Large collection of brain cancer data now easily, freely accessible to global researchers
Large collection of brain cancer data now easily, freely accessible to global researchers. A valuable cache of #BrainCancer biomedical data has been made freely available to researchers worldwide. Read more here and here.
A full collection of articles about this dataset can be obtained here:
Our work in Natural Language Processing and Text Mining Tools
Our work in Natural Language Processing and Text Mining Tools was profiled in February on Health Data Management.com, you can read more here .
On Friday, October 27th, 2017 our 6th Annual Biomedical Informatics Symposium will take place at the GeorgetownUniversity Conference Center and Hotel. This one-day event will include talks by academic, industry, and government leaders in clinical and translational sciences who will highlight technologies, applications of informatics science and tools to advance precision medicine. This symposium will bring together a dynamic community of innovators, research scientists, clinicians, program managers, educators, and students to exchange ideas and learn new methodologies. The symposium also offers an opportunity to network and socialize with colleagues during the evening reception and poster session. This year's symposium will include sessions on cancer networks, machine learning. Artificial intelligence and other emerging technologies in healthcare and precision medicine as well as a panel discussion on current and future needs for education programs in biomedical informatics and data science. We are delighted to have Dr. Patricia Brennan, NLM Director as the keynote speaker. You can read more about it here
A free new massive open online course (MOOC)
"Demystifying Biomedical Big Data: A User's Guide," a free new massive open online course (MOOC) directed by Georgetown faculty Drs. Bassem Haddad, Yuriy Gusev and Peter McGarvey, will launch on online educational platform edX on February 14, 2017. Watch the trailer for this course here. To register, please visit: http://bit.ly/biomedicalbigdata.
Mark your Calendar: ICBI's 5th Annual Biomedical Informatics Symposium - 10/14/2016
ICBI's 5th Annual Biomedical Informatics Symposium will be held on Friday, October 14, 2016 at the Georgetown University Conference Center. Dr. Jacob Corn from University of California, Berkeley will deliver the keynote address. Click here to register and to see more information about abstract submission for this year’s event.
Biomedical Data Science MeetUp - 5/5/2016
ICBI is hosting its next Biomedical Data Science MeetUp on May 5, 2016 at Georgetown University's campus Epicurean and Company from 6:15pm - 8:00pm. Our invited speakers Kris Schulz From Duke Medical and Alex Ulvila from SynGlyphX will talk about ‘Covering Insight in Complex Medical Data Using Interactive Data Visualization’, followed by a networking session with food and drinks. For further details and registration, please visit Biomedical Data Science Meetup and join us!
NCI Data catalog - 3/2016
Our G-DOC Plus portal is listed among many other R & D resources at the NCI Data catalog site.
Cancer ‘Moonshot’ needs Informatics - 1/2016
In-class Immersion of 'Big Data' Technologies to Improve Students' Understanding of Genomic Instability and Systems Biology - 1/2016
The Initiative on Technology-Enhanced Learning (ITEL) Center at Georgetown University highlights one of their ‘Big Data’ education projects involving Dr. Yuriy Gusev from ICBI in their 2015 ITEL reports. More details about this ITEL project here.
GUMC News: Triple Negative Breast Cancer in African-American Women has Distinct Difference - 4/22/2015
AMIA E-News: 2016, Symposium, Joint Summits and iHealth Chairs Selected - 2/5/2015
2014 Biomedical Informatics Symposium at Georgetown University - 10/3/2014
The 3rd annual Biomedical Informatics symposium at Georgetown was a huge success with over 300 participants and a poster session that included over 40 selected scientific projects from Georgetown, affiliated local universities, industry sponsors, and international collaborators. Keynote speaker, Dr. Atul Butte, MD PhD from Stanford University, inspired the crowd with ideas for transforming big data into clinical applications, much of which is happening now in transition to a more patient-controlled healthcare system. "Big data in biomedicine is the most promising platform for entrepreneurship,” he stated. Ruesch Center director, Dr. John Marshall, MD, presented a special session on "Finding Value in Cancer Care" where he illustrated the different stakeholder interests that can be a barrier in applying the best and most cost efficient care.
