API for Statistical Phylogenetics with HPC

January 25, 2012

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Researchers at the University of Maryland have developed BEAGLE, an application programming interface and specialized library for high-performance statistical phylogenetic inference that allows existing software packages to make more effective use of available computer hardware including GPUs, CPUs with Streaming SIMD Extensions, and multi-core CPUs via OpenMP.

The team profiled their research in Systematic Biology and write that "a specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future."

BEAGLE is compatible with Mac, Windows, and Linux operating systems. It is freely available for download here.

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Data presented in this webinar illustrates the value of live cell analysis at the single-cell level to identify differences in expression levels across populations of cells. The cells remain intact for downstream analysis. Our experts also discuss the use of SmartFlare RNA detection probes for the direct quantification of circulating miRNAs with rapid processing of blood plasma/serum, which is done without the use of enzymes. Using circulating miRNAs with established roles in cancer and quality control, we can accurately detect these miRNAs in plasma using a microplate fluorometer within an hour after plasma preparation.

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Optimization of NGS Library Preparation: Low Inputs and Fast, Streamlined Workflows

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Available here.
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Nicholas Tatonetti

Assistant Professor
Columbia University

New Computational Tools to Study Drug Effects

Studying for a dual degree in mathematics and molecular biology, Nick Tatonetti became interested in using computational models to study biology and make sense of its massive datasets. As a bioinformatics PhD student at Stanford, he developed new statistical models and computational approaches for analyzing drug effects and drug-drug interactions.

At Columbia, Tatonetti is now focusing on molecular mechanisms of drugs. "We can actually think of each time a patient is being given a drug as an experiment," he says. "When the drug goes into the human system, it interacts molecularly, and then phenotypes come out of this system," which can be connected to molecular mechanisms in new ways.

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GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

GenomeWeb and EMD Millipore invite you to view an archived webinar discussing new approaches to detect RNA at the single-cell level as well as new probes for the direct quantification of circulating miRNAs. In this free online seminar, recorded April 25, 2013, our expert panel shares protocols for improved RNA and miRNA detection.

On-demand recording available here.

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