RHadoop Project=Big Data Analytics with R and Hadoop

May 11, 2012

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By Matthew Dublin

Below is a video featuring data scientist and RHadoop project lead Antonio Piccolboni in which he introduces Hadoop and explains how to write map-reduce statements in the R language to drive the Hadoop cluster. The RHadoop project is an open-source initiative that aims to better enable researchers to extract data from Hadoop for analysis with R and to run R within the nodes of a Gadoop cluster.

While roughly two years-old, Pacific Northwest National Laboratories' Ronald Taylor has a paper that provides a thorough roundup of Hadoop use in bioinformatics.

Matthew Dublin is a senior writer at Genome Technology.

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Nicholas Tatonetti

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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.

In particular, he is developing techniques that use clinical data to develop networks that highlight interactions between different systems in the human body, such as two organs.
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High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
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The University of Würzburg's Cynthia Sharma and colleagues undertook a transcriptomics-based analysis of the gastroenteritis-causing bacterial species Campylobacter jejuni. The team used its so-called differential RNA sequencing strategy to sequence and compare the transcriptomes of four C. jejuni isolates (three from humans and one from a chicken), applying a new method to automatically annotate transcription start sites in each. "Overall," they write, "our study provides new insights into strain-specific transcriptome organization and [small RNAs], and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level."

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts
Hacquard, Kracher, et al. Proceedings of the National Academy of Sciences

The barley powdery mildew (Blumeria graminis f. sp. hordei) pathogen genome is comprised of chunks of sequence that are particularly rich or replete in polymorphisms, according to a study by researchers from the Max Planck Institute for Plant Breeding Research. The team sequenced the genomes of two Bgh isolates from Europe, comparing each to the barley powdery mildew reference genome. The newly sequenced isolates each contained distinct combinations of sequence blocks with high or low SNP concentrations — isolate-specific mosaic genomes that point to "exceptionally large standing genetic variation in the Bgh population," study authors say. Meanwhile, their transcriptome sequencing experiments offered a look at genes used by Bgh during attempted infiltration of barley or immunocompromised Arabidopsis.
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Hologic has appointed former Beckman Coulter head Scott Garrett to its board of directors, where he will serve on the corporate development committee.
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An international team has sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba. Their findings suggest that the carnivorous plant has ditched virtually all its non-coding DNA, retaining a set of sequences that's almost exclusively genic. "What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the ['junk' DNA]," said co-corresponding author Victor Albert.
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GenomeWebinar: Advances in Single-Cell Genomics: Live Cell RNA and Circulating miRNA Detection

Sponsor: EMD Millipore

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On-demand recording available here.

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