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1652 result(s) for 'natural language processing' within BMC Bioinformatics

Page 1 of 34

  1. During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipitant...

    Authors: Joel Zirkle, Xiaomei Han, Rebecca Racz, Mohammadreza Samieegohar, Anik Chaturbedi, John Mann, Shilpa Chakravartula and Zhihua Li
    Citation: BMC Bioinformatics 2023 24:413
  2. Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data ... the implementation of a state-of-the-art Natural Language Processing system tha...

    Authors: Carlos Rodríguez-Penagos, Heladia Salgado, Irma Martínez-Flores and Julio Collado-Vides
    Citation: BMC Bioinformatics 2007 8:293
  3. Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this...

    Authors: Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale and Ted Briscoe
    Citation: BMC Bioinformatics 2008 9:193
  4. The Enteropathogen Resource Integration Center (ERIC; http://​www.​ericbrc.​org) has a goal of providing bioinformatics support for the scientific communi...

    Authors: Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett III, Matthew Shaker and David Pot
    Citation: BMC Bioinformatics 2009 10:177
  5. Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database....

    Authors: K. M. Tahsin Hassan Rahit, Vladimir Avramovic, Jessica X. Chong and Maja Tarailo-Graovac
    Citation: BMC Bioinformatics 2024 25:84
  6. Many biomedical natural language processing systems demonstrated large differences between their previously...

    Authors: Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L Johnson, Christophe Roeder, Jinho D Choi, Christopher Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A Baumgartner Jr, Michael Bada, Martha Palmer and Lawrence E Hunter
    Citation: BMC Bioinformatics 2012 13:207
  7. Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify local r...

    Authors: Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema A. Khan, Susan E. Clare, Xia Jiang, Richard Neapolitan and Yuan Luo
    Citation: BMC Bioinformatics 2018 19(Suppl 17):498

    This article is part of a Supplement: Volume 19 Supplement 17

  8. We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification....

    Authors: Jin Mao, Lisa R. Moore, Carrine E. Blank, Elvis Hsin-Hui Wu, Marcia Ackerman, Sonali Ranade and Hong Cui
    Citation: BMC Bioinformatics 2016 17:528
  9. Applications of Natural Language Processing (NLP) technology to biomedical texts have...subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are chara...

    Authors: Thomas Lippincott, Diarmuid Ó Séaghdha and Anna Korhonen
    Citation: BMC Bioinformatics 2011 12:212
  10. Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...

    Authors: C Hart Poskar, Jan Huege, Christian Krach, Mathias Franke, Yair Shachar-Hill and Björn H Junker
    Citation: BMC Bioinformatics 2012 13:295
  11. Longitudinal data on key cancer outcomes for clinical research, such as response to treatment and disease progression, are not captured in standard cancer registry reporting. Manual extraction of such outcomes fr...

    Authors: Haitham A. Elmarakeby, Pavel S. Trukhanov, Vidal M. Arroyo, Irbaz Bin Riaz, Deborah Schrag, Eliezer M. Van Allen and Kenneth L. Kehl
    Citation: BMC Bioinformatics 2023 24:328
  12. Protein S-nitrosylation (SNO) plays a key role in transferring nitric oxide-mediated signals in both animals and plants and has emerged as an important mechanism for regulating protein functions and cell signa...

    Authors: Pawel Pratyush, Suresh Pokharel, Hiroto Saigo and Dukka B. KC
    Citation: BMC Bioinformatics 2023 24:41
  13. Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not b...

    Authors: Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang and Ningshao Xia
    Citation: BMC Bioinformatics 2024 25:35
  14. Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information ...

    Authors: Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek and Paolo Romano
    Citation: BMC Bioinformatics 2014 15(Suppl 1):S2

    This article is part of a Supplement: Volume 15 Supplement 1

  15. Gas chromatography–mass spectrometry (GC-MS) is a technique frequently used in targeted and non-targeted measurements of metabolites. Most existing software tools for processing of raw instrument GC-MS data ti...

    Authors: Sean O'Callaghan, David P De Souza, Andrew Isaac, Qiao Wang, Luke Hodkinson, Moshe Olshansky, Tim Erwin, Bill Appelbe, Dedreia L Tull, Ute Roessner, Antony Bacic, Malcolm J McConville and Vladimir A Likić
    Citation: BMC Bioinformatics 2012 13:115
  16. Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis...

    Authors: Thomas Stropp, Timothy McPhillips, Bertram Ludäscher and Mark Bieda
    Citation: BMC Bioinformatics 2012 13:102
  17. Monoclonal antibodies (mAbs) have been used as therapeutic agents, which must overcome many developability issues after the discovery from in vitro display libraries. Especially, polyreactive mAbs can strongly...

