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1648 result(s) for 'natural language processing' within BMC Bioinformatics

Page 9 of 33

  1. 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
    Content type: Proceedings Published on:

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

  4. 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
    Content type: Research article Published on:

  6. A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring c...

    Authors: Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra and Susanna-Assunta Sansone
    Citation: BMC Bioinformatics 2009 10:125
    Content type: Correspondence Published on:

  7. Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since...

    Authors: Atima Tharatipyakul, Somrak Numnark, Duangdao Wichadakul and Supawadee Ingsriswang
    Citation: BMC Bioinformatics 2012 13(Suppl 17):S9
    Content type: Proceedings Published on:

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

  8. Calculating the electrostatic surface potential (ESP) of a biomolecule is critical towards understanding biomolecular function. Because of its quadratic computational complexity (as a function of the number of at...

    Authors: Mayank Daga and Wu-chun Feng
    Citation: BMC Bioinformatics 2012 13(Suppl 5):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 5

  9. Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a tr...

    Authors: Lishuang Li, Jia Wan, Jieqiong Zheng and Jian Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 9):285
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 9

  10. A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up...

    Authors: Isabel Segura-Bedmar, Paloma Martínez and César de Pablo-Sánchez
    Citation: BMC Bioinformatics 2011 12(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 2

  11. Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole...

    Authors: Vincent Henry, Fatiha Saïs, Olivier Inizan, Elodie Marchadier, Juliette Dibie, Anne Goelzer and Vincent Fromion
    Citation: BMC Bioinformatics 2020 21:327
    Content type: Methodology article Published on:

  12. Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved ...

    Authors: Thomas Hladish, Vivek Gopalan, Chengzhi Liang, Weigang Qiu, Peter Yang and Arlin Stoltzfus
    Citation: BMC Bioinformatics 2007 8:191
    Content type: Software Published on:

  13. We propose a novel PPI extraction technique called PPISpotter by combining Deterministic Annealing-based SSL and an AL technique to extract protein-protein interaction. In addition, we extract a comprehensive set...

    Authors: Min Song, Hwanjo Yu and Wook-Shin Han
    Citation: BMC Bioinformatics 2011 12(Suppl 12):S4
    Content type: Proceedings Published on:

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

  15. CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications. Indel analysis has thus become on...

    Authors: Huancheng Fu, Ce Shan, Fanchen Kang, Ling Yu, Zhonghan Li and Yike Yin
    Citation: BMC Bioinformatics 2023 24:219
    Content type: Software Published on:

  16. 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
    Content type: Research Published on:

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

  18. Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as ...

    Authors: Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti and Etienne GJ Danchin
    Citation: BMC Bioinformatics 2005 6:198
    Content type: Software Published on:

  20. We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI),...

    Authors: Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun'ichi Tsujii and Sophia Ananiadou
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S2
    Content type: Proceedings Published on:

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

  21. maxdLoad2 is a relational database schema and Java® application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification...

    Authors: David Hancock, Michael Wilson, Giles Velarde, Norman Morrison, Andrew Hayes, Helen Hulme, A Joseph Wood, Karim Nashar, Douglas B Kell and Andy Brass
    Citation: BMC Bioinformatics 2005 6:264
    Content type: Software Published on:

  22. Blood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources ...

    Authors: Nícia Rosário-Ferreira, Victor Guimarães, Vítor S. Costa and Irina S. Moreira
    Citation: BMC Bioinformatics 2021 22:482
    Content type: Research Published on:

  23. Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect ...

    Authors: Jader M. Caldonazzo Garbelini, Danilo S. Sanches and Aurora T. Ramirez Pozo
    Citation: BMC Bioinformatics 2024 25:128
    Content type: Software Published on:

  24. Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated ...

    Authors: Yasmine Mansour, Annie Chateau and Anna-Sophie Fiston-Lavier
    Citation: BMC Bioinformatics 2021 22(Suppl 6):396
    Content type: Research Published on:

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

  25. Studies of functional modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approache...

    Authors: Jun Zhong Ji, Lang Jiao, Cui Cui Yang, Jia Wei Lv and Ai Dong Zhang
    Citation: BMC Bioinformatics 2014 15:325
    Content type: Methodology article Published on:

  26. For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers...

    Authors: John A. Bachman, Benjamin M. Gyori and Peter K. Sorger
    Citation: BMC Bioinformatics 2018 19:248
    Content type: Database Published on:

  28. The use of ontologies to control vocabulary and structure annotation has added value to genome-scale data, and contributed to the capture and re-use of knowledge across research domains. Gene Ontology (GO) is ...

