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brian m. bot | principal scientist |
2016 april 18
sage bionetworks
pnw life science executive forum
biomedical research in an increasingly digital world
opportunities when problems are bigger than
a single organization
sage bionetworks
sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines
our approach
opportunities when problems are bigger than
a single organization
sage bionetworks
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
analysis of:
12 tumor types
6 molecular profiling platforms
TCGA Pan-Cancer Consortium
18NPG papers
68core projects
248researchers
28institutions
1070datasets
1723results
TCGA Pan-Cancer Consortium
TCGA Pan-Cancer Consortium
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
CommonMind Consortium
large public / private partnership
phase I: prefrontal cortex
~300 SCZ, 300 control, 60 BD
processing pipelines developed in collaboration
between sage and mssm
CommonMind Consortium
CommonMind Consortium
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
expert team data subtype
CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
...
expert team data subtype
CRC Subtyping Consortium
CRC Subtyping Consortium
collaborative analyses
cloud-based file storage
CRC Subtyping Consortium
code associated
with results
CRC Subtyping Consortium
doi:10.1038/nm.3967 doi:10.7303/syn2623706
CRC Subtyping Consortium
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
public / private partnership between NIH,
10 biopharmaceutical companies
and several non-profit organizations
Accelerating Medicines Partnership
($ Millions)
Total
Project
Total NIH
Total
Industry
Alzheimer’s
Disease
129.5 67.6 61.9
Type 2
Diabetes
58.4 30.4 28
Rheumatoid
Arthritis
41.6 20.9 20.7
TOTAL 229.5 118.9 110.6
Accelerating Medicines Partnership
mt sinai mayo / ufl / isb
broad / rush emory
integrated network analysis
target discovery
300 case-control
rnaseq, genotype, clinical
1000 case-control
rnaseq, methylation,
genotype, clinical
300 ad, tauopathy, control
rnaseq, clinical
200 AD, MCI, control
Proteomic, clinical data
Accelerating Medicines Partnership
iPS neurons and astrocytes
Mouse hippocamal slices
Drosophila model
Genetic analysis
aB and Tau mouse models
rAAV delivered models
Proteomics
Cultured neurons & astrocytes
iPS compound screens
Proteomics
Cell Culture, Mouse Models
Drosophila model
mt sinai mayo / ufl / isb
broad / rush emory
target validation
2
3
5
12
Accelerating Medicines Partnership
Target
Discovery
Target
Discovery
Target
Discovery
Target
Discovery
Target
Validation
Target
Validation
Target
Validation
Target
Validation
Shared
Information for
Target Identification
coordinate sharing of early-phase
target identification insights
Accelerating Medicines Partnership
AMP-AD
Collaborative
Workspace
Quarterly
Depositions
Broad/
RUSH
Mt.
Sinai
U Fl/
ISB/
Mayo
Emory
Sage
Other
Partners
Individual Partner Workspaces AMP-AD
Data Portal
Consortium Space
Public space
AMP-AD Synapse
Project Structure
Accelerating Medicines Partnership
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
DREAM Challenges
Columbia Professor Dimitris Anastassiou
MPEG-2 compression of digital audio and video signals
Modules of co-expressed genes shared across cancers
Belief that these ‘attractors’ represent underlying biological
mechanisms (bioinformatic ‘hallmarks of cancer’1)
1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)
DREAM Challenges
17 April 2013
DREAM Challenges
CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
mHealth
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
33
mHealth
34
48,104 downloads from app store - first six months
16,585 participants consented
14,684 participants enrolled
9,520 agreed to ‘share broadly’
1,087 self reported a professional diagnosis of Parkinson
mPower
Passive
Measures
GPS -
Displacement
Vectors
GPS -
Displacement
Vectors
- -
Structured
Activities
Tapping
Activity
Walking/
Standing
Activity
Voice Activity
Memory
Game
Surveys
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
MDS-UPDRS
PDQ8
four symptoms of PD
Motor
Initiation
Gait/Balance Hypophonia Memory
Motor
Initiation
Gait/Balance Hypophonia Memory
mPower activities
increasingly decentralized research ecosystem
democratization of research
de-coupling of data collection and analysis
cloud infrastructure
gov’t agencies and public pushing for > sharing
increasingly decentralized research ecosystem
brian m. bot
————————
principal scientist
community manager
brian.bot@sagebase.org
@BrianMBot
thank you
sage bionetworks

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