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 Summer 2016 Newsletter

BioInformatics is a Vocation,
Not a Job!

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Director's Blog Post By Subha Madhavan, PhD

  
Bioinformatics is at the heart of modern day clinical translational research. And while experts define this as an interdisciplinary field that develops and improves methods and tools for storing, retrieving, organizing, and analyzing biological (biomedical) data – it is much, much more!
 
Bioinformatics helps researchers connect the dots between disparate datasets; improve extraction of signal from noise; predict or explain outcomes; and improves acquisition and interpretation of clinical evidence. Ultimately, it allows us to tell the real data stories.
 
To effectively tell these stories, and to see this all-encompassing domain in biomedical research and its true super powers, we must pursue bioinformatics as a vocation – or a calling – and not just a job.
 
Spring’16 has been a busy season for us Bioinformaticians at the Georgetown
ICBI. I carefully curated six of our recent impact stories that you may find useful.
 
AMIA’16
The perfect triangulation between clinical practitioners, researchers and industry can be seen at AMIA annual conferences. I was honored to chair the Scientific Planning Committee for this year’s AMIA Translational Bioinformatics (TBI) Summits, featuring sessions on the NIH Precision Medicine initiative, BD2K program, and ClinGen. I sat down with GenomeWeb’s
Uduak Grace Thomas for a Q&A on this year’s Summit, which attracted over 500 informaticians. Come join us at the AMIA Joint Summits 2017 to discuss the latest developments in Bioinformatics.

Cyberattack
Response! 
We were in the middle of responding to NIH’s request for de-identified health record data for our Precision Medicine collaborative when MedStar Health, our health care partner’s computer systems, were crippled by a cyberattack virus. Thousands of patient records were inaccessible and the system reverted to paper records, seldom used in modern hospital systems. Thanks to the hard work and dedication of the IT staff, MedStar Health systems were restored within days with no evidence of any compromised data, according to the MedStar Health spokesperson. However, our research team had to act fast and improvise a way to fulfill the NIH’s data request. We ended up providing a complete synthetic linked dataset for over 200 fields. As our collaborator
Josh Denny, a leader in the NIH Precision Medicine Initiative put it – “this experience you had to go through will help us be better prepared for research access to EHRs for nationwide clinical networks”. We sure hope so!
 
Amazon Web Service (AWS) 
The AWS Public Sector
Summit was buzzing with energy from an active ecosystem of users and developers in federal agencies, small and large businesses, and nonprofit organizations—a community created over just the past few years. It was enlightening for me to participate on a panel discussing Open Data for Genomics: Accelerating Scientific Discovery in the Cloud, with NIH’s Senior Data Science Advisor, Vivien Bonazzi, FDA’s former Chief Health Informatics Officer, Taha Kass-Hout and AWS’s Scientific Computing Lead, Angel Pizarro. Three take homes from the Summit - (1) a growing need for demand-driven open data; (2) concern over the future administration’s commitment (or lack thereof) to #opendata; and (3) moving beyond data storage, and the future of on-demand analytics.  
 
Massive Open Online Course (MOOC) on Big Data 
Want to begin demystifying biomedical big data? Start with this
MOOC – to be available through Open edX late Fall. Georgetown University was recently awarded a BD2K training grant to develop an online course titled “Demystifying Biomedical Big Data: A User’s Guide”. The course aims to facilitate the understanding, analysis, and interpretation of biomedical big data for basic and clinical scientists, researchers, and librarians who have limited/no significant experience in bioinformatics. My colleagues Yuriy Gusev, Peter McGarvey and Bassem Haddad, who are leading the course, are recording interviews and lectures with experts on practical aspects of use of various genotype and phenotype datasets to help advance Precision Medicine.
 
Know Your TumorSM 
Patients with pancreatic cancer can obtain molecular tumor profiling through the
Pancreatic Cancer Action Network’s Know Your TumorSM precision medicine initiative. It is an innovative partnership with Perthera, a personalized medicine service company that facilitates the multi-omic profiling and generates reports to patients and physicians. Check out the results from over 500 KYT patients presented at AACR’16 by our multi-disciplinary team of patient coordinators, oncologists, molecular diagnostic experts and data scientists.

Moonshot
 
Latest announcement from VP Biden’s
Cancer Moonshot program unveiled a major database initiative at ASCO’16. I had the opportunity to comment in Scientific American on the billions of bits of information that such a database would capture to help drive an individual’s precise cancer treatment. Continue to watch the Moonshot program if you are involved with cancer research or care continuum.

It is personally gratifying to see Bioinformaticians, BioIT professionals, and data scientists continue to solidify their role as an integral part of advancing biomedicine. I have yet to meet a bioinformatician who thinks of her/his work as just a job. Engage your bioinformatics colleagues in your work, we will all be better for it!

              Let's continue the conversation:

      Symposium Registration 
Now Open!

ICBI's 5th Annual Biomedical Informatics Symposium will be held on Friday, October 14, 2016 at the Georgetown University Conference Center. There will be many opportunities for networking and socializing with colleagues.

Dr. Jacob Corn from University of California, Berkeley and Dr. Heidi Rehm from Harvard University Medical will deliver the keynote addresses.

            Topics covered will include:

Advances in the area of genomics

Approaches to health data analytics


Women in biomedical informatics

Click HERE for more information on the event and abstract submission.
REGISTER TODAY !


