EMBnet.news Morphs into New Bioinformatics Journal

August 15, 2011

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EMBnet.news magazine has now expanded to become an open access, peer-reviewed journal, EMBnet.journal. The new journal will focus on routine data-analysis tasks, multi-faceted IT architectural infrastructures, and the challenges of data-driven life sciences research.

The first issue is available online now and focuses on next-generation sequencing data analysis.

Included in the maiden issue is a letter to the editor that discusses the Dicode EU project, an initiative that aims to exploit cloud computing, MapReduce, Hadoop, Mahout, and column databases to analyze and aggregate data existing in large and diverse sources.

Also included in the current issue is a paper entitled “GRID distribution supports clustering validation of large mixed microarray data sets.”

This paper describes a grid computing approach that drastically speeds up an unsupervised hierarchical clustering algorithm, called Chaotic Map Clustering, for sorting through microarray databases. Instead of taking days, this approach reduces search time to a few hours. They also offer an online service to cluster large microarray data sets via the Job Submission Tool portal.

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Careers
Who's an Author?
The Daily Scan
Moriguchi's at it Again
The Daily Scan
This Week in PNAS
The Daily Scan
Now the Fastest
The Daily Scan
Difficulties After the Freeze

GenomeWebinars

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

Sponsor: EMD Millipore

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.

On-demand recording is available here.

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

Sponsor: New England Biolabs

Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.

Available here.
Young Investigator Profile

Lei Xie

Associate Professor
City University of New York

Changing Approaches in Drug Development

After finishing his postdoc, Lei Xie started working at a pharmaceutical company where he saw firsthand the weaknesses of the one-drug-one-gene-one disease approach. Upon leaving industry, Xie returned to academia, set upon finding ways to improve the success rate of investigational treatments through so-called polypharmacology, an approach that aims to advance drugs that target disease-causing networks instead of inhibiting individual receptors.

In his research at CUNY's computational systems biology, molecular modeling, and bioinformatics lab, Xie aims to identify the targets of drugs across the whole genome and then map them into biological pathways and networks.
Blog

Moriguchi's at it Again

Hisashi Moriguchi now says he has supercooled oocytes as well as used iPS cells to treat liver cancer and heart failure, but the Nature News blog isn't so sure.

Who's an Author?

To be included on the author list, investigators should meet certain criteria.

Difficulties After the Freeze

A new survey says that UK researchers are experiencing funding and recruiting issues as the science research budget is kept flat.

Now the Fastest

The current fastest supercomputer is China's Tianhe-2, Top500 says.
Papers of Note

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us
El Baidouri, Diancourt, et al. PLOS Neglected Tropical Diseases

Through a multilocus sequence analysis of 222 African and Eurasian Leishmania isolates, French researchers identified seven genetic clusters of Leishmania in the regions tested. For the most part, those clusters corresponded to existing Leishmania classification schemes, the study authors note, though their analysis suggests genetic distinctions are somewhat hazier for three Leishmania species implicated in visceral forms of leishmaniasis. "Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles," they say, "they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago."

Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna
Nakamura, Mori, et al. Proceedings of the National Academy of Sciences

AJapanese team describes findings from a genome sequencing study focused on the Pacific bluefin tuna, Thunnus orientalis. An analysis of the genome revealed more than 26,400 predicted protein-coding genes, including genes coding for rhodopsin and opsin pigments poised to pick up blue, green, red, and UV light. Within genes coding for the color-sensing proteins, researchers found substitutions and duplications suspected of helping bluefish tuna differentiate between blue and green. If so, that could confer an evolutionary advantage in the fish's ocean environment, they say, perhaps explaining some aspects of the tuna's predatory proficiency.
People on the Move

Direct-to-consumer genetic testing firm 23andMe has appointed Andy Page as its president, a newly created post. Page, who has served as a member of 23andMe's board of directors for the past year, will report to CEO and co-founder Anne Wojcicki. He was previously president of the Gilt Groupe, an online luxury shopping website, and chief operating and financial officer at PlayPhone.

The Ludwig Institute for Cancer Research has appointed David Lane to be its new scientific director, effective June 1. He succeeds Andrew Simpson, who was scientific director for five years, from 2007 to 2012. Lane is chief scientist at Singapore's Agency for Science, Technology, and Research, and he will retain that post in addition to his new role at Ludwig.

Kevin Hrusovsky is resigning his post at PerkinElmer as senior VP and president of the Life Science and Technology division. Hrusovsky will serve as a consultant to the company for up to one year, beginning in June. He joined PerkinElmer through the company's acquisition of Caliper Life Sciences, where he was CEO and president.
Upcoming Events

Conferences, Meetings & Deadlines

International Meeting on Cell-Free DNA
June 20-21 / Copenhagen
Copenhagen University Hospital

Intelligent Systems for Molecular Biology
July 21-23 / Berlin
International Society for Computational Biology

2013 AACC Annual Meeting
July 28-August 1 / Houston
American Association for Clinical Chemistry

NGS for Drug Developers
July 31-August 2 / Boston
Wyss Institute

Cancer Cytogenomics Microarray Consortium meeting
August 5-7 / Chicago
Cancer Cytogenomics Microarray Consortium

Abstract & Registration Deadlines

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Science
An international research team has uncovered unexpected genetic diversity in the miniscule marine algae Emiliania huxleyi, a species now known to have the type of variable 'pan genome' previously described in some bacterial species. They detected an array of genes and repetitive sequences that are present in some E. huxleyi strains but not in others, varying with each strain's habitat, physical features, and metabolic capabilities, among others.
Business
The US Supreme Court unanimously ruled that human genes are not patentable, but synthetic DNA, or cDNA, is patent eligible because it does not occur naturally. Its decision had broad implications for the biotech industry and for Myriad Genetics, in particular, whose patents on the BRCA1 and BRCA2 genes were at the center of the case. The ruling runs counter to the US Patent and Trademark Office's policy of granting patents on isolated gene sequences.
Funding
The US investment in the Human Genome Project and the ensuing federal funding for genome science has reaped massive economic benefits, according to a new study from Battelle. It found that genomics-related fields from biomedicine to energy and agriculture have had a $965 billion impact on the US economy, stemming from a total of $14.5 billion in federal investments between 1988 and 2012. Genomics-related funding has yielded a $65 return on every $1 invested.
GenomeWebinars
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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EMBnet.news Morphs into New Bioinformatics Journal

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