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1641 result(s) for 'natural language processing' within BMC Bioinformatics

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  1. Handling genotype data typed at hundreds of thousands of loci is very time-consuming and it is no exception for population structure inference. Therefore, we propose to apply PCA to the genotype data of a popu...

    Authors: Chih Lee, Ali Abdool and Chun-Hsi Huang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S73
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  2. Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene reg...

    Authors: Ichcha Manipur, Ilaria Granata, Lucia Maddalena and Mario R. Guarracino
    Citation: BMC Bioinformatics 2020 21(Suppl 10):349
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

    The Correction to this article has been published in BMC Bioinformatics 2020 21:494

  3. Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown t...

    Authors: Tim Lu, Christine M Costello, Peter JP Croucher, Robert Häsler, Günther Deuschl and Stefan Schreiber
    Citation: BMC Bioinformatics 2005 6:37
    Content type: Methodology article Published on:

  5. The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final rep...

    Authors: Jin-Dong Kim, Jung-jae Kim, Xu Han and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  6. Survival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly int...

    Authors: Jiarui Feng, Heming Zhang and Fuhai Li
    Citation: BMC Bioinformatics 2021 22:47
    Content type: Methodology article Published on:

  7. Optimality principles have been used to explain the structure and behavior of living matter at different levels of organization, from basic phenomena at the molecular level, up to complex dynamics in whole pop...

    Authors: Nikolaos Tsiantis and Julio R. Banga
    Citation: BMC Bioinformatics 2020 21:472
    Content type: Methodology article Published on:

  8. The detection of the glomeruli is a key step in the histopathological evaluation of microscopic images of the kidneys. However, the task of automatic detection of the glomeruli poses challenges owing to the di...

    Authors: Tsuyoshi Kato, Raissa Relator, Hayliang Ngouv, Yoshihiro Hirohashi, Osamu Takaki, Tetsuhiro Kakimoto and Kinya Okada
    Citation: BMC Bioinformatics 2015 16:316
    Content type: Research Article Published on:

  10. Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of di...

    Authors: Afrah Shafquat, Ronald G. Crystal and Jason G. Mezey
    Citation: BMC Bioinformatics 2020 21:178
    Content type: Research article Published on:

  11. Cancer subtype classification is helpful for personalized cancer treatment. Although, some approaches have been developed to classifying caner subtype based on high dimensional gene expression data, it is diff...

    Authors: Junwei Luo, Yading Feng, Xuyang Wu, Ruimin Li, Jiawei Shi, Wenjing Chang and Junfeng Wang
    Citation: BMC Bioinformatics 2023 24:289
    Content type: Research Published on:

  12. Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve bia...

    Authors: P Andrew Nevarez, Christopher M DeBoever, Benjamin J Freeland, Marissa A Quitt and Eliot C Bush
    Citation: BMC Bioinformatics 2010 11:462
    Content type: Research article Published on:

  13. The prediction of conformational B-cell epitopes is one of the most important goals in immunoinformatics. The solution to this problem, even if approximate, would help in designing experiments to precisely map...

    Authors: Yan Xin Huang, Yong Li Bao, Shu Yan Guo, Yan Wang, Chun Guang Zhou and Yu Xin Li
    Citation: BMC Bioinformatics 2008 9:538
    Content type: Software Published on:

  16. DNA-Binding Proteins (DBP) plays a pivotal role in biological system. A mounting number of researchers are studying the mechanism and detection methods. To detect DBP, the tradition experimental method is time...

    Authors: Yuqing Qian, Limin Jiang, Yijie Ding, Jijun Tang and Fei Guo
    Citation: BMC Bioinformatics 2021 22(Suppl 3):291
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  18. Since the function of a protein is largely dictated by its three dimensional configuration, determining a protein's structure is of fundamental importance to biology. Here we report on a novel approach to dete...

    Authors: James R Green, Michael J Korenberg and Mohammed O Aboul-Magd
    Citation: BMC Bioinformatics 2009 10:222
    Content type: Research article Published on:

  21. Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is ...

    Authors: Richard G Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler and Henning Hermjakob
    Citation: BMC Bioinformatics 2007 8:401
    Content type: Software Published on:

  22. Immunological prevention of cancer has been obtained in HER-2/neu transgenic mice using a vaccine that combines 3 different immune stimuli (Triplex vaccine) that is repeatedly administered for the entire lifes...

    Authors: Pier-Luigi Lollini, Santo Motta and Francesco Pappalardo
    Citation: BMC Bioinformatics 2006 7:352
    Content type: Methodology article Published on:

  23. Deep learning methods are a proven commodity in many fields and endeavors. One of these endeavors is predicting the presence of adverse drug–drug interactions (DDIs). The models generated can predict, with rea...

    Authors: Rogia Kpanou, Mazid Abiodoun Osseni, Prudencio Tossou, Francois Laviolette and Jacques Corbeil
    Citation: BMC Bioinformatics 2021 22:477
    Content type: Research Published on:

  24. Methods for the integrative analysis of multi-omics data are required to draw a more complete and accurate picture of the dynamics of molecular systems. The complexity of biological systems, the technological ...

    Authors: Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani and Luciano Milanesi
    Citation: BMC Bioinformatics 2016 17(Suppl 2):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 2

  25. Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of indi...

    Authors: Sean M Hoban, Massimo Mezzavilla, Oscar E Gaggiotti, Andrea Benazzo, Cock van Oosterhout and Giorgio Bertorelle
    Citation: BMC Bioinformatics 2013 14:309
    Content type: Research article Published on:

  26. The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares contro...

    Authors: Gennady V. Khvorykh and Andrey V. Khrunin
    Citation: BMC Bioinformatics 2020 21(Suppl 12):304
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  27. Single nucleotide polymorphisms (SNPs) located within the human genome have been shown to have utility as markers of identity in the differentiation of DNA from individual contributors. Massively parallel DNA ...