New Initiatives 


Oncore Clinical trial management system launch
We are working with clinicians, researchers and administrators at Georgetown-MedStar Health to implement the Oncore CTMS for clinical research studies

I2b2 clinical research
data warehouse

We are working with Georgetown-Howard Universities CTSA to enable access to de-identified MedStar health record datasets through i2b2 for cohort discovery and translational research

Human factors
We are collaborating with the National Center for human factors research at MedStar health to apply human factors engineering approaches to our precision medicine software development project

G-DOC
We are building tools to support exploration and analysis of cancer patient molecular diagnostic data for new hypothesis generation and decision support

New Appointments


ICBI is delighted to welcome new team members, collaborators and students

Dr. Shaojun Tang  joined ICBI as a new faculty member in January 2016. His research primarily focuses on the development of tools and methods for the analysis of cancer immunotherapy data, including breast cancer and melanoma datasets. Dr. Tang is also interested in the study of multi-'omics' data using various machine learning tools.  

Dr. Vishakha Sharma joined ICBI as a Postdoctoral Research Fellow in January 2016. She is currently working on NIH’s BD2K project to develop a data portal that will host clinical, molecular and therapeutic information extracted through a custom built natural language processing software. In addition to this she will also be responsible for building a user interface for the data portal, optimized by cognitive analysis for human-computer interaction method.

Philippa Hogstadius Counter joined ICBI in May as the Department Administrator. She holds a Masters of Public Health from Tulane University and a Bachelors Degree in Political Science from Loyola University New Orleans. She studied Government and Sociology at Umea University in Sweden, where she is also from. Philippa looks forward to working with and learning from the ICBI team.
      


Recent Publications


Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P Hoffman, Yetrib Hathout and Subha Madhavan. Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study. PLOS ONE, April 15, 2016
 
Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M Johnson, Lei Song, Adil Alaoui, Michael A Harris, Robert Clarke, Louis M Weiner, Yuriy Gusev, Subha Madhavan. G-DOC Plus - an integrative bioinformatics platform for precision medicine. BMC Bioinformatics, April 2016.

Chen, Cong, Li, Nicole, Shentu, Yue, Pang, Lei, and Robert A. Beckman. Adaptive Informational Design of Confirmatory Phase III Trials with an Uncertain Biomarker Effect to Improve the Probability of Success. Statistics in Biopharmaceutical Research, in press (2016). 

Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan and Yuriy Gusev. CINdex: Chromosome Instability Index. Bioconductor package (2016)

Midrar Al Hossiny, Linlin Luo, William R Frazier, Noriko Steiner, Yuriy Gusev, Bhaskar Kallakury, Eric Glasgow, Karen Creswell, Subha Madhavan, Rakesh Kumar and Geeta Upadhyay. Ly6E/K signaling to TGF-ß promotes breast cancer progression, immune escape and drug resistance. Cancer Research (2016)

Guy Tal, Simina M. Boca, Jay Mittenthal, Gustavo Caetano-Anollés. A dynamic model for the evolution of protein structure." Journal of Molecular Evolution, Accepted (2016)

  
 

ICBI in the Community

ICBI members participated in the following
recent conferences and events: 

 

Posters


MACE2K: Molecular and Clinical Extraction: A Natural Language Processing Tool For Personalized Medicine. S. Rao, K. Vijay-Shanker, V. Sharma, S. Boca, K. Ross, M. Harris, P. McGarvey, R. Beckman, C. Wu, S. Madhavan. Curating the Clinical Genome, Hinxton, United Kingdom 2016
Retrospective Analysis of Patient Molecular Profiles to Inform Cancer Precision Medicine. B. Conkright, S. Rao, S. Boca, R. Beckman, J. Marshall, S. Madhavan, AMIA Joint Summits 2016
Combining Protein Annotation and Genome Variation. P. McGarvey, M. Harris, S. Rao, H. Huang, S. Madhavan, C. Wu, M. Martin, A. Nightingale, A. Bateman, the UniProt Consortium. AMIA Joint Summits 2016

viGEN – A Novel Bioinformatics Pipeline for Viral RNA Detection and Quantification in Human RNAseq Data. K. Bhuvaneshwar, L. Song, Y. Gusev. AMIA Joint Summits 2016
Molecular profiling of TOPO1: A way to evaluate irinotecan treatment in colorectal cancer. JM. Cunningham, P. Prins, B. Conkright, S. Boca, S. Rao, A. Gabrielson, A. Oseran, R. Beckman, M. Al-hajeili, S.Madhavan, J. Marshall. In ASCO Annual Meeting Proceedings 2016 Feb 1 (Vol. 34, No. 4_suppl, p. 546).

Talks


Trastuzumab Treatment and Cardiotoxicity in Breast Cancer Patients, Simina Boca. AMIA Joint Summits 2016
Quantifying the Impact of Precision Medicine, Robert Beckman, Ruesch Center for the Cure of Gastrointestinal Cancers Advisory Board, March 3, 2016.
Dynamic Precision Medicine Strategies for Cancer May Improve Patient Outcomes, Robert Beckman, Molecular and Computational Biology Department, University of Southern California, Los Angeles, California, February 12, 2016.
Clinical and Statistical Considerations in Design of Basket Trials. Robert Beckman. Drug Information Association (DIA) Key Opinion Leader (KOL) Lecture Series, online lecture, February, 2016.
Biomedical Informatics Driving Clinical & Translational Team Science, Subha Madhavan, Joint Team Science Symposium, D.C, April 12, 2016.
Amazon Web Services Summit. Subha Madhavan, June 20, 2016
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                 ICBI Consultation and Support

Our data scientists would love to collaborate with you. We provide consultation and support to answer your research questions, help choose the most insightful analyses for your studies and run your data through our bioinformatics pipelines. We recently organized an effort to survey and assess GUMC’s researcher needs for next generation sequencing. This will enable us to identify the computational and technological requirements and implement them for GUMC to be at the cutting edge in sequencing and genomics data research. Read more here.

For more information on collaboration please contact us by completing the ICBI Service Request Form


 
 
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 Innovation Center for Biomedical Informatics
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Phone: 
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