    Authors: Hocheol Lim and Kyoung Tai No
    Citation: BMC Bioinformatics 2022 23:520
  18. We introduced a novel way to represent protein sequences as continuous vectors (embeddings) by using the language model ELMo taken from natural language processing. By modeling protein sequences, ELMo effectively...

    Authors: Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes and Burkhard Rost
    Citation: BMC Bioinformatics 2019 20:723
  19. The recognition of pharmacological substances, compounds and proteins is essential for biomedical relation extraction, knowledge graph construction, drug discovery, as well as medical question answering. Although...

    Authors: Cong Sun, Zhihao Yang, Lei Wang, Yin Zhang, Hongfei Lin and Jian Wang
    Citation: BMC Bioinformatics 2021 22(Suppl 1):602

    This article is part of a Supplement: Volume 22 Supplement 1

  20. Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estima...

    Authors: Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban and Ora Schueler-Furman
    Citation: BMC Bioinformatics 2023 24:433
  21. The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protein...

    Authors: William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber and Mahdi Belcaid
    Citation: BMC Bioinformatics 2024 25:165
  22. Decisions in healthcare usually rely on the goodness and completeness of data that could be coupled with heuristics to improve the decision process itself. However, this is often an incomplete process. Structured...

    Authors: Giuseppe Sgroi, Giulia Russo, Anna Maglia, Giuseppe Catanuto, Peter Barry, Andreas Karakatsanis, Nicola Rocco and Francesco Pappalardo
    Citation: BMC Bioinformatics 2022 22(Suppl 14):631

    This article is part of a Supplement: Volume 22 Supplement 14

  23. Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...

    Authors: Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner Jr, Helen L Johnson, Philip V Ogren and K Bretonnel Cohen
    Citation: BMC Bioinformatics 2008 9:78
  24. Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to ... the neural network and large scale pre-trained language model have largely improved its perf...

    Authors: Gezheng Xu, Wenge Rong, Yanmeng Wang, Yuanxin Ouyang and Zhang Xiong
    Citation: BMC Bioinformatics 2021 22:272
  25. Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...

    Authors: Halil Kilicoglu and Sabine Bergler
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S10

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

  26. The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level ...

    Authors: Leonardo Giannantoni, Roberta Bardini, Alessandro Savino and Stefano Di Carlo
    Citation: BMC Bioinformatics 2024 25:166
  27. This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for bi...

    Authors: David Campos, Sérgio Matos and José Luís Oliveira
    Citation: BMC Bioinformatics 2013 14:281
  28. Glaucoma can cause irreversible blindness to people’s eyesight. Since there are no symptoms in its early stage, it is particularly important to accurately segment the optic disc (OD) and optic cup (OC) from fu...

    Authors: Yun Jiang, Zeqi Ma, Chao Wu, Zequn Zhang and Wei Yan
    Citation: BMC Bioinformatics 2022 23:523
  29. Calcium (Ca2+) propagates within tissues serving as an important information carrier. In particular, cilia beat frequency in oviduct cells is partially regulated by Ca2+ changes. Thus, measuring the calcium de...

    Authors: Carlos Milovic, Carolina Oses, Manuel Villalón, Sergio Uribe, Carlos Lizama, Claudia Prieto, Marcelo E Andia, Pablo Irarrazaval and Cristian Tejos
    Citation: BMC Bioinformatics 2013 14:162
  30. We present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein...bibliosphere. We illustrate the extent of the desc...

    Authors: Christopher JO Baker, Rajaraman Kanagasabai, Wee Tiong Ang, Anitha Veeramani, Hong-Sang Low and Markus R Wenk
    Citation: BMC Bioinformatics 2008 9(Suppl 1):S5

    This article is part of a Supplement: Volume 9 Supplement 1

  31. Medical information has rapidly increased on the internet and has become one of the main targets of search engine use. However, medical information on the internet is subject to the problems of quality and acc...

    Authors: Li Zhang, Xiaoran Yang, Shijian Li, Tianyi Liao and Gang Pan
    Citation: BMC Bioinformatics 2022 23:136
  32. Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that pr...

    Authors: Leila Ranandeh Kalankesh, Robert Stevens and Andy Brass
    Citation: BMC Bioinformatics 2012 13:127
  33. During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they c...

    Authors: Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro and Luciano Milanesi
    Citation: BMC Bioinformatics 2016 17(Suppl 12):346

    This article is part of a Supplement: Volume 17 Supplement 12

  34. Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...

    Authors: K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer and Lawrence E. Hunter
    Citation: BMC Bioinformatics 2017 18:372
  35. This paper presents novel datasets providing numerical representations of ICD-10-CM codes by generating description embeddings using a large language model followed by a dimension reduction via autoencoder. Th...

    Authors: Michael J. Kane, Casey King, Denise Esserman, Nancy K. Latham, Erich J. Greene and David A. Ganz
    Citation: BMC Bioinformatics 2023 24:482

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