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1661 result(s) for 'natural language processing' within BMC Bioinformatics

Page 6 of 34

  1. Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data ext...

    Authors: Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael Müller and Paul W Sternberg
    Citation: BMC Bioinformatics 2009 10:228
    Content type: Methodology article Published on:

  2. We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP) technology. For the protein annotation ... We also expanded the ...

    Authors: Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo and Iaroslav Ispolatov
    Citation: BMC Bioinformatics 2007 8:243
    Content type: Research article Published on:

  3. Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence,...

    Authors: Eli J. Draizen, John Readey, Cameron Mura and Philip E. Bourne
    Citation: BMC Bioinformatics 2024 25:11
    Content type: Software Published on:

  4. Natural History science is characterised by a single immense goal (to document, describe and synthesise all facets pertaining to the diversity of life) that can only be addressed through a seemingly infinite s...

    Authors: Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott and David Roberts
    Citation: BMC Bioinformatics 2009 10(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 14

  5. In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person’s genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch, James I Hoath, Ira J Kalet and David L Veenstra
    Citation: BMC Bioinformatics 2010 11(Suppl 9):S10
    Content type: Proceedings Published on:

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

  6. The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA ...

    Authors: Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne and Joshua M Stuart
    Citation: BMC Bioinformatics 2008 9:463
    Content type: Research article Published on:

  7. Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health inf...

    Authors: Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2018 19:34
    Content type: Research Article Published on:

  8. Although rare diseases are characterized by low prevalence, approximately 400 million people are affected by a rare disease. The early and accurate diagnosis of these conditions is a major challenge for general p...

    Authors: Isabel Segura-Bedmar, David Camino-Perdones and Sara Guerrero-Aspizua
    Citation: BMC Bioinformatics 2022 23:263
    Content type: Research Published on:

  10. Orphan gene play an important role in the environmental stresses of many species and their identification is a critical step to understand biological functions. Moso bamboo has high ecological, economic and cu...

    Authors: Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin and Shaowen Li
    Citation: BMC Bioinformatics 2022 23:162
    Content type: Research Published on:

  12. Stroke has an acute onset and a high mortality rate, making it one of the most fatal diseases worldwide. Its underlying biology and treatments have been widely studied both in the “Western” biomedicine and the...

    Authors: Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang and Kai Lu
    Citation: BMC Bioinformatics 2021 22(Suppl 10):387
    Content type: Research Published on:

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

    The Correction to this article has been published in BMC Bioinformatics 2021 22:585

  13. Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked...

    Authors: Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger and Katharina Nöh
    Citation: BMC Bioinformatics 2019 20:452
    Content type: Software Published on:

  15. Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data durin...

    Authors: Hyunjung Lee, Utku Ozbulak, Homin Park, Stephen Depuydt, Wesley De Neve and Joris Vankerschaver
    Citation: BMC Bioinformatics 2024 25:170
    Content type: Research Published on:

  16. Sphingosine 1-phosphate (S1P), a lysophospholipid, is involved in various cellular processes such as migration, proliferation, and survival. To date, the impact of S1P on human glioblastoma is not fully unders...

    Authors: Jeyakumar Natarajan, Daniel Berrar, Werner Dubitzky, Catherine Hack, Yonghong Zhang, Catherine DeSesa, James R Van Brocklyn and Eric G Bremer
    Citation: BMC Bioinformatics 2006 7:373
    Content type: Research article Published on:

  17. Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that i...

    Authors: Eider B Moore, Andrew V Poliakov, Peter Lincoln and James F Brinkley
    Citation: BMC Bioinformatics 2007 8:389
    Content type: Software Published on:

  18. In this paper, a novel building block of proteins called Top-n-grams is presented, which contains the evolutionary information extracted from the protein sequence frequency profiles. The protein sequence frequenc...

    Authors: Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong and Xuan Wang
    Citation: BMC Bioinformatics 2008 9:510
    Content type: Research article Published on:

  19. Computing semantic relatedness between textual labels representing biological and medical concepts is a crucial task in many automated knowledge extraction and processing applications relevant to the biomedica...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  20. Text mining has become a useful tool for biologists trying to understand the genetics of diseases. In particular, it can help identify the most interesting candidate genes for a disease for further experimenta...

    Authors: Shi Yu, Leon-Charles Tranchevent, Bart De Moor and Yves Moreau
    Citation: BMC Bioinformatics 2010 11:28
    Content type: Methodology article Published on:

  21. Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory me...

    Authors: Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun and Lin Zhang
    Citation: BMC Bioinformatics 2024 25:32
    Content type: Research Published on:

  22. The widely spreading coronavirus disease (COVID-19) has three major spreading properties: pathogenic mutations, spatial, and temporal propagation patterns. We know the spread of the virus geographically and te...

    Authors: Inyoung Sung, Sangseon Lee, Minwoo Pak, Yunyol Shin and Sun Kim
    Citation: BMC Bioinformatics 2022 23(Suppl 3):149
    Content type: Research Published on:

    This article is part of a Supplement: Volume 23 Supplement 3

  23. The Turku Event Extraction System (TEES) is a text mining program developed for the extraction of events, complex biomedical relationships, from scientific literature. Based on a graph-generation approach, the...

