Best of ICBI in 2017

By


2017 was a busy year at the Georgetown Innovation Center for Biomedical Informatics, ICBI!

Driven by our mission to apply data insights and informatics in advancing human health, our team led or contributed to numerous innovation, service and education projects. I share a few of our aha moments from 2017 here with you.

1. Innovation

Text2Action: Clinicians and patients must know the strength of scientific evidence that associates genes to drugs to advance personalized care. A pubmed search for 50 cancer genes with FDA approved on label or off label treatments and/or investigational drugs in clinical trials yielded 47,558 articles on Nov 13, 2017. This would take a trained biocurator roughly 142,674 hours or 17,834 work days or 8 years to complete. Sounds like a project ripe for automation, right? In collaboration with the Computer scientists at University of Delaware, we developed a NIST TREC Challenge award winning natural language processing method that not only automates extraction of gene-drug associations but also ranks enrolling clinical trials based on patient’s tumor gene signature.

Know Your Tumor: Pancreatic cancer will likely become the second leading cause of cancer-related death in the United States by 2020. In an effort to “democratize” access to and implementation of precision medicine in the care of pancreatic cancer patients, the Know Your Tumor (KYT) program was initiated as an academic, industry, and advocacy group collaboration with The Pancreatic Cancer Action Network (PanCAN) and Perthera, a therapeutic intelligence small business. So far, > 1000 patients’ tumor samples were molecularly profiled through KYT from >300 academic and local community practices covering 44 states. We established a virtual tumor board as a cloud-based, asynchronous, one-stop-shop for patient’s past medical history, lab tests and clinician recommended treatment plans. Look out for many more publications and talks at cancer meetings from the KYT program in 2018!

Medical Cannabis: Cannabinoids are being tested for relief in patients with Glaucoma, inflammatory disease and even cancer. Our industry partner Teewinot Life Science, global leader in cannabinoid biosynthesis can produce commercial quantities for 18 different non-psychotic cannabinoids for medical research. We partnered with Teewinot to identify novel cannabinoid biosynthetic genes with medicinal properties through genome analysis and bioinformatic approaches. Results were presented at Cann10’2-17.

2. Service

At ICBI, we imbibe Georgetown University mission “…to be responsible and active participants in civic life and to live generously in service to others”.

In 2017, we actively participated in the data science mission of many consortia including the Lombardi Comprehensive Cancer Center to advance basic, translational, clinical and population cancer research, NHGRI’s ClinGen to curate clinical genome, GHUCCTS to create a living clinical translational laboratory in the DC metro area, NCI’ ITCR program to develop open-source cancer research technologies to advance reproducibility in research, CPTAC consortium to advance our understanding of the cancer proteome and MedStar Health to implement practical precision medicine in cancer, cardiology and anesthesiology service lines.

3. Education:

MOOC: Our massive open online course on the edX platform, “Demystifying Big Data in Biomedicine” supported by the NIH BD2K program enrolled >4000 students worldwide. This course trains scientists and bench researchers on big data tools and methods, geared towards those who dread or just don’t care for the command line. More sessions of the MOOC coming up in 2018!

Big Data in Biomedicine Annual Symposium: 2017 marked the 6th Annual Big Data in Biomedicine Symposium on October 27th held at the beautiful Georgetown Conference Center facility. We hosted over 300 registrants from academia, government and industry. The breadth and depth of the challenges and opportunities in informatics were highlighted in the keynote address “Data powered health” by Patricia Flatley Brennan, RN, PhD, Director of the National Library of Medicine. Vibrant panel discussions followed on current topics including open, shareable, cancer data networks, artificial intelligence in healthcare, disease surveillance among heterogeneous populations and educating next generation of data scientists. You can find the full account of the Symposium here.

I wish you joy, peace and prosperity in the New Year.

Happy holidays.

Comments

Post a Comment

Popular posts from this blog

Not all news about COVID-19 is bad - Part 3

By
Image
Dear friends, This is part 3 in my blogpost series titled " Not all news about COVID-19 is bad"  where I attempt to capture scientifically-rigorous, evidence-based, and data-driven synthesis of promising news items and peer-reviewed articles relating to the COVID-19 global pandemic. My goal is to present topics in health care, life sciences and health IT in a simple language for anyone who may be interested. I prioritize current topics from medical/scientific literature and social media that overlap with the interests of folks in my personal and professional networks. You can read part 1 and part 2  of this series here . In this post, I review contact tracing, saliva-based rapid test for COVID , open COVID clinical trials platform and COVID-19 State-by-state testing data and plans for reopening in the US. Exhibit 1: Aarogya Setu - Indian Government's contract tracing mobile App 1. Apple and Google are partnering on contact tracing . How often do we see thes
Read more

Not all news about COVID-19 is bad - Part 2

By
Image
As a not-so-regular blogger, I was delighted to see >1000 views/reads of my post from last week -  Not all news about COVID-19 is bad: as a data scientist, here is what you can do to help . This has inspired me to write another post on reliable good news backed by data-driven science regarding  COVID-19 in a simple language that anyone interested can understand. Amidst all the dire reports that focus on worst case scenarios, people are coming together (mostly virtually or following distancing guidelines ) to do many amazing things during these strange times. The following good news caught my attention and I wish to share them here: Remdesivir is working in patients with severe COVID-19.   Remdesivir  is an anti-viral drug Exhibit 1. Clinical improvements were seen in all age groups in the study developed by Gilead Sciences that is showing benefits in patients with severe COVID-19. In a recent  study  published in the highly-reputed New England Journal of Medicine,
Read more

DS-I Africa initiative brings together researchers, entrepreneurs, innovators and educators through a global virtual forum

By
Image
" Rapid advances in data science coming from all over the globe and largely accessible to anybody with internet connection, are expected to be rather transforming and biomedical research..investing now, to develop data science expertise in Africa has the potential to pay really big dividends...We are all Africans. We know this is the cradle of humanity. This is where we all came from. Want to understand genomics, the best place to do that is in Africa " --- Keynote speech Dr. Francis Collins, Director, NIH. Aisha Walcott-Bryant, IBM Research Africa, AI Innovations to Transform Healthcare in Africa From August 10, 2020 through August 19, 2020, the US National Institutes of Health hosted an online-only virtual symposium to communicate the key priorities of the new NIH common fund initiative - Harnessing Data Science for Health Discovery and Innovation in Africa (DS-I Africa). The virtual platform hosted by Know Innovation attracted over 1000 participants globally and provided
Read more