Polina Pine

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There is a critical need for standard approaches to assess, report and compare the technical performance of genome-scale differential gene expression experiments. Here we assess technical performance with a proposed standard 'dashboard' of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with(More)
BACKGROUND Highly multiplexed assays for quantitation of RNA transcripts are being used in many areas of biology and medicine. Using data generated by these transcriptomic assays requires measurement assurance with appropriate controls. Methods to prototype and evaluate multiple RNA controls were developed as part of the External RNA Controls Consortium(More)
Spike-in RNAs are valuable controls for a variety of gene expression measurements. The External RNA Controls Consortium developed test sets that were used in a number of published reports. Here we provide an authoritative table that summarizes, updates, and corrects errors in the test version that ultimately resulted in the certified Standard Reference(More)
Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM)-P103.1) was performed in order to(More)
The spatial volume occupied by an atom depends on its electronic density. Although this density can only be evaluated exactly for hydrogen-like atoms, there are many excellent algorithms and packages to calculate it numerically for other materials. Three-dimensional vi-sualization of charge density is challenging, especially when several molecular/atomic(More)
Genome-scale “-omics” measurements are challenging to benchmark due to the enormous variety of unique biological molecules involved. Mixtures of previously-characterized samples can be used to benchmark repeatability and reproducibility using component proportions as truth for the measurement. We describe and evaluate experiments characterizing the(More)
Carbon takes many different forms, each with its own electronic structure and has a fantastic range of properties. As well as graphite/diamond, a hexagonal diamond called londsdaleite, and amorphous carbons of sp2, sp3 and mixed natures there are all the fullerenes, graphene, nanotubes etc. Fortunately, their different electronic structures take distinct(More)
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