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1645 result(s) for 'natural language processing' within BMC Bioinformatics

Page 22 of 33

  5. Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell pote...

    Authors: Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu and Chengchen Zhao
    Citation: BMC Bioinformatics 2021 22:289
    Content type: Database Published on:

  6. The omics fields promise to revolutionize our understanding of biology and biomedicine. However, their potential is compromised by the challenge to analyze the huge datasets produced. Analysis of omics data is...

    Authors: Martin Eklund, Ola Spjuth and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2010 11:282
    Content type: Methodology article Published on:

  8. Trait heterogeneity, which exists when a trait has been defined with insufficient specificity such that it is actually two or more distinct traits, has been implicated as a confounding factor in traditional st...

    Authors: Tricia A Thornton-Wells, Jason H Moore and Jonathan L Haines
    Citation: BMC Bioinformatics 2006 7:204
    Content type: Research article Published on:

  9. Single cell RNA sequencing (scRNAseq) has provided invaluable insights into cellular heterogeneity and functional states in health and disease. During the analysis of scRNAseq data, annotating the biological i...

    Authors: H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens and Ryan M. O’Connell
    Citation: BMC Bioinformatics 2020 21:191
    Content type: Software Published on:

  10. In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a use...

    Authors: Sergio Gonzalez, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo and Norma Paniego
    Citation: BMC Bioinformatics 2017 18:121
    Content type: Software Published on:

  11. A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D structure patterns in proteins. Ex...

    Authors: Kevin Nagel, Antonio Jimeno-Yepes and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2009 10(Suppl 8):S4
    Content type: Research Published on:

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

  12. The Genia task, when it was introduced in 2009, was the first community-wide effort to address a fine-grained, structural information extraction from biomedical literature. Arranged for the second time as one ...

    Authors: Jin-Dong Kim, Ngan Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi and Akinori Yonezawa
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S1
    Content type: Proceedings Published on:

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

  15. The high growth of Next Generation Sequencing data currently demands new knowledge extraction methods. In particular, the RNA sequencing gene expression experimental technique stands out for case-control studi...

    Authors: Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi and Giovanni Felici
    Citation: BMC Bioinformatics 2018 19(Suppl 10):354
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  16. The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The prot...

    Authors: Alessandro Dal Palù, Agostino Dovier and Federico Fogolari
    Citation: BMC Bioinformatics 2004 5:186
    Content type: Research article Published on:

  17. The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is nece...

    Authors: Jianwei Li, Xiaoyu Ma, Xichuan Li and Junhua Gu
    Citation: BMC Bioinformatics 2020 21:236
    Content type: Methodology article Published on:

  18. Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA ...

    Authors: Matthew J Wakefield, Peter Maxwell and Gavin A Huttley
    Citation: BMC Bioinformatics 2005 6:130
    Content type: Software Published on:

  19. Inflammatory mediators play havoc in several diseases including the novel Coronavirus disease 2019 (COVID-19) and generally correlate with the severity of the disease. Interleukin-13 (IL-13), is a pleiotropic ...

    Authors: Pooja Arora, Neha Periwal, Yash Goyal, Vikas Sood and Baljeet Kaur
    Citation: BMC Bioinformatics 2023 24:141
    Content type: Research Published on:

  20. Recurrent neural network(RNN) is a good way to process sequential data, but the capability of RNN to compute long sequence data is inefficient. As a variant of RNN, long short term memory(LSTM) solved the prob...

    Authors: Jiale Liu and Xinqi Gong
    Citation: BMC Bioinformatics 2019 20:609
    Content type: Methodology Article Published on:

  22. Accuracy of document retrieval from MEDLINE for gene queries is crucially important for many applications in bioinformatics. We explore five information retrieval-based methods to rank documents retrieved by P...

    Authors: Aditya K Sehgal and Padmini Srinivasan
    Citation: BMC Bioinformatics 2006 7:220
    Content type: Research article Published on:

  23. Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational too...

    Authors: Pasquale Claudio Africa, Roberto Piersanti, Francesco Regazzoni, Michele Bucelli, Matteo Salvador, Marco Fedele, Stefano Pagani, Luca Dede’ and Alfio Quarteroni
    Citation: BMC Bioinformatics 2023 24:389
    Content type: Software Published on:

  24. T cell receptors (TCRs) play critical roles in adaptive immune responses, and recent advances in genome technology have made it possible to examine the T cell receptor (TCR) repertoire at the individual sequen...

    Authors: Meiling Liu, Juna Goo, Yang Liu, Wei Sun, Michael C. Wu, Li Hsu and Qianchuan He
    Citation: BMC Bioinformatics 2022 23:152
    Content type: Research Published on:

  27. Plant variety identification is the one most important of agricultural systems. Development of DNA marker profiles of released varieties to compare with candidate variety or future variety is required. However...