    Authors: M. Heath Farris, Andrew R. Scott, Pamela A. Texter, Marta Bartlett, Patricia Coleman and David Masters
    Citation: BMC Bioinformatics 2018 19:126
    Content type: Research article Published on:

  28. Numerous studies have demonstrated that long non-coding RNAs are related to plenty of human diseases. Therefore, it is crucial to predict potential lncRNA-disease associations for disease prognosis, diagnosis ...

    Authors: Zhuangwei Shi, Han Zhang, Chen Jin, Xiongwen Quan and Yanbin Yin
    Citation: BMC Bioinformatics 2021 22:136
    Content type: Research article Published on:

  29. Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be ...

    Authors: Jie Hao, Youngsoon Kim, Tae-Kyung Kim and Mingon Kang
    Citation: BMC Bioinformatics 2018 19:510
    Content type: Methodology article Published on:

  31. Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes ...

    Authors: Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Cinzia Di Pietro, Michele Purrello and Marco Ragusa
    Citation: BMC Bioinformatics 2007 8:58
    Content type: Software Published on:

  32. Missing values are commonly present in microarray data profiles. Instead of discarding genes or samples with incomplete expression level, missing values need to be properly imputed for accurate data analysis. ...

    Authors: Yang Yang, Zhuangdi Xu and Dandan Song
    Citation: BMC Bioinformatics 2016 17(Suppl 1):S10
    Content type: PROCEEDINGS Published on:

    This article is part of a Supplement: Volume 17 Supplement 1

  33. Multi-omics experimental approaches are becoming common practice in biological and medical sciences underlining the need to design new integrative techniques and applications to enable the multi-scale characte...

    Authors: Johanna Zoppi, Jean-François Guillaume, Michel Neunlist and Samuel Chaffron
    Citation: BMC Bioinformatics 2021 22:6
    Content type: Software Published on:

  35. The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing...

    Authors: Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun and Zexuan Zhu
    Citation: BMC Bioinformatics 2017 18:179
    Content type: Software Published on:

  36. Researchers in systems biology use network visualization to summarize the results of their analysis. Such networks often include unconnected components, which popular network alignment algorithms place arbitra...

    Authors: Miha Štajdohar, Minca Mramor, Blaž Zupan and Janez Demšar
    Citation: BMC Bioinformatics 2010 11:475
    Content type: Research article Published on:

  38. Haplotype phasing is an important problem in the analysis of genomics information. Given a set of DNA fragments of an individual, it consists of determining which one of the possible alleles (alternative forms...

    Authors: Andrea Bracciali, Marco Aldinucci, Murray Patterson, Tobias Marschall, Nadia Pisanti, Ivan Merelli and Massimo Torquati
    Citation: BMC Bioinformatics 2016 17(Suppl 11):342
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 11

  39. The growth of the biomedical information requires most information retrieval systems to provide short and specific answers in response to complex user queries. Semantic information in the form of free text tha...

    Authors: Qinmin Hu, Jimmy Xiangji Huang and Xiaohua Hu
    Citation: BMC Bioinformatics 2012 13(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 13 Supplement 9

  41. Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern...

    Authors: Elham Khodayari Moez, Morteza Hajihosseini, Jeffrey L. Andrews and Irina Dinu
    Citation: BMC Bioinformatics 2019 20:650
    Content type: Methodology article Published on:

  42. Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations ...

    Authors: James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl and Bjoern Peters
    Citation: BMC Bioinformatics 2019 20(Suppl 5):182
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  43. Although there have been some recent cell and animal experiments indicating that expression of the gene encoding apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) is closely related to cancer, ...

    Authors: Jiacheng Wu, Ni Li, Linwen Zhu, Dawei Zhen, Mengqi Li, Hang Chen, Mengmeng Ye, Yiqin Wei and Guofeng Shao
    Citation: BMC Bioinformatics 2022 23:312
    Content type: Research Published on:

  44. Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemble...

    Authors: Min Xie, Linfeng Yang, Chenglin Jiang, Shenshen Wu, Cheng Luo, Xin Yang, Lijuan He, Shixuan Chen, Tianquan Deng, Mingzhi Ye, Jianbing Yan and Ning Yang
    Citation: BMC Bioinformatics 2022 23:68
    Content type: Software Published on:

  45. Performing statistical tests is an important step in analyzing genome-wide datasets for detecting genomic features differentially expressed between conditions. Each type of statistical test has its own advanta...

    Authors: Yuanzhe Bei and Pengyu Hong
    Citation: BMC Bioinformatics 2016 17:541
    Content type: Methodology article Published on:

  47. There has been a lot of interest in recent years focusing on the modeling and simulation of Gene Regulatory Networks (GRNs). However, the evolutionary mechanisms that give rise to GRNs in the first place are s...

    Authors: Anton Kratz, Masaru Tomita and Arun Krishnan
    Citation: BMC Bioinformatics 2008 9:541
    Content type: Software Published on:

  48. A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false...

    Authors: Isabella Mendolia, Salvatore Contino, Ugo Perricone, Edoardo Ardizzone and Roberto Pirrone
    Citation: BMC Bioinformatics 2020 21(Suppl 8):310
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  49. As in many different areas of science and technology, most important problems in bioinformatics rely on the proper development and assessment of binary classifiers. A generalized assessment of the performance ...

    Authors: Ismael A Vergara, Tomás Norambuena, Evandro Ferrada, Alex W Slater and Francisco Melo
    Citation: BMC Bioinformatics 2008 9:265
    Content type: Software Published on:

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