    Authors: Jari Björne and Tapio Salakoski
    Citation: BMC Bioinformatics 2015 16(Suppl 16):S4
    Content type: Research Published on:

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

  24. From a comparative perspective, the combination of retrieval and natural language processing methods we designed, achieved very competitive performances...

    Authors: Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno and Patrick Ruch
    Citation: BMC Bioinformatics 2005 6(Suppl 1):S23
    Content type: Report Published on:

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

  25. Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects task...

    Authors: Anthony Goddard, Nathan Wilson, Phil Cryer and Grant Yamashita
    Citation: BMC Bioinformatics 2011 12(Suppl 15):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 15

  26. Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through po...

    Authors: Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis and Karin Verspoor
    Citation: BMC Bioinformatics 2022 23:4
    Content type: Research Published on:

  27. Computational Biology needs computer-readable information records. Increasingly, meta-analysed and pre-digested information is being used in the follow up of high throughput experiments and other investigation...

    Authors: Barend Mons
    Citation: BMC Bioinformatics 2005 6:142
    Content type: Commentary Published on:

  28. Manual extraction of information from electronic pathology (epath) reports to populate the Surveillance, Epidemiology, and End Result (SEER) database is labor intensive. Systematizing the data extraction automati...

    Authors: Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian and Tanmoy Bhattacharya
    Citation: BMC Bioinformatics 2018 19(Suppl 18):485
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  29. Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However,...

    Authors: Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain and Robert Gentleman
    Citation: BMC Bioinformatics 2009 10:106
    Content type: Software Published on:

  30. This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semanti...

    Authors: Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner Jr, K Bretonnel Cohen, Karin Verspoor, Judith A Blake and Lawrence E Hunter
    Citation: BMC Bioinformatics 2012 13:161
    Content type: Research article Published on:

  31. Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...

    Authors: Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S3
    Content type: Research Published on:

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

  32. Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information ... the WSD problem for a number of text processing

    Authors: Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu and Carol Friedman
    Citation: BMC Bioinformatics 2006 7:334
    Content type: Research article Published on:

  34. The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-l...

    Authors: BD Pascal, MJ Chalmers, SA Busby, CC Mader, MR Southern, NF Tsinoremas and PR Griffin
    Citation: BMC Bioinformatics 2007 8:156
    Content type: Software Published on:

  35. Microbes have been shown to play a crucial role in various ecosystems. Many human diseases have been proved to be associated with bacteria, so it is essential to extract the interaction between bacteria for me...

    Authors: Xusheng Li, Chengcheng Fu, Ran Zhong, Duo Zhong, Tingting He and Xingpeng Jiang
    Citation: BMC Bioinformatics 2019 20(Suppl 16):583
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  36. Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. Th...

    Authors: Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2006 7(Suppl 5):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 5

  37. Many biomedical relation extraction systems are machine-learning based and have to be trained on large annotated corpora that are expensive and cumbersome to construct. We developed a knowledge-based relation ...

    Authors: Ning Kang, Bharat Singh, Chinh Bui, Zubair Afzal, Erik M van Mulligen and Jan A Kors
    Citation: BMC Bioinformatics 2014 15:64
    Content type: Research article Published on:

  38. Our main effort was to provide a robust integrated research environment, giving a particular emphasis to the integration process and facing different challenges, consecutively listed: ... ETL) operations; develop...

    Authors: Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G Priori and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2012 13(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 4

  40. Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq ex...

    Authors: John A. Hadish, Tyler D. Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman B. McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren Honaas and Stephen P. Ficklin
    Citation: BMC Bioinformatics 2022 23:156
    Content type: Software Published on:

  42. Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new en...

    Authors: Nicolas Fiorini, Sylvie Ranwez, Jacky Montmain and Vincent Ranwez
    Citation: BMC Bioinformatics 2015 16:83
    Content type: Research Article Published on:

  43. Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the prolifer...

    Authors: G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman, J Darlington, L Game, MJE Sternberg and SA Butcher
    Citation: BMC Bioinformatics 2008 9:493
    Content type: Software Published on:

  44. Plate design is a necessary and time-consuming operation for GC/LC-MS-based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a ...

    Authors: Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An, Jiawei Wang and Changbin Yu
    Citation: BMC Bioinformatics 2023 24:489
    Content type: Software Published on:

  46. DNA-binding proteins are vital for the study of cellular processes. In recent genome engineering studies, the identification of proteins with certain functions has become increasingly important and needs to be...

    Authors: Li Song, Dapeng Li, Xiangxiang Zeng, Yunfeng Wu, Li Guo and Quan Zou
    Citation: BMC Bioinformatics 2014 15:298
    Content type: Research article Published on:

  47. Relationships between entities such as genes, chemicals, metabolites, phenotypes and diseases in MEDLINE are often directional. That is, one may affect the other in a positive or negative manner. Detection of ...

    Authors: Cory B Giles and Jonathan D Wren
    Citation: BMC Bioinformatics 2008 9(Suppl 9):S11
    Content type: Proceedings Published on:

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

  50. Biomarkers and target-specific phenotypes are important to targeted drug design and individualized medicine, thus constituting an important aspect of modern pharmaceutical research and development. More and mo...

    Authors: Carlo A Trugenberger, Christoph Wälti, David Peregrim, Mark E Sharp and Svetlana Bureeva
    Citation: BMC Bioinformatics 2013 14:51
    Content type: Research article Published on:

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