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Finding and sharing GIS methods based on the questions they answer
Geographic information has become central for data scientists of many disciplines to put their analyzes into a spatio-temporal perspective. However, just as the volume and... -
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... -
Automated joining element design by predicting spot-weld locations using 3D c...
Joining element design is mainly a manual task resulting in costly and prolonged development trajectories. Current limited automation solutions support engineers, but still lead... -
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.... -
The artificial patents in the PATSTAT database: how much do they matter when ...
International audience; This paper proposes to broaden by more than 10%-compared with the current practice-the set of applications for priority patents, which is used to compute... -
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... -
A bibliometric analysis of NOAA’s Office of Ocean Exploration and Research
Bibliometric analysis techniques are increasingly being used to analyze and evaluate scientific research produced by institutions and grant funding agencies. This article uses... -
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...