Archive for October, 2013


Oct 24 2013

Poster Winners!

by at 4:46 pm


First place

Dr. Robert Clarke, Dean of Research at the Lombardi Cancer Center presented the best poster awards during the reception for the 2nd annual biomedical informatics symposium held October 11, 2013.

The first place prize went to ICBI’s own Difei Wang (see below). The top poster winners were chosen through crowdsourcing by conference attendees, with first place receiving an iPAD mini. Dr. Wang, who was quite grateful to be selected, was also very surprised and humbly said to a small group of us, “I didn’t even vote for myself!”

Second place was a tie between two groups: one group at George Washington University on data mining of gene expression and microarray data, and the other group from Georgetown University Medical Center on the impact of pager delays on trauma teams (see below).  The third place winner went to ICBI’s Michael Harris and team on pharmacogenomics.

First Place:  SNP2Structure: A public database for mapping and modeling nsSNPs on human protein structuresSecond place- a
Difei Wang, Kevin Rosso, Shruti Rao, Lei Song, Varun Singh, Shailendra Singh, Michael Harris and Subha Madhavan Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington DC

Second Place (tie): Biologically Inspired Data Mining Framework for Detecting Outliers in Gene Expression Microarray Data
Abdelghani Bellaachia and Anasse Bari Department of Computer Science, School of Engineering and Applied Science,The George Washington University

Second Place (tie):The impact of pager notification delays on trauma team dynamics Second place b
Kayvon I. Izadpanah, MS1,2; Imran T. Siddiqui, MS1,2; Sarah H. Parker, PhD2; 1Georgetown University School of Medicine, Washington, DC; 2National Center for Human Factors in Healthcare, Washington DC

Third Place: Pharmacogenomics to clinical care 
Michael Harris, Krithika Bhuvaneshwar, Varun Singh, Subha Madhavan Innovation Center for Biomedical Informatics, Georgetown University Medical Center (award accepted by Krithika) 3rd place

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Oct 24 2013

Keynote Talks at ICBI symposium: Stephen Friend and Eric Hoffman

by at 4:40 pm

Big Data in Precision Medicine was the focus of the 2nd Annual Biomedical Informatics Symposium at Georgetown, which drew nearly 250 people to hear about topics from direct-to-consumer (DTC) testing to mining data from Twitter.

The morning plenary on Genomics and Translational Medicine was kicked off by Stephen Friend, MD, PhD, President, Co-founder, and Director of Sage Bionetworks who discussed the “discontinuity between the state of our institutions and the state of our technology.”   This disconnect stems from the way results are presented in the literature and compared with one another in different scenarios, and sometimes interpreted into the clinic. “We are going to get different answers at the DNA, RNA, and functional levels,” said Friend, and different groups working on the same data can get different answers because science “context dependent” – dependent on the samples, technologies, and statistical parameters.  Our minds are wired for a “2D narrative” but the fact is we are all just “alchemists.”

Friend is a champion of open data sharing and turning the current system on its head.  We need “millions of eyes looking at biomedical data…not just one group, it’s immoral to do so,” Friend said.  We need to get rid of the paradigm, “I can’t tell you because I haven’t published yet.”   He said that GitHub has over 4M people sharing code with version tracking, and in fact hiring managers for software engineering jobs are more likely to look for a potential candidate’s work on GitHub than to considering credentials on a CV.

Sage created Synapse, a collaborative and open platform for data sharing, which he hopes could be the GitHub for biomedical scientists.   He would like to see large communities of scientists worldwide working together on a particular problem and sharing data in real time. As an example of this sort of effort, check out the Sage Crowdsourcing genetic prediction of clinical utility in the Rheumatoid Arthritis Responder Challenge.  His excitement for this future model for large scale collaboration was palpable in his closing remarks—a prediction for a future Nobel prize for “theoretical medicine.”

The afternoon plenary on Big Data in Biomedicine was led by a keynote talk from Eric Hoffman, PhD, Director of the Research Center for Genetic Medicine at Children’s National Medical Center who discussed “data integration in systems biology”  -which is a topic very close to the heart of ICBI.  He presented a new tool, miRNAVis, to integrate and visualize microRNA and mRNA expression data, which he referred to as “vertical” data integration or the integration of heterogeneous data types.  This tool will soon be released for public use.

Hoffman is considered one of the top world experts in muscular dystrophy research, having cloned the dystrophin gene in Louis Kunkel’s lab in 1987.  He has made an enormous contribution to research in this field along with dedicating countless hours to volunteering with children affected by the horrible disease.  He discussed a very exciting project in his lab on a promising new drug – VBP15, which has anti-inflammatory properties, and shows strong inhibition of NF-κB, and repair of skeletal muscle.  Most importantly, VBP15 does not have the side effects of glucocorticoids, which are currently the standard treatment for Duchenne muscular dystrophy. Hoffman said this new drug may potentially be effective against other chronic inflammatory diseases.  Let’s hope this drug will make it into clinical trial testing very soon!

More information about the keynote and other talks can be found on ICBI’s Twitter feed and at #GUinformatics, which provided snapshots of the day.

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