    Authors: Melissa J Davis, Muhammad Shoaib B Sehgal and Mark A Ragan
    Citation: BMC Bioinformatics 2010 11:498
    Content type: Methodology article Published on:

  30. The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool ret...

    Authors: Pengli Cai, Sheng Liu, Dachuan Zhang, Huadong Xing, Mengying Han, Dongliang Liu, Linlin Gong and Qian-Nan Hu
    Citation: BMC Bioinformatics 2023 24:152
    Content type: Database Published on:

  32. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from meta...

    Authors: Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B Kell and Norman W Paton
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  33. Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced cate...

    Authors: Yongping Du, Yunpeng Pan, Chencheng Wang and Junzhong Ji
    Citation: BMC Bioinformatics 2018 19(Suppl 20):502
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  34. Medical databases normally contain large amounts of data in a variety of forms. Although they grant significant insights into diagnosis and treatment, implementing data exploration into current medical databas...

    Authors: Jero Schäfer, Ming Tang, Danny Luu, Anke Katharina Bergmann and Lena Wiese
    Citation: BMC Bioinformatics 2022 23:537
    Content type: Software Published on:

  35. Identification of discourse relations, such as causal and contrastive relations, between situations mentioned in text is an important task for biomedical text-mining. A biomedical text corpus annotated with di...

    Authors: Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind Joshi and Hong Yu
    Citation: BMC Bioinformatics 2011 12:188
    Content type: Research article Published on:

  36. We find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid.....

    Authors: Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez and Michael Krauthammer
    Citation: BMC Bioinformatics 2021 22:412
    Content type: Research Published on:

  37. Biomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials su...

    Authors: Ahmed AbdoAziz Ahmed Abdulla, Hongfei Lin, Bo Xu and Santosh Kumar Banbhrani
    Citation: BMC Bioinformatics 2016 17(Suppl 7):238
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 7

  38. We participated in the BioCreAtIvE Task 2, which addressed the annotation of proteins into the Gene Ontology (GO) based on the text of a given document and the selection of evidence text from the document just...

    Authors: Karin Verspoor, Judith Cohn, Cliff Joslyn, Sue Mniszewski, Andreas Rechtsteiner, Luis M Rocha and Tiago Simas
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S20
    Content type: Report Published on:

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

  40. The COVID-19 pandemic has increasingly accelerated the publication pace of scientific literature. How to efficiently curate and index this large amount of biomedical literature under the current crisis is of g...

    Authors: Jinghang Gu, Rong Xiang, Xing Wang, Jing Li, Wenjie Li, Longhua Qian, Guodong Zhou and Chu-Ren Huang
    Citation: BMC Bioinformatics 2022 23:259
    Content type: Research Published on:

  41. Named entity recognition is critical for biomedical text mining, where it is not unusual to find entities labeled by a wide range of different terms. Nowadays, ontologies are one of the crucial enabling technolog...

    Authors: Maria Taboada, Hadriana Rodriguez, Ranga C. Gudivada and Diego Martinez
    Citation: BMC Bioinformatics 2017 18:446
    Content type: Research Article Published on:

  42. Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies ...

    Authors: Alexander Garcia Castro, Philippe Rocca-Serra, Robert Stevens, Chris Taylor, Karim Nashar, Mark A Ragan and Susanna-Assunta Sansone
    Citation: BMC Bioinformatics 2006 7:267
    Content type: Methodology article Published on:

  43. In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences....

    Authors: Daniel Quest, Kathryn Dempsey, Mohammad Shafiullah, Dhundy Bastola and Hesham Ali
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S6
    Content type: Proceedings Published on:

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

  45. The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spati...

    Authors: Frédéric Pont, Juan Pablo Cerapio, Pauline Gravelle, Laetitia Ligat, Carine Valle, Emeline Sarot, Marion Perrier, Frédéric Lopez, Camille Laurent, Jean Jacques Fournié and Marie Tosolini
    Citation: BMC Bioinformatics 2023 24:30
    Content type: Software Published on:

  46. Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manag...

    Authors: Wei Yu, Ajay Yesupriya, Anja Wulf, Junfeng Qu, Muin J Khoury and Marta Gwinn
    Citation: BMC Bioinformatics 2007 8:436
    Content type: Methodology article Published on:

  47. Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling sing...

    Authors: Lei Cai, Yufeng Wu and Jingyang Gao
    Citation: BMC Bioinformatics 2019 20:665
    Content type: Research article Published on:

  48. In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional...

    Authors: Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos García, Francisco Tirado and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2015 16:43
    Content type: Software Published on:

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