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Short Reads: Oct 1, 2012


In papers appearing in Nature, Science, Genome Research, Genome Biology, as well as other journals, the Encyclopedia of DNA Elements project consortium describes the approaches it used to define some four million regulatory regions in the genome. The ENCODE team was able to assign biological function, loosely termed, to around 80 percent of the genome.

Ivan Trifunovich has left his position as CEO of Helicos BioSciences. He took over the top spot at Helicos in October 2010. Additionally, Noubar Afeyan and Peter Barrett resigned from Helicos' board of directors. Afeyan is a cofounder of Helicos as well as a founder and CEO of Flagship Ventures, a Helicos investor.

Francisco De La Vega is to head Real Time Genomics' commercial operations as VP of genome science. De La Vega spent 13 years at Applied Biosystems.

The New York Genome Center has appointed Dirk Evers as its senior vice president of bioinformatics and Kevin Shianna as senior vice president of sequencing operations team. Previously, Evers led Illumina's computational biology efforts in the UK, and Shianna was the director of operations for Duke University's Center for Human Genome Variation.

The US National Human Genome Research Institute has undergone a reorganization that has split its Extramural Research program into four new research divisions: genome sciences, genomic medicine, genomics and society, and extramural operations. The genome sciences division is being led by Jeffrey Schloss, while Teri Manolio is heading up genomic medicine and Bettie Graham is overseeing extramural operations. Mark Guyer has taken on the acting director role for the genomics and society division. NHGRI says the changes will enable it to better pursue its mission of advancing genomic science and medicine.

A federal court has ruled in Illumina's favor in a patent infringement lawsuit filed by Helicos BioSciences. In the decision, District Judge Sue Robinson of the US District Court for the District of Delaware granted Illumina's motion for summary judgment declaring US Patent No 7,593,109 held by Helicos invalid for "lack of written description."

PathGen Dx, a spinoff from the Genome Institute of Singapore, plans to develop a pathogen detection diagnostic kit based on the Affymetrix GeneChip. Its test, called the PathChip, is to detect the presence of more than 70,000 viral and bacterial genomes in human samples.

Sam Levy is the new chief scientific officer at Genomic Health. He replaces Joffre Baker, who resigned. Levy directed genomic sciences efforts at Scripps Translational Science Institute and Scripps Genomic Medicine.

Monsanto and Alnylam Pharmaceuticals have entered into a $29.2 million deal that gives Monsanto worldwide rights to Alnylam's RNAi technology and intellectual property for agricultural applications.

Daniel O'Day has taken over as COO of Roche Pharma. He replaces Pascal Soriot, who left the company to head up AstraZeneca. Previously, O'Day was the COO of Roche Diagnostics. Roland Diggelmann has succeeded O'Day as COO of Roche Diagnostics.

Baylor College of Medicine's Margaret Spitz has received the Association of American Cancer Institute's 2012 Distinguished Scientist Award.

The University of Florida has named Patrick Concannon to be the new director of its Genetics Institute, beginning in 2013. He will succeed Kenneth Burns, who is retiring. Concannon currently is the associate director of the Center for Public Health Genomics at the University of Virginia.

The UK government plans to establish a center focused on synthetic biology, to be called the Innovation and Knowledge Centre for Synthetic Biology, as part of an initiative to cultivate new national industries.

The US National Science Foundation has awarded $10 million to Cold Spring Harbor Laboratory and Oregon State University to develop public data resources to contain genomic information about crop plants, such as corn, rice, wheat, barley, and Arabidopsis.

Mariana Kuras is the new chief technology officer at Ariana Pharma, a provider of an association rules-based clinical data analysis technology. Prior to joining the company, Kuras worked as the director of research at Biosystems International.

The US National Aeronautics and Space Administration has granted $40 million to five new research efforts to develop biological tools and technologies to study the origin of life and evolution, including about $8 million to the University of Illinois at Urbana-Champaign to use genomic tools to understand early states of life.

Idaho Technology has changed its name to BioFire Diagnostics.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.