Skip to main content

Articles

Page 200 of 248

  2. Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed mi...

    Authors: Da Meng, Shira L Broschat and Douglas R Call
    Citation: BMC Bioinformatics 2008 9:328
    Content type: Software Published on:

  4. Real-time PCR analysis is a sensitive DNA quantification technique that has recently gained considerable attention in biotechnology, microbiology and molecular diagnostics. Although, the cycle-threshold (Ct) meth...

    Authors: Michele Guescini, Davide Sisti, Marco BL Rocchi, Laura Stocchi and Vilberto Stocchi
    Citation: BMC Bioinformatics 2008 9:326
    Content type: Methodology article Published on:

  5. A better understanding of the mechanisms involved in gas-phase fragmentation of peptides is essential for the development of more reliable algorithms for high-throughput protein identification using mass spect...

    Authors: Cong Zhou, Lucas D Bowler and Jianfeng Feng
    Citation: BMC Bioinformatics 2008 9:325
    Content type: Research article Published on:

  7. Testing for selection is becoming one of the most important steps in the analysis of multilocus population genetics data sets. Existing applications are difficult to use, leaving many non-trivial, error-prone ...

    Authors: Tiago Antao, Ana Lopes, Ricardo J Lopes, Albano Beja-Pereira and Gordon Luikart
    Citation: BMC Bioinformatics 2008 9:323
    Content type: Software Published on:

  9. GenBank flatfile (GBF) format is one of the most popular sequence file formats because of its detailed sequence features and ease of readability. To use the data in the file by a computer, a parsing process is...

    Authors: Tae-Ho Lee, Yeon-Ki Kim and Baek Hie Nahm
    Citation: BMC Bioinformatics 2008 9:321
    Content type: Software Published on:

  11. Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deplo...

    Authors: Alexander Statnikov, Lily Wang and Constantin F Aliferis
    Citation: BMC Bioinformatics 2008 9:319
    Content type: Research article Published on:

  12. Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines,...

    Authors: Kengo Sato, Toutai Mituyama, Kiyoshi Asai and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2008 9:318
    Content type: Methodology article Published on:

  13. The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability a...

    Authors: Andrew M Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas Down, Robert D Finn, Henning Hermjakob, Tim JP Hubbard, Rafael C Jimenez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R Macías, Gabrielle A Reeves and Andreas Prlić
    Citation: BMC Bioinformatics 2008 9(Suppl 8):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 8

  14. Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation work is slow and expensive. Au...

    Authors: Samira Jaeger, Sylvain Gaudan, Ulf Leser and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2008 9(Suppl 8):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 8

  16. Correctly merged data sets that have been independently genotyped can increase statistical power in linkage and association studies. However, alleles from microsatellite data sets genotyped with different expe...

    Authors: Angela P Presson, Eric M Sobel, Paivi Pajukanta, Christopher Plaisier, Daniel E Weeks, Karolina Åberg and Jeanette C Papp
    Citation: BMC Bioinformatics 2008 9:317
    Content type: Software Published on:

  17. A goal of proteomics is to distinguish between states of a biological system by identifying protein expression differences. Liu et al. demonstrated a method to perform semi-relative protein quantitation in shotgu...

    Authors: Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, John R Yates III and Valmir C Barbosa
    Citation: BMC Bioinformatics 2008 9:316
    Content type: Software Published on:

    The Related Article to this article has been published in Nature Protocols 2015 11:nprot.2015.133

  18. Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an e...

    Authors: Li Ma, H Birali Runesha, Daniel Dvorkin, John R Garbe and Yang Da
    Citation: BMC Bioinformatics 2008 9:315
    Content type: Software Published on:

  19. A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that ...

    Authors: Ruixiao Lu, Geun-Cheol Lee, Michael Shultz, Chris Dardick, Kihong Jung, Jirapa Phetsom, Yi Jia, Robert H Rice, Zelanna Goldberg, Patrick S Schnable, Pamela Ronald and David M Rocke
    Citation: BMC Bioinformatics 2008 9:314
    Content type: Research article Published on:

  20. Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays....

    Authors: Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland, Ari B Kahn, Hongfang Liu and John N Weinstein
    Citation: BMC Bioinformatics 2008 9:313
    Content type: Database Published on:

  21. Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is...

    Authors: Adel Golovin and Kim Henrick
    Citation: BMC Bioinformatics 2008 9:312
    Content type: Software Published on:

  22. Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies...

    Authors: Don L Armstrong, Chaim O Jacob and Raphael Zidovetzki
    Citation: BMC Bioinformatics 2008 9:311
    Content type: Software Published on:

  24. Large-scale genetic association studies can test hundreds of thousands of genetic markers for association with a trait. Since the genetic markers may be correlated, a Bonferroni correction is typically too str...

    Authors: Brian L Browning
    Citation: BMC Bioinformatics 2008 9:309
    Content type: Software Published on:

  25. Biomedical researchers often want to explore pathogenesis and pathways regulated by abnormally expressed genes, such as those identified by microarray analyses. Literature mining is an important way to assist ...

    Authors: Zhong-Xi Huang, Hui-Yong Tian, Zhen-Fu Hu, Yi-Bo Zhou, Jin Zhao and Kai-Tai Yao
    Citation: BMC Bioinformatics 2008 9:308
    Content type: Software Published on:

  26. Random forests are becoming increasingly popular in many scientific fields because they can cope with "small n large p" problems, complex interactions and even highly correlated predictor variables. Their vari...

    Authors: Carolin Strobl, Anne-Laure Boulesteix, Thomas Kneib, Thomas Augustin and Achim Zeileis
    Citation: BMC Bioinformatics 2008 9:307
    Content type: Methodology article Published on:

  27. We propose a multiple sequence alignment (MSA) algorithm and compare the alignment-quality and execution-time of the proposed algorithm with that of existing algorithms. The proposed progressive alignment algo...

    Authors: David J Russell, Hasan H Otu and Khalid Sayood
    Citation: BMC Bioinformatics 2008 9:306
    Content type: Research article Published on:

  28. Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of micro...

    Authors: Ivan Borozan, Limin Chen, Bryan Paeper, Jenny E Heathcote, Aled M Edwards, Michael Katze, Zhaolei Zhang and Ian D McGilvray
    Citation: BMC Bioinformatics 2008 9:305
    Content type: Methodology article Published on:

  29. Two problems complicate the study of selection in viral genomes: Firstly, the presence of genes in overlapping reading frames implies that selection in one reading frame can bias our estimates of neutral mutat...

    Authors: Saskia de Groot, Thomas Mailund, Gerton Lunter and Jotun Hein
    Citation: BMC Bioinformatics 2008 9:304
    Content type: Research article Published on:

  30. False discovery rate (FDR) methods play an important role in analyzing high-dimensional data. There are two types of FDR, tail area-based FDR and local FDR, as well as numerous statistical algorithms for estim...

    Authors: Korbinian Strimmer
    Citation: BMC Bioinformatics 2008 9:303
    Content type: Methodology article Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

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 

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us