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NetAffx: Affymetrix probesets and annotations
NetAffx details and annotates probesets on Affymetrix GeneChip microarrays, and lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context.
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
The Integrated Genome Browser is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers or local files; and dynamic manipulation of quantitative data via genome graphs.
Integrated genome browser: visual analytics platform for genomics
To support future visualization needs as new genome-scale assays enter wide use, the IGB codebase was transformed into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.
RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing1[C][W][OA]
- A. Loraine, S. McCormick, A. Estrada, Ketan Patel, P. Qin
- Biology, Environmental SciencePlant Physiology
- 16 April 2013
The robustness of splicing patterns in plants is highlighted and the importance of ongoing annotation and visualization of RNA-Seq data using interactive tools such as Integrated Genome Browser is highlighted.
Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm1[W]
- M. Mutwil, B. Usadel, M. Schütte, A. Loraine, O. Ebenhöh, S. Persson
- Computer SciencePlant Physiology
- 4 November 2009
This work constructed an interactive coexpression network for the Arabidopsis genome using a novel Heuristic Cluster Chiseling Algorithm (HCCA) that supports weighted edges and that may control average cluster sizes and shows that the HCCA-partitioned network constitutes an ideal "cartographic” platform for visualization of correlation networks.
CressExpress: A Tool For Large-Scale Mining of Expression Data from Arabidopsis1[W][OA]
- V. Srinivasasainagendra, G. Page, Tapan Mehta, I. Coulibaly, A. Loraine
- Computer SciencePlant Physiology
- 8 May 2008
It is shown that subselecting sample types produces a richer network for genes involved in flowering in Arabidopsis, and CressExpress provides direct access to expression values via an easy-to-use URL-based Web service, allowing users to determine quickly if their query genes are coexpressed with each other and likely to yield informative pathway-level coexpression results.
Identification of Cytokinin-Responsive Genes Using Microarray Meta-Analysis and RNA-Seq in Arabidopsis1[C][W][OA]
A meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokin in-regulated gene expression in Arabidopsis identified a set of 226 genes differentially regulated by cytokinIn, a subset of which has previously been validated by other methods.
Transcriptional Coordination of the Metabolic Network in Arabidopsis1[W][OA]
Using a network-analysis algorithm based on coexpression with multiple pathway members (pathway-level coexpression), novel candidate pathway members, regulators, and cross pathway transcriptional control points for over 140 metabolic pathways are identified and prioritized.
Large‐scale transposon mutagenesis of Mycoplasma pulmonis
- C. T. French, P. Lao, A. Loraine, B. Matthews, Huilan Yu, K. Dybvig
- Biology, MedicineMolecular microbiology
- 1 July 2008
To obtain mutants for the study of the basic biology and pathogenic mechanisms of mycoplasmas, the insertion site of transposon Tn4001T was determined for 1700 members of a library of Mycoplasma pulmonis mutants and 321 of the 782 protein coding regions were inactivated.
Efficient quantification of the health-relevant anthocyanin and phenolic acid profiles in commercial cultivars and breeding selections of blueberries ( Vaccinium spp.).
- G. Yousef, Allan F. Brown, M. Lila
- Chemistry, MedicineJournal of agricultural and food chemistry
- 13 May 2013
An improved protocol was developed for the accurate, efficient, and rapid comparative screening for large blueberry sample sets and different genotypes frequently had comparable overall levels of total anthocyanins and phenolic acids, but differed dramatically in individual profiles of compounds.