    Authors: Xiong Yuan, Zirong Li, Liwen Xiong, Sufeng Song, Xingfei Zheng, Zhonghai Tang, Zheming Yuan and Lanzhi Li
    Citation: BMC Bioinformatics 2022 23:30
    Content type: Research Published on:

  28. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma and accounts for cancer-related deaths. Survival rates are very low when the tumor is discovered in the late-stage. Th...

    Authors: Fangjun Li, Mu Yang, Yunhe Li, Mingqiang Zhang, Wenjuan Wang, Dongfeng Yuan and Dongqi Tang
    Citation: BMC Bioinformatics 2020 21:232
    Content type: Research article Published on:

  29. Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an import...

    Authors: Shuwei Yin, Xiao Tian, Jingjing Zhang, Peisen Sun and Guanglin Li
    Citation: BMC Bioinformatics 2021 22:10
    Content type: Software Published on:

  30. Analysis of high-throughput multi-’omics interactions across the hierarchy of expression has wide interest in making inferences with regard to biological function and biomarker discovery. Expression levels acr...

    Authors: Gregory M. Parkes and Mahesan Niranjan
    Citation: BMC Bioinformatics 2019 20:536
    Content type: Research Article Published on:

  33. Cellular systems are highly dynamic and responsive to cues from the environment. Cellular function and response patterns to external stimuli are regulated by biological networks. A protein-protein interaction ...

    Authors: Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen and Yi Pan
    Citation: BMC Bioinformatics 2011 12:339
    Content type: Methodology article Published on:

  34. The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, ...

    Authors: Nigam H Shah, Daniel L Rubin, Inigo Espinosa, Kelli Montgomery and Mark A Musen
    Citation: BMC Bioinformatics 2007 8:296
    Content type: Software Published on:

  37. We present a statistical method of analysis of biological networks based on the exponential random graph model, namely p2-model, as opposed to previous descriptive approaches. The model is capable to capture g...

    Authors: Svetlana Bulashevska, Alla Bulashevska and Roland Eils
    Citation: BMC Bioinformatics 2010 11:46
    Content type: Research article Published on:

  38. Automated biomedical named entity recognition and normalization serves as the basis for many downstream applications in information management. However, this task is challenging due to name variations and enti...

    Authors: Huiwei Zhou, Shixian Ning, Zhe Liu, Chengkun Lang, Zhuang Liu and Bizun Lei
    Citation: BMC Bioinformatics 2020 21:35
    Content type: Research article Published on:

  39. Networks are ubiquitous in modern cell biology and physiology. A large literature exists for inferring/proposing biological pathways/networks using statistical or machine learning algorithms. Despite these adv...

    Authors: Phillip D Yates and Nitai D Mukhopadhyay
    Citation: BMC Bioinformatics 2013 14:94
    Content type: Methodology article Published on:

  41. Ensemble attribute profile clustering is a novel, text-based strategy for analyzing a user-defined list of genes and/or proteins. The strategy exploits annotation data present in gene-centered corpora and util...

    Authors: JR Semeiks, A Rizki, MJ Bissell and IS Mian
    Citation: BMC Bioinformatics 2006 7:147
    Content type: Methodology article Published on:

  44. The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield...

    Authors: Garth L. Kong, Thai T. Nguyen, Wesley K. Rosales, Anjali D. Panikar, John H. W. Cheney, Theresa A. Lusardi, William M. Yashar, Brittany M. Curtiss, Sarah A. Carratt, Theodore P. Braun and Julia E. Maxson
    Citation: BMC Bioinformatics 2024 25:142
    Content type: Software Published on:

  45. Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best app...

    Authors: Catia Pesquita, Daniel Faria, Hugo Bastos, António EN Ferreira, André O Falcão and Francisco M Couto
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S4
    Content type: Proceedings Published on:

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

  48. Authors: Eric C. Rouchka, Julia H. Chariker, David A. Tieri, Juw Won Park, Shreedharkumar Rajurkar, Vikas Singh, Nishchal K. Verma, Yan Cui, Mark Farman, Bradford Condon, Neil Moore, Jerzy Jaromczyk, Jolanta Jaromczyk, Daniel Harris, Patrick Calie, Eun Kyong Shin…
    Citation: BMC Bioinformatics 2017 18(Suppl 9):377
    Content type: Meeting abstracts Published on:

    This article is part of a Supplement: Volume 18 Supplement 9

    The Correction to this article has been published in BMC Bioinformatics 2017 18:490

  49. In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still c...

    Authors: Giulia Russo, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Miguel A. Juarez, Pere-Joan Cardona, Santo Motta, Kenneth B. Walker, Epifanio Fichera, Marco Viceconti and Francesco Pappalardo
    Citation: BMC Bioinformatics 2020 21(Suppl 17):458
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  50. Genome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experienc...

    Authors: Dao-Feng Zhang, Wei He, Zongze Shao, Iftikhar Ahmed, Yuqin Zhang, Wen-Jun Li and Zhe Zhao
    Citation: BMC Bioinformatics 2023 24:390
    Content type: Software Published on:

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