17:249
  31. This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a g...

    Authors: Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey and Patrick Ruch
    Citation: BMC Bioinformatics 2008 9(Suppl 3):S9

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

  32. Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...

    Authors: Mehrdad Kashefi and Mohammad Reza Daliri
    Citation: BMC Bioinformatics 2021 22:26

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