Skip to main content

Articles

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

Page 23 of 33

  1. General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificia...

    Authors: Andy Pang, Andrew D Smith, Paulo AS Nuin and Elisabeth RM Tillier
    Citation: BMC Bioinformatics 2005 6:236
  2. MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs...

    Authors: Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li and Shu-Hong Zhao
    Citation: BMC Bioinformatics 2007 8:341
  3. The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessio...

    Authors: Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan and Degui Zhi
    Citation: BMC Bioinformatics 2018 19(Suppl 17):492

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

  4. Simulation of DNA-microarray data serves at least three purposes: (i) optimizing the design of an intended DNA microarray experiment, (ii) comparing existing pre-processing and processing methods for best anal...

    Authors: Casper J Albers, Ritsert C Jansen, Jan Kok, Oscar P Kuipers and Sacha AFT van Hijum
    Citation: BMC Bioinformatics 2006 7:205
  5. Identifying differentially expressed genes (DEG) is a fundamental step in studies that perform genome wide expression profiling. Typically, DEG are identified by univariate approaches such as Significance Anal...

    Authors: Neil R Clark, Kevin S Hu, Axel S Feldmann, Yan Kou, Edward Y Chen, Qiaonan Duan and Avi Ma’ayan
    Citation: BMC Bioinformatics 2014 15:79
  6. Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software...

    Authors: Bastiaan A van den Berg, Marcel JT Reinders, Johannes A Roubos and Dick de Ridder
    Citation: BMC Bioinformatics 2014 15:93
  7. RNA metabolism, through 'combinatorial splicing', can generate enormous structural diversity in the proteome. Alternative domains may interact, however, with unpredictable phenotypic consequences, necessitatin...

    Authors: Mark C Emerick, Giovanni Parmigiani and William S Agnew
    Citation: BMC Bioinformatics 2007 8:16
  8. The ability to compare RNA secondary structures is important in understanding their biological function and for grouping similar organisms into families by looking at evolutionarily conserved sequences such as...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli
    Citation: BMC Bioinformatics 2023 23(Suppl 6):575

    This article is part of a Supplement: Volume 23 Supplement 6

  9. In cluster analysis, the validity of specific solutions, algorithms, and procedures present significant challenges because there is no null hypothesis to test and no 'right answer'. It has been noted that a re...

    Authors: Nikhil R Garge, Grier P Page, Alan P Sprague, Bernard S Gorman and David B Allison
    Citation: BMC Bioinformatics 2005 6(Suppl 2):S10

    This article is part of a Supplement: Volume 6 Supplement 2

  10. Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, suc...

    Authors: You Tang, Zhuo Li, Chao Wang, Yuxin Liu, Helong Yu, Aoxue Wang and Yao Zhou
    Citation: BMC Bioinformatics 2020 21:461
  11. DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorith...

    Authors: Mark D. Temple
    Citation: BMC Bioinformatics 2017 18:221
  12. Single cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of ...

    Authors: Jiajie Peng, Xiaoyu Wang and Xuequn Shang
    Citation: BMC Bioinformatics 2019 20(Suppl 8):284

    This article is part of a Supplement: Volume 20 Supplement 8

  13. Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensi...

    Authors: Daniel Wüstner
    Citation: BMC Bioinformatics 2022 23:334
  14. Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer opti...

    Authors: Melissa J Morine, Jolene McMonagle, Sinead Toomey, Clare M Reynolds, Aidan P Moloney, Isobel C Gormley, Peadar Ó Gaora and Helen M Roche
    Citation: BMC Bioinformatics 2010 11:499
  15. Inspired by a recent application of the Latent Dirichlet Allocation (LDA) model for conducting structural comparisons of proteins, we propose higher-order LDA-obtained topic-based representations of protein struc...

    Authors: Kevin Molloy, M Jennifer Van, Daniel Barbara and Amarda Shehu
    Citation: BMC Bioinformatics 2014 15(Suppl 8):S4

    This article is part of a Supplement: Volume 15 Supplement 8

  16. As an important task in bioinformatics, clustering analysis plays a critical role in understanding the functional mechanisms of many complex biological systems, which can be modeled as biological networks. The...

    Authors: Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu and Lun Hu
    Citation: BMC Bioinformatics 2023 24:451
  17. Automated assignment of functions to unknown proteins is one of the most important task in computational biology. The development of experimental methods for genome scale analysis of molecular interaction netw...

    Authors: Qingyao Wu, Yunming Ye, Michael K Ng, Shen-Shyang Ho and Ruichao Shi
    Citation: BMC Bioinformatics 2014 15(Suppl 2):S9

    This article is part of a Supplement: Volume 15 Supplement 2

  18. Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and ...

    Authors: Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan and Jaewoo Kang
    Citation: BMC Bioinformatics 2018 19:21
  19. Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, ...

    Authors: Vladimir A. Ivanisenko, Pavel S. Demenkov, Timofey V. Ivanisenko, Elena L. Mishchenko and Olga V. Saik
    Citation: BMC Bioinformatics 2019 20(Suppl 1):34

    This article is part of a Supplement: Volume 20 Supplement 1

  20. An organism’s observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic ...

    Authors: Katharina Munk, Daria Ilina, Lisa Ziemba, Günter Brader and Eva M. Molin
    Citation: BMC Bioinformatics 2024 25:93
  21. Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation approaches are available to the ...