Georgetown University Medical Center (GUMC) executive leadership provided introductory remarks and chaired the sessions, including GUMC Dean of Research, Dr. Bob Clarke, PhD; Georgetown CTSA director, Dr. Joseph Verbalis, MD; Director of the Lombardi Comprehensive Cancer Center (LCCC), Dr. Lou Weiner, MD; and LCCC deputy director, Dr. Michael Atkins, MD. The plenary session, "Science on the Cloud" was chaired by Dr. Ian Foster, director of the Computation Institute, University of Chicago and Argonne National Laboratory.
The program included talks from world-renowned speakers discussing immunotherapies, big data applications in healthcare, cloud computing, a new paradigm for cancer research and care, and many other related topics. Networking as always was one of the most important outcomes of the symposium with numerous opportunities for interaction with colleagues in academia and industry.
The symposium program committee included Subha Madhavan (Symposium Chair), Yuriy Gusev (Poster Session), Adil Alaoui (Sponsorships), Laura Sheahan (Communications), Alfreda Walker (Event Planning), Ming Tan and Ophir Frieder (Planning Committee). We are very grateful for the support from numerous sponsors and colleagues, who have enabled us to keep this event free for all registrants. See more highlights and pictures from the day here.
Featured in Frontiers' Top 10 2013 Most Viewed Genetic Research Articles - 5/2/2014
We are honored to be #2 on this list! The article is open access so enjoy reading.
AAAS Big Data Blog - 3/12/2014
American Association for the Advancement of Science (AAAS.org) - Subha Madhavan, Director of the Innovation Center for Biomedical Informatics at the Georgetown University Medical Center, discusses current and future applications of Big Data within the biomedical field, and the potential challenges Big Data might confer to biomedical research and patient care.
The term “Big Data” is a hot phrase in a variety of sectors, from the biomedical and environmental sciences to team sports. But what is “Big Data” and how is it different from other kinds of data? How is Big Data being used, and what challenges does it bring? To answer these questions, we have spoken to scientists, scholars and big data gurus. We will share their responses to these questions through a series of blog posts leading up to the AAAS Center for Science, Technology, and Security Policy (CSTSP) and Federal Bureau of Investigation’s public event on April 1, “Big Data, Life Sciences, and National Security.”
Today’s expert, Subha Madhavan, Director of the Innovation Center for Biomedical Informatics at the Georgetown University Medical Center, discusses current and future applications of Big Data within the biomedical field, and the potential challenges Big Data might confer to biomedical research and patient care.
Washington Post: Infusing Data into Cancer Therapy - 3/7/2014
Subha Madhavan has worked 60-hour weeks regularly for the past 10 years, and she doesn’t show any sign of slowing down. Madhavan splits her time between two main jobs — one as director of the Innovation Center for Biomedical Informatics at the Georgetown University Medical Center, and the other, more recently, as the chief data officer at Perthera, a McLean-based cancer therapy advisory service. She is also an associate professor of oncology at Georgetown, and leads a Georgetown-Howard University joint clinical research program for students.
How does she have time for it all? The Potomac resident said she gets in a couple of hours of work before her husband and 10-year-old son wake up in the morning, and another few after they go to sleep. She spends a few days a week at Georgetown and the remainder at Perthera. But when she’s on the move, she’s accessing medical databases on her iPhone, videoconferencing or advising her team over the phone. Throughout her busy career, Madhavan has had one goal: to bring computer science into medical treatment.
Madhavan is a proponent of “precision therapy” — a medical approach that assumes patients are unique, and some are more likely to respond to treatment than others because of genetic or environmental factors. After analyzing large volumes of data about past patients, doctors can better advise current patients about which treatments are likely to work, she thinks. At Perthera — a mashup of “personal” and “therapy” — Madhavan oversees the software-based processing of tissue samples. Click on the link above to read the full article.
