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. Research Article

    On the association analysis of CNV data: a fast and robust family-based association method

    Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won

    BMC Bioinformatics 2017 18:217

    Published on: 18 April 2017

  2. Research article

    Comparison of different cell type correction methods for genome-scale epigenetics studies

    Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang

    BMC Bioinformatics 2017 18:216

    Published on: 14 April 2017

  3. Database

    DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

    Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding ...

    Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou and Ji-Hua Wang

    BMC Bioinformatics 2017 18:206

    Published on: 5 April 2017

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:194

  10. 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

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