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1632 result(s) for 'natural language processing' within BMC Bioinformatics

Page 27 of 33

  1. Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computa...

    Authors: Hamid Younesy, Torsten Möller, Matthew C Lorincz, Mohammad M Karimi and Steven JM Jones
    Citation: BMC Bioinformatics 2015 16(Suppl 11):S2

    This article is part of a Supplement: Volume 16 Supplement 11

  2. Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selec...

    Authors: Venkata Thodima, Mehdi Pirooznia and Youping Deng
    Citation: BMC Bioinformatics 2006 7(Suppl 2):S6

    This article is part of a Supplement: Volume 7 Supplement 2

  3. Longitudinal single-cell sequencing experiments of patient-derived models are increasingly employed to investigate cancer evolution. In this context, robust computational methods are needed to properly exploit...

    Authors: Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti and Alex Graudenzi
    Citation: BMC Bioinformatics 2023 24:99
  4. Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains pattern...

    Authors: Nicholas J Hudson, Laercio R Porto-Neto, James Kijas, Sean McWilliam, Ryan J Taft and Antonio Reverter
    Citation: BMC Bioinformatics 2014 15:66
  5. Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally develope...

    Authors: Mutlu Doğruel, Thomas A Down and Tim JP Hubbard
    Citation: BMC Bioinformatics 2008 9:19
  6. Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to ...

    Authors: Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang and Shiaofen Fang
    Citation: BMC Bioinformatics 2021 22:223
  7. Several techniques have been tailored to the quantification of microRNA expression, including hybridization arrays, quantitative PCR (qPCR), and high-throughput sequencing. Each of these has certain strengths ...

    Authors: Matthew N. McCall, Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer and Marc K. Halushka
    Citation: BMC Bioinformatics 2016 17:138
  8. Comparative analysis of gene expression profiling of multiple biological categories, such as different species of organisms or different kinds of tissue, promises to enhance the fundamental understanding of th...

    Authors: Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu and Kun Zhang
    Citation: BMC Bioinformatics 2010 11:338
  9. The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used fo...

    Authors: Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis and Marianne Rooman
    Citation: BMC Bioinformatics 2011 12:151
  10. The biomedical literature is expanding at ever-increasing rates, and it has become extremely challenging for researchers to keep abreast of new data and discoveries even in their own domains of expertise. We i...

    Authors: Patricia Maraver, Rubén Armañanzas, Todd A. Gillette and Giorgio A. Ascoli
    Citation: BMC Bioinformatics 2019 20:50
  11. As more complete genome sequences become available, bioinformatics challenges arise in how to exploit genome sequences to make phenotypic predictions. One type of phenotypic prediction is to determine sets of ...

    Authors: Steven Eker, Markus Krummenacker, Alexander G Shearer, Ashish Tiwari, Ingrid M Keseler, Carolyn Talcott and Peter D Karp
    Citation: BMC Bioinformatics 2013 14:114
  12. RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology ...

    Authors: MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu and Henry W. Long
    Citation: BMC Bioinformatics 2018 19:135
  13. The next-generation of sequencing technologies, along with the development of bioinformatics, are generating a growing number of reads every day. For the convenience of further research, these reads should be ...

    Authors: Song Liu, Yi Wang and Fei Wang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):466

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

  14. Microarray and other high-throughput technologies are producing large sets of interesting genes that are difficult to analyze directly. Bioinformatics tools are needed to interpret the functional information i...

    Authors: Bing Zhang, Denise Schmoyer, Stefan Kirov and Jay Snoddy
    Citation: BMC Bioinformatics 2004 5:16
  15. Microbes perform a fundamental economic, social, and environmental role in our society. Metagenomics makes it possible to investigate microbes in their natural environments (the complex communities) and their ...

    Authors: Raíssa Silva, Kleber Padovani, Fabiana Góes and Ronnie Alves
    Citation: BMC Bioinformatics 2021 22:87
  16. The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models,...

    Authors: Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander and Laurent Excoffier
    Citation: BMC Bioinformatics 2010 11:116
  17. With a growing amount of (multi-)omics data being available, the extraction of knowledge from these datasets is still a difficult problem. Classical enrichment-style analyses require predefined pathways or gen...

    Authors: Sebastian Winkler, Ivana Winkler, Mirjam Figaschewski, Thorsten Tiede, Alfred Nordheim and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2022 23:139
  18. Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that al...

    Authors: Vasyl Pihur, Susmita Datta and Somnath Datta
    Citation: BMC Bioinformatics 2009 10:62
  19. An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have bee...

    Authors: Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis and Steven Watts
    Citation: BMC Bioinformatics 2021 22:51
  20. Genomic selection (GS) promises to improve accuracy in estimating breeding values and genetic gain for quantitative traits compared to traditional breeding methods. Its reliance on high-throughput genome-wide ...

    Authors: Isaak Y Tecle, Jeremy D Edwards, Naama Menda, Chiedozie Egesi, Ismail Y Rabbi, Peter Kulakow, Robert Kawuki, Jean-Luc Jannink and Lukas A Mueller
    Citation: BMC Bioinformatics 2014 15:398
  21. Facing the diversity of omics data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce rob...

    Authors: Galadriel Brière, Élodie Darbo, Patricia Thébault and Raluca Uricaru
    Citation: BMC Bioinformatics 2021 22:361
  22. Recombination plays an important role in the maintenance of genetic diversity in many types of organisms, especially diploid eukaryotes. Recombination can be studied and used to map diseases. However, recombin...

    Authors: Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhi-Ming Ma and Shuhua Xu
    Citation: BMC Bioinformatics 2014 15:273
  23. Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes and have been confirmed to be concerned with various diseases. Largely uncharacterized of the physiological role and functions...

    Authors: Long Yang, Li-Ping Li and Hai-Cheng Yi
    Citation: BMC Bioinformatics 2022 22(Suppl 12):621

    This article is part of a Supplement: Volume 22 Supplement 12

  24. miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed signif...

    Authors: Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li and Thuc Duy Le
    Citation: BMC Bioinformatics 2018 19(Suppl 19):514

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

  25. Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutati...

    Authors: Sebastien Tempel, Christine Rousseau, Fariza Tahi and Jacques Nicolas
    Citation: BMC Bioinformatics 2010 11:474
  26. Due to the advent of deep learning, the increasing number of studies in the biomedical domain has attracted much interest in feature extraction and classification tasks. In this research, we seek the best comb...

    Authors: Zolzaya Dashdorj and Min Song
    Citation: BMC Bioinformatics 2019 20(Suppl 10):244

    This article is part of a Supplement: Volume 20 Supplement 10

  27. qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the st...

    Authors: Michael T. Ganger, Geoffrey D. Dietz and Sarah J. Ewing
    Citation: BMC Bioinformatics 2017 18:534
  28. A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA spe...

    Authors: Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio and Cecilia Saccone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S15

    This article is part of a Supplement: Volume 10 Supplement 6

  29. 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

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

  30. 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

    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

  31. 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
  32. 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

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

  33. 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
  34. 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
  35. 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

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