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Orchestrating high-throughput genomic analysis with Bioconductor

An overview of Bioconductor, an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology, which comprises 934 interoperable packages contributed by a large, diverse community of scientists.
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Contrapuntal Networks of Gene Expression during Arabidopsis Seed Filling Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.000877.

We have used cDNA microarrays to examine changes in gene expression during Arabidopsis seed development and to compare wild-type and mutant wrinkled1 (wri1) seeds that have an 80% reduction in oil.…
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The Vegetative Vacuole Proteome of Arabidopsis thaliana Reveals Predicted and Unexpected Proteinsw⃞

Evidence is presented of four tonoplast-localized soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs), representing each of the four groups of SNARE proteins necessary for membrane fusion in Arabidopsis thaliana.
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Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis

This study provides an in silico dataset for recognition of differentially expressed genes at the cell-, region-, and organ-specific levels.
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Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

An enrichment of DNA repair and chromatin modification pathways in stem cells is revealed suggesting that maintenance of genome stability and flexible chromatin may be crucial for stem cell function.
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Microarray analysis of developing Arabidopsis seeds.

The Arabidopsis arrays were also found to be useful for transcriptional profiling of mRNA isolated from developing oilseed rape (Brassica napus) seeds and expression patterns correlated well between the two species.
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ChemmineR: a compound mining framework for R

This work presents the first open-source compound mining framework for the popular statistical programming environment R, ChemmineR, which contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of classification algorithms and various utilities for managing complex compound data.
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WUSCHEL protein movement mediates stem cell homeostasis in the Arabidopsis shoot apex.

It is shown that maintenance of the WUS gradient is essential to regulate stem cell number and Migration of a stem cell-inducing transcription factor into adjacent cells to activate a negative regulator, thereby restricting its own accumulation, is a theme that is unique to plant stem cell niches.
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Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

The precise mapping of ribosome footprints on mRNAs is used to investigate translational regulation under control and sublethal hypoxia stress conditions in seedlings of Arabidopsis thaliana and illuminates prevalent and nuanced regulation of protein synthesis under optimal and energy-limiting conditions.
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Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana.

The abundance of PS mRNA may provide a more accurate estimate of gene expression than total cellular mRNA because of extensive differential translational regulation.
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