    Authors: Johannes Tuikkala, Laura L Elo, Olli S Nevalainen and Tero Aittokallio
    Citation: BMC Bioinformatics 2008 9:202
  22. The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several...

    Authors: Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao and Xiaokun Li
    Citation: BMC Bioinformatics 2009 10:123
  23. There are many methods for analyzing microarray data that group together genes having similar patterns of expression over all conditions tested. However, in many instances the biologically important goal is to...

    Authors: Joseph C Roden, Brandon W King, Diane Trout, Ali Mortazavi, Barbara J Wold and Christopher E Hart
    Citation: BMC Bioinformatics 2006 7:194
  24. The phenome represents a distinct set of information in the human population. It has been explored particularly in its relationship with the genome to identify correlations for diseases. The phenome has been a...

    Authors: Halil Bisgin, Zhichao Liu, Hong Fang, Reagan Kelly, Xiaowei Xu and Weida Tong
    Citation: BMC Bioinformatics 2014 15:267
  25. A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metaboli...

    Authors: Martin A Ott and Gert Vriend
    Citation: BMC Bioinformatics 2006 7:517
  26. Protein–protein interaction (PPI) plays an important role in regulating cells and signals. Despite the ongoing efforts of the bioassay group, continued incomplete data limits our ability to understand the mole...

    Authors: Xiao-Rui Su, Lun Hu, Zhu-Hong You, Peng-Wei Hu and Bo-Wei Zhao
    Citation: BMC Bioinformatics 2022 23:234
  27. Modern proteomes evolved by modification of pre-existing ones. It is extremely important to comparative biology that related proteins be identified as members of the same cognate group, since a characterized p...

    Authors: Adriano Barbosa-Silva, Venkata P Satagopam, Reinhard Schneider and J Miguel Ortega
    Citation: BMC Bioinformatics 2008 9:141
  28. Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In thi...

    Authors: Shashank Agarwal, Feifan Liu and Hong Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S10

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

  29. Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations an...

    Authors: Xiaoshi Zhong and Jagath C. Rajapakse
    Citation: BMC Bioinformatics 2020 21(Suppl 16):560

    This article is part of a Supplement: Volume 21 Supplement 16

  30. Phosphorylation events direct the flow of signals and metabolites along cellular protein networks. Current annotations of kinase-substrate binding events are far from complete. In this study, we scanned the en...

    Authors: Yichuan Liu and Aydin Tozeren
    Citation: BMC Bioinformatics 2010 11:349
  31. Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past dec...

    Authors: ShanShan Hu, Chenglin Zhang, Peng Chen, Pengying Gu, Jun Zhang and Bing Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 25):689

    This article is part of a Supplement: Volume 20 Supplement 25

  32. There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using ba...

    Authors: Antonio Carvajal-Rodríguez
    Citation: BMC Bioinformatics 2008 9:223
  33. Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most wi...

    Authors: Jiongmin Zhang, Ke Jia, Jinmeng Jia and Ying Qian
    Citation: BMC Bioinformatics 2018 19:161
  34. The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste ar...

    Authors: Peter Murray-Rust, John BO Mitchell and Henry S Rzepa
    Citation: BMC Bioinformatics 2005 6:180
  35. DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The re...

    Authors: Stephan Hutter, Albert J Vilella and Julio Rozas
    Citation: BMC Bioinformatics 2006 7:409
  36. Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitat...

    Authors: Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato and Stefania Bortoluzzi
    Citation: BMC Bioinformatics 2009 10:201
  37. Gene set analysis based on Gene Ontology (GO) can be a promising method for the analysis of differential expression patterns. However, current studies that focus on individual GO terms have limited analytical ...

    Authors: Tao Xu, JianLei Gu, Yan Zhou and LinFang Du
    Citation: BMC Bioinformatics 2009 10:240
  38. The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaff...

    Authors: Sen Wang, Hengchao Wang, Fan Jiang, Anqi Wang, Hangwei Liu, Hanbo Zhao, Boyuan Yang, Dong Xu, Yan Zhang and Wei Fan
    Citation: BMC Bioinformatics 2022 23:528
  39. The identification of protein-protein interaction sites is a computationally challenging task and important for understanding the biology of protein complexes. There is a rich literature in this field. A broad...

    Authors: Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke and Stephan Waack
    Citation: BMC Bioinformatics 2014 15:277
  40. Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these t...

    Authors: Francisco Fernandes, Paulo GS da Fonseca, Luis MS Russo, Arlindo L Oliveira and Ana T Freitas
    Citation: BMC Bioinformatics 2011 12:163
  41. Biomedical event extraction has attracted substantial attention as it can assist researchers in understanding the plethora of interactions among genes that are described in publications in molecular biology. W...

    Authors: Andreas Vlachos and Mark Craven
    Citation: BMC Bioinformatics 2012 13(Suppl 11):S5

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

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Sign up for article alerts and news from this journal