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Studying grant decision-making: a linguistic analysis of review reports
Peer and panel review are the dominant forms of grant decision-making, despite its serious weaknesses as shown by many studies. This paper contributes to the understanding of... -
Cnidaria: fast, reference-free clustering of raw and assembled genome and tra...
Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying... -
Je, a versatile suite to handle multiplexed NGS libraries with unique molecul...
Background The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes... -
RGmatch: matching genomic regions to proximal genes in omics data integration
© The Author(s). 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License... -
DensityMap: a genome viewer for illustrating the densities of features
Background Several tools are available for visualizing genomic data. Some, such as Gbrowse and Jbrowse, are very efficient for small genomic regions, but they are not suitable... -
"A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative pro...
Background Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach... -
A multiple testing procedure for multi-dimensional pairwise comparisons with ...
Background Often researchers are interested in comparing multiple experimental groups (e.g. tumor size) with a reference group (e.g. normal tissue) on the basis of thousands of... -
Joint use of over- and under-sampling techniques and cross-validation for the...
Background Prediction models are used in clinical research to develop rules that can be used to accurately predict the outcome of the patients based on some of their... -
Bioinformatics identification of new targets for improving low temperature st...
Background Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes.... -
Exact p-values for pairwise comparison of Friedman rank sums, with applicatio...
Background The Friedman rank sum test is a widely-used nonparametric method in computational biology. In addition to examining the overall null hypothesis of no significant... -
Combining location-and-scale batch effect adjustment with data cleaning by la...
Background In the context of high-throughput molecular data analysis it is common that the observations included in a dataset form distinct groups; for example, measured at... -
TCGA2BED: Extracting, extending, integrating, and querying The Cancer Genome ...
Background Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical... -
SoftPanel: a website for grouping diseases and related disorders for generati...
Background Targeted next-generation sequencing is playing an increasingly important role in biological research and clinical diagnosis by allowing researchers to sequence high... -
EchinoDB, an application for comparative transcriptomics of deeply-sampled cl...
Background One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation... -
A fast exact sequential algorithm for the partial digest problem
Background Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the... -
A decision analysis model for KEGG pathway analysis
Background The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis... -
Drug-target interaction prediction via class imbalance-aware ensemble learning
Background Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data... -
IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRN...
Background The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S... -
PyPedia: using the wiki paradigm as crowd sourcing environment for bioinforma...
Background Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the... -
Evaluation of logistic regression models and effect of covariates for case–co...
Background Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression...