NCI Cracks Open Cancer Research by Moving it to the Cloud - 1/6/2014
Dr. Subha Madhavan was quoted in Government Computing News. To read the full article, click here.
ICBI Publishes in Frontiers on Genetics - 12/12/2013
Multi-omics analysis of early stage colorectal cancer
The use and benefit of adjuvant chemotherapy to treat stage II colorectal cancer (CRC) patients is not well understood since the majority of these patients are cured by surgery alone. Identification of biological markers of relapse is a critical challenge to effectively target treatments to the ~20% of patients destined to relapse. We have integrated molecular profiling results of several “omics” data types to determine the most reliable prognostic biomarkers for relapse in CRC using data from 40 stage I and II CRC patients. We identified 31 multi-omics features that highly correlate with relapse. The data types were integrated using multi-step analytical approach with consecutive elimination of redundant molecular features. For each data type a systems biology analysis was performed to identify pathways biological processes and disease categories most affected in relapse. The biomarkers detected in tumors urine and blood of patients indicated a strong association with immune processes including aberrant regulation of T-cell and B-cell activation that could lead to overall differences in lymphocyte recruitment for tumor infiltration and markers indicating likelihood of future relapse. The immune response was the biologically most coherent signature that emerged from our analyses among several other biological processes and corroborates other studies showing a strong immune response in patients less likely to relapse.
GUMC Feature: Symposium Drives Connections Between Big Data and Precision Medicine - 10/17/2013
The Georgetown University Medical Center (GUMC) Newsletter featured the 2nd Annual Georgetown Biomedical Informatics symposium hosted by ICBI. Click here to read the article on GUMC's website.
SYMPOSIUM DRIVES CONNECTIONS BETWEEN BIG DATA AND PRECISION MEDICINE
Sister Grace Miriam Usala (M’16) sits squarely at the intersection of two related –- but still somewhat disconnected –- fields.
A medical student at Georgetown University School of Medicine, Usala is also simultaneously pursuing her master’s degree in systems medicine through a unique joint MD/MS program offered at Georgetown.
Through this two-year-old program, Usala is immersing herself for an entire academic year in the informatics-driven and computational side of medicine – in other words, in learning how to make sense of massive quantities of patient data in a way that will actually make a difference in patient care. It is a new paradigm, to be sure, and Usala readily admits she is not quite sure how this convergence will play out in her medical career.
Seeking more information, perspective and clarity, Usala eagerly attended the 2nd Annual Biomedical Informatics Symposium on “Big Data in Precision Medicine,” an all-day event held at Georgetown University Oct. 11 that convened the leading thinkers in the fields of genomics, informatics and computational analysis.
Igniting New Collaborations
The Innovation Center for Biomedical Informatics (ICBI), part of Georgetown University Medical Center, hosted the event, which drew nearly 250 people. ICBI is an academic hub for research in the field of data science to facilitate a more individualized approach to health care -- or what has come to be known as precision medicine.
The rich and varied content included two prominent keynote speakers: Stephen Friend, MD, PhD, president of Seattle-based Sage Bionetworks, and Eric Hoffman, PhD, director of the Research Center for Genetic Medicine at Children’s National Medical Center in Washington.
“Our main mission was to bring together, not just people from our Georgetown community, but from an array of institutions to hopefully ignite new ideas and collaborations,” said ICBI Director Subha Madhavan, PhD, who is also a professor at Georgetown Lombardi Comprehensive Cancer Center and head of the cancer center’s clinical informatics group.
“If you look around this room, you will see physicians, bench researchers and technologists; typically we would bring these teams together only for specific projects,” Madhavan said. “But I find it very inspiring to have them in one place for a day so we can collectively think about creative and novel solutions [to data problems] that are outside our individual fields.” This year’s symposium drew about 100 more people than last year’s -- a fact Madhavan attributes to a slow but steady groundswell of interest in the intersection of medicine and informatics.
