September 2011

With a new academic year comes the return of the IGSP's usual menu of weekly seminars in Genomic and Personalized Medicine, Genome Biology, Computational Biology & Bioinformatics, Systems Biology and more. In addition to the long-standing Genome Academy, the IGSP Education Office also plans to hold a session this fall for those interested in exploring health careers and another on "thinking about grad school." Check back on genome.duke.edu for details and the latest updates.

We're also fortunate to have a number of special events and seminars to look foward to this fall. The Center for Systems Biology will hold its 6th Annual Duke Systems Biology Symposium on campus on Thursday, September 29th. Attendance is free and open to all. The focus of this year's symposium is "International Perspectives on Systems Biology." Registration is open now.

Shubha Chandrasekharan will give a special seminar on property rights, commercialization models and their impact on access to genetic and genomic diagnostics on Thursday, September 22nd at 9 am in CIEMAS 2240.

The Thursday, October 13th Genomic and Personalized Medicine Forum will feature Sir Richard J. Roberts, 1993 winner of The Nobel Prize in Physiology or Medicine (along with Phillip A. Sharp) for the discovery of split genes. He will give a talk in Schiciano Auditorium called "Why I Love Bacteria!" Details are available online.

There will be a special visit by Sir John Sulston and Bob Waterston, whom the IGSP will honor as distinguished lecturers on Monday, November 14th. This will be a major event, so mark your calendars and keep an eye out for details.

Also note that the Monday, October 10th Basic Science Day 2011, organized by the School of Medicine with support from the Chancellor's Science Advisory Council, will feature the IGSP's Beth Sullivan and Uwe Ohler. See full details of the schedule here.

Last but certainly not least, we extend a hearty welcome to Raluca Gordan, Tim Reddy and Barbara Engelhardt, the three successful recruits from last spring's computational biology search. All three will be based in the CIEMAS building. Look for a cover story on computational biology in the September/October issue of GenomeLIFE - coming soon.

'Stealth Transmitters' of the Flu Activate Different Genes
Study shows the difference in gene activity between people who become ill with the flu and those who contract the virus but show no symptoms, Fox News reports. The work was also featured by MSNBC and others. Read the original report in PLoS Genetics.

Genomics Research Effort Aims to Enlist Military, Obtain $20M
The Business Journal reports that a partnership between Cone Health, UNC-Greensboro's Center of Biotechnology, Genomics and Health Research and the IGSP is seeking up to $20 million in federal defense funding to roll out a tool that uses genetic information to detect diseases.

Don't Throw It Out: 'Junk DNA' Essential In Evolution
Greg Wray told NPR's Joe Palca that protein-coding genes are "only half the picture." Among the human genome's approximately 20,000 genes are as many as 1 million regulatory elements.

Genetic Differences Distinguish Stomach Cancers, Treatment Response
A team led by Patrick Tan in Singapore found that stomach cancer is actually two distinct diseases that respond differently to chemotherapy. Read the original report in Gastroenterology.

U.S. Appeals Court Backs Gene Patents in Myriad Case
After a long-awaited ruling in the Myriad case in which a U.S. appeals court decided that genes can be patented, Bob Cook-Deegan told Science Insider that he "wouldn't be surprised if both sides appealed to the Supreme Court." Cook-Deegan also appeared in coverage on the case by GenomeWeb and others. More about his take on the case here.

Interaction of FKBP5 Gene Variants and Adverse Life Events in Predicting Depression Onset: Results From a 10-Year Prospective Community Study
In The American Journal of Psychiatry, Avshalom Caspi and Terrie Moffitt are coauthors on a study connecting variation in the main receptor of the stress hormone system, adverse life events, and the onset of depression.

Repeated Phenotypic Changes Highlight Molecular Targets of Convergent Evolution
In Genome Biology, Tom Mitchell-Olds and colleague say that an example of repeated evolution in rice and Brassica illustrates how selection might preferentially target certain genes and mutations.

Glutamine Synthetase Is a Genetic Determinant of Cell Type-Specific Glutamine Independence in Breast Epithelia
In PLoS Genetics, Hsiu-Ni Kung, Jeffrey Marks and Ashley Chi report the discovery of a systematic variation in glutamine dependence among breast tumor subtypes associated with mammary differentiation.

