Biomedicine – from Stethoscope to Computer Philip E. Bourne NIH Associate Director for Data Science Emerging Researchers National Conference in STEM February 20, 2015
Jul 15, 2015
Biomedicine – from
Stethoscope to Computer
Philip E. Bourne
NIH Associate Director for Data Science
Emerging Researchers National Conference in STEM
February 20, 2015
What I do…I run a program at the NIH which supports projects that
advance the contribution of the computational and
quantitative sciences to biomedical discovery.
I also run a research lab at the NIH where we do
computational biology with an emphasis on
protein structure.
How I think I got here…
• I embrace change
• I make and keep lots of friends and colleagues
• I keep questioning assumptions
• I follow my heart
• I learned to live with regret
• I try to make the most of every day
• I go after the big problems
• I give back to the scientific community and society
Google “PLOS Ten Simple Rules”
The Life of One Scientist – The Early YearsSo That You Might Not Make the Same Mistakes
• My high school teacher Mr. Wilson said I would be a failure at chemistry
• My PhD is in chemistry
• The opportunity to live in different places shaped my life
• Good friends are forever
Postdoctoral Work – The Molecular Basis of How the Body Works
• Regrets: never learnt another language
Senior Scientist HHMI Columbia University New York
• Driven not by career but wanting to live in New York City
~1990 Got Involved withThe Human Genome
• Was only possible by applying computers to problems in biology
• Developed algorithms to support physical and genetic mapping of Chromosome 13
Went to UCSD to Apply Computers to Big Biological Problems
In 1993 possibly the best place in the world to do computational biology
Realized that there is still more
work for me to do… it isn’t all in the
lab… and it is in Washington, D.C.
New Job! Associate Director for Data
Science (ADDS)
at the National Institutes of
Health (NIH)
Mission: To accelerate
and support the integration
of the computational and
quantitative sciences and
the biomedical sciences.
I also got to move my lab to the NIH – my group’s research in
protein structure biology continues here in the D.C. area and with
collaborations all over the world.
1. Josh Sommer and Chordoma
Disease
http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation#fullprogram
Josh Sommer – A Remarkable Young Man
Co-founder & Executive Director the Chordoma Foundation
http://sagecongress.org/Presentations/Sommer.pdf
Chordoma
• A rare form of brain
cancer
• No known drugs
• Treatment – surgical
resection followed by
intense radiation
therapy
http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
Open Data leads to faster cures
Collaboration
• Open Data generates collaborations and supports Team Science
• Collaborations bring in more researchers
Big Data
• More researchers create more data
• More researchers create different types of data
Faster Cures
• Computational Science helps biologists do more with all that Big Data
• Big Data leads to new discoveries.
The Worst of Times
Source: http://www.pharmafocusasia.com/strategy/drug_discovery_india_force_to_reckon.htm
Here is One Reason Why• Tykerb – Breast cancer
• Gleevac – Leukemia, GI cancers
• Nexavar – Kidney and liver cancer
• Staurosporine – natural product – alkaloid – uses many e.g., antifungal antihypertensive
Collins and Workman 2006 Nature Chemical Biology 2 689-700
Bioinformatics – Reverse Engineering
Drug Discovery
Characterize ligand binding
site of primary target
(Geometric Potential)
Identify off-targets by ligand
binding site similarity
(Sequence order independent
profile-profile alignment)
Extract known drugs
or inhibitors of the
primary and/or off-targets
Search for similar
small molecules
Dock molecules to both
primary and off-targets
Statistics analysis
of docking score
correlations
…
Xie and Bourne 2009
Bioinformatics 25(12) 305-312
2. HARNESSING SOCIETY FOR
SCIENCE
A Team of scientists is great but….what if ordinary people could
help us do science. Computer games are the key.
Nature’s ReductionismThere are ~ 20300 possible proteins
>>>> all the atoms in the Universe
11.2M protein sequences from
10,854 species (source RefSeq)
38,221 protein structures
yield 1195 domain folds (SCOP 1.75)
Bridging fields to support
innovationSometimes biomedical research is mind-numbingly BORING! How can we manage time-intensive, low-skill tasks without biologist burn out??? Crowdsourcing?
Think Tank: Game Developers and
Biomedical Researchers
9 biomedical researchers &
10 game developersDecember 9-10, 2014 @
NIH
To address challenges of how these two communities
collaborate, exchange data science & visualization
expertise, and develop games for enabling and
performing biomedical research
“And that’s why we’re here today. Because something
called precision medicine … gives us one of the greatest
opportunities for new medical breakthroughs that we
have ever seen.”
President Barack ObamaJanuary 30, 2015
Precision Medicine Concept is not new• Consider prescription eyeglasses, blood transfusions…
• Prospects for broader application raised by recent advances
in basic research, technology development, genomics,
proteomics, metabolomics, EMRs, Big Data, mHealth, etc.
• Reinforced by 2011 National Research Council report
What is needed now• Development of rigorous research program to provide
scientific evidence needed to turn concept into reality
• Recruitment of the best and brightest from multiple disciplines
to join the team
Precision Medicine Initiative:
The Time Is Right
Ten Years AgoNow – 2014
(most recent data)
Cost of sequencing a
human genome$22,000,000 $1000 - $5000
Amount of Time to
Sequence a Human
Genome
2 years <1 day
Number of smart
phones in the United
States
1 million (<2%) 160 million (58%)
EMR Adoption,
(% providers)20-30% >90%
Computing Power n n x 16
Precision Medicine:
What Success Might Look Like
50-year-old woman with type 2 diabetes
visits her doctor
• Now
– Though woman’s glucose control has been
suboptimal, doctor renews her prescription for
drug often used for type 2 diabetes
– Continues to monitor blood glucose with
fingersticks and glucometer, despite
dissatisfaction with these methods
Precision Medicine:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her doctor
• Future: + 2 years
– Volunteers for new national research network• Sample of her DNA, along with her health information, sent to
researchers for sequencing/analysis
• Can view her health/research data via smartphone
– Agrees to researchers’ request to track her glucose levels via tiny implantable chip that sends wireless signals to her watch, researchers’ computers
• Using these data, she changes diet, medicine dose schedule
Other Diseases:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits her doctor
• Future: + 5 years
– Receives word from her doctor about a new drug based upon improved molecular understanding of type 2 diabetes
– When she enters drug’s name into her smartphone’s Rx app, her genomic data show she’ll metabolize the drug slowly
• Her doctor alters the dose accordingly
Other Diseases:
What Success Might Look Like
50-year-old woman with type 2 diabetes visits
her doctor
• Future: + 10 years
– Celebrates her 60th birthday and reflects with her
family about how proud she is to be part of cohort
study
– Her glucose levels remain well controlled; she’s
suffered no diabetes-related complications
– Her children decide to volunteer for cohort study