Bridging the Divide
Usala said this type of conference helps her understand how the practice of medicine is already incorporating bioinformatics in the patient care and clinical research and visualize how it might look if the clinical and informatics communities were more harmoniously integrated.
“As someone just starting in medicine, I think about how to be of service. I know I want to be with patients -- I am not interested in a tenure track [in informatics] -- however I am looking for ways that this information can be applied to a future clinical practice,” she said.
Usala said hearing from experts at an event such as that organized by ICBI gives her hope that bridging the divide between these two great fields may be more within reach than she realized.
“While it will take a while for all this to be translated into clinical practice, it is essential that we seek out the clinical relevance of this. I think such [events] as this are important stepping blocks,” she said.
By Lauren Wolkoff, GUMC Communications
2nd Annual Biomedical Informatics Symposium - 10/11/2013
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!
CNN: Forms at the Doctor's Office Just Got Fun - 1/24/2013
GUMC Feature: Leaders in Biomedical Informatics Explore Vast Potential at Inaugural Symposium - 10/19/2012
The Georgetown University Medical Center (GUMC) Newsletter featured a nice article on the first Georgetown Biomedical Informatics symposium hosted by ICBI on October 12, 2012. Click here to read it on GUMC's website.
Informatics has become an essential component of modern medicine. Properly employed, it is the key that allows us to unravel the secrets of genomic and molecular data with the goal of improving patient care.
Without it, the vast amount of biomedical data available today to researchers and clinicians lacks organization and any meaningful relevance for translation to clinical knowledge and patient care.
Georgetown hosted a symposium to explore the immense challenges and opportunities in the field of biomedical informatics at a symposium held October 12.
The symposium was the inaugural event held by the Innovation Center for Biomedical Informatics (ICBI), a new center launched this past summer at Georgetown University Medical Center. The center was established as an academic hub for innovative research in the field of biomedical informatics, with the goal of enabling a more individualized approach to health care based on a patient’s molecular makeup.
Era of ‘Big Data’
In this era of so-called “big data”, with an increasing volume and rapid output of genomics and other molecular information, scientists need more sophisticated tools to rapidly integrate, analyze and apply it, according to ICBI Director Subha Madhavan, Ph.D.
“How do you go from terabytes of data to those seven or eight data elements that you want to put in front of a basic scientist or a clinician to make effective decisions?” Madhavan said in her remarks.
The answer is not simple, and requires a multidisciplinary effort involving informaticians, statisticians, computer scientists, basic scientists and clinicians, she said.
“Our vision is to bring these groups of people together to enhance translational research and clinical care into a multidisciplinary and collaborative approach that will ultimately enable a more individualized approach to health care,” Madhavan said.
Sorting Genetic Needles from the Haystack
The day-long symposium featured opening remarks from Louis M. Weiner, M.D., director of Georgetown Lombardi Comprehensive Cancer Center, and Robert Clarke, Ph.D., D.Sc., dean for research at Georgetown University Medical Center.
There were two keynote presentations: John Quackenbush, Ph.D., professor of computational biology and bioinformatics at the Harvard School of Public Health, and John Niederhuber, M.D., executive vice president and CEO of Inova Translational Medicine Institute and former director of the National Cancer Institute.
As Quackenbush phrased it, the real challenge of biomedical informatics lies in convening the right people and creating the right tools to “begin to sort the genetic needles from the haystack.”
The predecessor to the ICBI, the clinical informatics group, was first established at Georgetown Lombardi in 2008. The clinical informatics group developed the Georgetown Database of Cancer (G-DOC®), a cutting-edge software platform that allows researchers and clinicians to analyze genomic data across numerous cancer studies and clinical trials.
This event was co-sponsored by the Georgetown-Howard Universities Center for Clinical and Translational Science,Georgetown Center for Cancer Systems Biology and Georgetown Lombardi Comprehensive Cancer Center.
