Results and data

This section incorporates novel results, useful tools, and methods using bioinformatics in new ways, including but not limited to: biological conclusions that are only supported by bioinformatics analyses.

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  1. Software

    StrAuto: automation and parallelization of STRUCTURE analysis

    Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data...

    Vikram E. Chhatre and Kevin J. Emerson

    BMC Bioinformatics 2017 18:192

    Published on: 24 March 2017

  2. Methodology article

    MOST: most-similar ligand based approach to target prediction

    Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested t...

    Tao Huang, Hong Mi, Cheng-yuan Lin, Ling Zhao, Linda L. D. Zhong, Feng-bin Liu, Ge Zhang, Ai-ping Lu and Zhao-xiang Bian

    BMC Bioinformatics 2017 18:165

    Published on: 11 March 2017

  3. Software

    stpm: an R package for stochastic process model

    The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relate...

    Ilya Y. Zhbannikov, Konstantin Arbeev, Igor Akushevich, Eric Stallard and Anatoliy I. Yashin

    BMC Bioinformatics 2017 18:125

    Published on: 23 February 2017

  4. Methodology article

    A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies

    Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorith...

    Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng and Stephan Beck

    BMC Bioinformatics 2017 18:105

    Published on: 13 February 2017

  5. Software

    VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

    MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estim...

    Raja H. Ali, Mikael Bark, Jorge Miró, Sayyed A. Muhammad, Joel Sjöstrand, Syed M. Zubair, Raja M. Abbas and Lars Arvestad

    BMC Bioinformatics 2017 18:97

    Published on: 10 February 2017

  6. Research Article

    How can functional annotations be derived from profiles of phenotypic annotations?

    Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requ...

    Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché and Juan A. G. Ranea

    BMC Bioinformatics 2017 18:96

    Published on: 10 February 2017

  7. Methodology article

    MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes

    Tracing stable isotopes, such as 13C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information re...

    Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W. N. Lee, Silvia Marin and Marta Cascante

    BMC Bioinformatics 2017 18:88

    Published on: 3 February 2017

  8. Methodology article

    Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp

    ERp is a variable selection and classification method for metabolomics data. ERp uses minimized classification error rates, based on data from a control and experimental group, to test the null hypothesis of n...

    Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke and J Hendrik Venter

    BMC Bioinformatics 2017 18:83

    Published on: 2 February 2017

  9. Research Article

    A systematic comparative evaluation of biclustering techniques

    Biclustering techniques are capable of simultaneously clustering rows and columns of a data matrix. These techniques became very popular for the analysis of gene expression data, since a gene can take part of ...

    Victor A. Padilha and Ricardo J. G. B. Campello

    BMC Bioinformatics 2017 18:55

    Published on: 23 January 2017

  10. Database

    ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana

    Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides wit...

    Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue and Vera van Noort

    BMC Bioinformatics 2017 18:37

    Published on: 17 January 2017

  11. Research Article

    Predicting probable Alzheimer’s disease using linguistic deficits and biomarkers

    The manual diagnosis of neurodegenerative disorders such as Alzheimer’s disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic crit...

    Sylvester O. Orimaye, Jojo S-M. Wong, Karen J. Golden, Chee P. Wong and Ireneous N. Soyiri

    BMC Bioinformatics 2017 18:34

    Published on: 14 January 2017

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