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  1. Methodology article

    Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies

    High throughput metabolomics makes it possible to measure the relative abundances of numerous metabolites in biological samples, which is useful to many areas of biomedical research. However, missing values (M...

    Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar and Guy N. Brock

    BMC Bioinformatics 2017 18:114

    Published on: 20 February 2017

  2. Software

    Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

    Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate ort...

    Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof and Oliver Niehuis

    BMC Bioinformatics 2017 18:111

    Published on: 16 February 2017

  3. Software

    MARV: a tool for genome-wide multi-phenotype analysis of rare variants

    Genome-wide association studies have enabled identification of thousands of loci for hundreds of traits. Yet, for most human traits a substantial part of the estimated heritability is unexplained. This and rec...

    Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris and Inga Prokopenko

    BMC Bioinformatics 2017 18:110

    Published on: 16 February 2017

  4. Software

    VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology

    With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides ...

    Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan and Amjad Ali

    BMC Bioinformatics 2017 18:106

    Published on: 13 February 2017

  5. 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

  6. Software

    TipMT: Identification of PCR-based taxon-specific markers

    Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attr...

    Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes and Daniella C. Bartholomeu

    BMC Bioinformatics 2017 18:104

    Published on: 11 February 2017

  7. Research article

    The Drosophila Gene Expression Tool (DGET) for expression analyses

    Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help ...

    Yanhui Hu, Aram Comjean, Norbert Perrimon and Stephanie E. Mohr

    BMC Bioinformatics 2017 18:98

    Published on: 10 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. Methodology Article

    Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO

    Conventional differential gene expression analysis by methods such as student’s t-test, SAM, and Empirical Bayes often searches for statistically significant genes without considering the interactions among them....

    Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li and Habtom W. Ressom

    BMC Bioinformatics 2017 18:99

    Published on: 10 February 2017

  10. 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

  11. Methodology Article

    An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data

    The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer...

    W. Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A. Shelbourne and Marina Vannucci

    BMC Bioinformatics 2017 18:94

    Published on: 8 February 2017

  12. Software

    PyHLA: tests for the association between HLA alleles and diseases

    Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughp...

    Yanhui Fan and You-Qiang Song

    BMC Bioinformatics 2017 18:90

    Published on: 6 February 2017

  13. Methodology article

    Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis

    Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression measurements. Although Negative Binomial (NB) r...

    Seung Hoan Choi, Adam T. Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis and Anita L. DeStefano

    BMC Bioinformatics 2017 18:91

    Published on: 6 February 2017

  14. 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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