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Trimmomatic: a flexible trimmer for Illumina sequence data
TLDR
Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
TLDR
RobiNA is an integrated solution that consolidates all steps of RNA-Seq-based differential gene-expression analysis in one user-friendly cross-platform application featuring a rich graphical user interface and supports quality checking, flexible filtering and statistical analysis of differential gene expression based on state of the art biostatistical methods developed in the R/Bioconductor projects.
Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses1
TLDR
New developments are presented, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize.
TLDR
These analyses illustrate how MapMan can be used to analyse and compare global transcriptional responses between phylogenetically distant species, and show that analyses at the level of functional categories are especially useful in cross-species comparisons.
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments
TLDR
PageMan is introduced, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies, enabling researchers to gain a rapid overview of the biological responses in the experiments.
Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus.
TLDR
Differentially expressed and highly P-specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition.
Sugars and Circadian Regulation Make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis[W][OA]
TLDR
It is confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm, and a set of candidate regulatory genes are identified that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle.
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.
TLDR
The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences using the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data.
Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.
TLDR
Examples from the literature, wherein co-expression has been used to corroborate and discover various aspects of plant biology are presented, and statistical issues including how normalization of gene expression data can influence co- expression results are discussed.
GMD@CSB.DB: the Golm Metabolome Database
TLDR
GD, The Golm Metabolome Database is presented, an open access metabolome database, which provides public access to custom mass spectral libraries, metabolite profiling experiments as well as additional information and tools, e.g. with regard to methods, spectral information or compounds.
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