By Lauren Wolkoff, Georgetown Lombardi Communications
Ist Annual Biomedical Informatics Symposium - 10/12/2012
Co-sponsored by Georgetown-Howard Universities Center for Clinical and Translational Science (GHUCCTS) & Georgetown Center for Cancer Systems Biology (CCSB)
October 12, 2012
The first annual Georgetown Informatics Symposium will serve to both introduce and showcase several exciting applications in the field of biomedical informatics to the Georgetown University community. This free, one-day event will include a variety of talks by leaders in the field of clinical and translational sciences who will highlight the applications of informatics tools and resources that can help to advance research from bench to bedside.
7:30 - 8:30 am: Registration Check-In and Continental Breakfast
8:30-8:45 am: Dr. Louis Weiner, Director, Lombardi Cancer Center: Welcome message
8:45-9:00 am: Dr. Robert Clarke, Dean of Research: Overview of research priorities at GU
9:00-9:15 am: Dr. Subha Madhavan, Director ICBI: Informatics at Georgetown
Session 1: INFORMATICS ENABLES TRANSLATIONAL RESEARCH (Chair: Dr. Subha Madhavan, Georgetown)
9:15 – 10:00 am: KEYNOTE SPEAKER: Dr. John Quackenbush, Harvard School of Public Health
10:00-10:30 am: COFFEE BREAK
10:30-11:00 am: Dr. Kenna Shaw - Director, The Cancer Genome Atlas Program Office, NCI
The Cancer Genome Atlas: A Community Resource in Search of a Community
11:00-11:30 am: Dr. ShaAvhrée Buckman, Director, Office of Translational Sciences, FDA
11:30-12:00 pm: Dr. Dan Gallahan – Project Director, Integrative Cancer Biology Program, NCI
Unraveling the Complexity of Cancer
12:00-1:00 pm: LUNCH and Informal Poster Viewing
1:00 – 1:45 pm: KEYNOTE SPEAKER: Dr. John Niederhuber, Inova Translational Medicine Institute
Session 2: TECHNOLOGY DRIVEN SYSTEMS MEDICINE (Chair: Dr. Ophir Frieder, Georgetown)
2:00-2:30 pm: Dr. Joel Saltz, – Director, Center for Comprehensive Informatics, Emory University Chair and Professor, Department of Biomedical Informatics (Integrative Multi-Scale Biomedical Informatics)
2:30-3:00 pm: Dr. Eliot Siegel, Professor, Diagnostic Radiology and Nuclear Medicine; Director, Baltimore VA Medical Center Radiology; Associate Vice Chairman for Informatics, University of Maryland (Artificial Intelligence and the Next Generation of Personalized Medicine)
3:00-3:30 pm: COFFEE BREAK and Informal Poster Viewing
Session 3: GEORGETOWN RESOURCES (Chair: Dr. Sona Vasudevan, Georgetown)
3:30-4:00 pm: Dr. Sona Vasudevan, Associate Professor; Director, MD/MS program in Systems Medicine (Informatics Educational Programs at GU)
4:00-4:20 pm: Dr. Cathy Wu, Professor, Department of Oncology at GU (Protein Information Resource/Uniprot)
4:20-4:40 pm: Dr. Yuriy Gusev, Sr. Bioinformatics Scientist at GU (G-DOC/G-CODE)
4:40-5:00 pm: Rachel Kidwiler, Program Director and AVP, Research Information Systems at GU (REDCap)
5:00-5:20 pm: Dr. Nawar Shara, – Director, Biostatistics and Epidemiology, MedStar Research Institute; Assistant Professor of Medicine, Georgetown University Medical School (Enterprise management of big data in healthcare (Explorys))
5:20-5:30 pm: Closing Remarks, Dr. Subha Madhavan
RECEPTION AND FORMAL POSTER SESSION
5:30-7:00 pm: Wine reception, posters, and networking event (presenters please stand by your posters during the event) *Poster Awards will be announced at 6:30pm*