PARalyzer: Definition of RNA Binding Sites from PAR-CLIP Short-Read Sequence Data
In Genome Biology, Uwe Ohler, Jack Keene and David Corcoran present an approach, centered on the novel PARalyzer tool, for mapping high-confidence sites from PAR-CLIP deep-sequencing data. The software is available for download.

Peripheral Blood Signatures of Lead Exposure
In PLoS One, Heather Labreche, Joe Nevins and John Chute report evidence that lead exposure alters gene expression patterns in peripheral blood cells and that those changes reflect dose-specific alterations in the activity of particular pathways.

Effects of Inversions on Within- and Between-Species Recombination and Divergence
In Genome Biology and Evolution, Mohamed Noor and colleagues present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence.

Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models
In PLoS Computational Biology, Iulian Pruteanu-Malinici and Uwe Ohler outline a computational method for comparing, annotating, and modeling gene expression based on images.

Living With Sickle Cell Disease: Traversing 'Race' and Identity
In Ethnicity & Health, a study by Charmaine Royal and Laura De Castro illustrates the complex interplay between 'racial' identity beliefs and patients' experiences with sickle cell disease.

The National Institutes of Health is calling for applications from institutions and organizations that propose to develop basic and applied projects utilizing systems science methodologies relevant to human behavioral and social sciences and health.

The National Heart, Lung, and Blood Institute will fund exome sequencing projects aimed at discovering the genetic basis of Mendelian or single gene disorders.

The National Institutes of Health will fund efforts to build a genetic and genomic knowledge base in dental, oral and craniofacial diseases and disorders with the ultimate goal of driving the development of diagnostic, therapeutic, and preventive approaches.

The National Institutes of Health will fund pilot studies aimed to explore the biology, etiology, detection, prevention, and treatment of pancreatic cancer.

For details and updates on IGSP seminars and events, see the Events Calendar.

A selection of upcoming events:

Tuesday, September 6th
Tuesday Seminar Series
Matthew Hahn of Indiana University speaks on "Gene Gain, Gene Loss and Gene Movement in Evolution"

Wednesday, September 7th
Systems Biology Seminar
Jaimie Van Norman from Philip Benfey's lab speaks on "Exploring the Root Clock as a Molecular Mechanism for Periodic Branching in Arabidopsis Roots"

Thursday, September 8th
Genomic and Personalized Medicine Forum
Geoff Ginsburg kicks off the weekly series.

Friday, September 9th
Science & Society Journal Club
Bob Cook-Deegan will lead the discussion. Stay tuned for details.

Monday, September 12th
Computational Biology Seminar
Andreas Pfenning on "Convergent Transcriptional Specializations in the Brains of Humans and Song Learning Birds"

Thursday, September 22nd
Special Seminar
Shubha Chandrasekharan speaks on property rights, commercialization models and their impact on access to genetic and genomic diagnostics at 9 am in CIEMAS 2240.

Thursday, September 29th
6th Annual Duke Systems Biology Symposium
An all-day event on "International Perspectives on Systems Biology." Register by Sept. 18th.

The IGSP, OIT, the School of Medicine, Department of Biology, Duke Human Vaccine Institute, Department of Biomedical Engineering, and Mohamed Noor have combined resources to bring DNASTAR's Lasergene Core Suite to the Duke teaching and research community at no cost to individual labs, faculty, staff, or students. Download the software here.

Bob Cook-Deegan and Arti Rai will participate in a Congressional Briefing about the Myriad/BRCA case and issues related to gene patents more broadly on Thursday, September 15th.

Steve Haase has taken over as the new Director of Graduate Studies for the Computational Biology & Bioinformatics Program. The program's NIH-supported T32 training grant has also been renewed for another term.

The IGSP has formed a relationship with the new Center for Microbial Genomics & Microbiomics, to be headed up by Raphael Valdivia. The new center is based in the MGM Department, but will maintain a close relationship to IGSP programs, including the Genome Sequencing & Analysis Core Resource.