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Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Structure and function of the global ocean microbiome
This work identifies ocean microbial core functionality and reveals that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
The EMBL Nucleotide Sequence Database
Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data.
Eukaryotic plankton diversity in the sunlit ocean
Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.
Patterns and ecological drivers of ocean viral communities
These investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.
QDD version 3.1: a user‐friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate
The QDD pipeline has been modified to include these most pertinent factors in the output to help the selection of markers, and QDD3 is now also available imbedded into a virtual machine making installation easier and operating system independent.
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus.
This RNA-seq study confirmed the AAAATTGA sequence as an early promoter element, as well as the presence of palindromes at most of the polyadenylation sites, and revealed a new promoter element correlating with late gene expression, which is also prominent in Sputnik, the recently described Mimivirus "virophage".
A Holistic Approach to Marine Eco-Systems Biology
The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes
Open science resources for the discovery and analysis of Tara Oceans data
An overview of Tara Oceans Data is presented, and detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events are provided.