How can we put abundant public data to use in the biological sciences? Here I discuss one of our new methods and its application to phosphate starvation.

1. Public data as a
lab resource.
Casey Greene
@GreeneScientist
Image: William R Shepherd

3. 2,087,215 assays
~$2.1 billion

4. • Pseudomonas aeruginosa compendium
• > 100 different experiments
• Many different labs
Image: Nathan Reading

5. Image from You Don’t Know Jack. Vol 3.

6. If you showed 16,000 computers 10 million
images from youtube, what would they see?
Le et al. 2012

7. ADAGE analysis of publicly available
gene expression data collections
illuminates Pseudomonas aeruginosa-
host interactions
bioRxiv: http://dx.doi.org/10.1101/030650
github: http://github.com/greenelab/adage
Tan, Hammond, Hogan, and Greene. mSystems. 2016

8. I didn’t want to just know the
names of things. I remember really
wanting to know how it all worked.
- Elizabeth Blackburn
Image: US Embassy Sweden

9. eADAGE node 164 captures
phosphate concentration in
media.
Georgia Doing and Jie Tan

10. Production of alkaline
phosphatase indicates phosphate
limitation.
Low Phosphate
PhoB (TF)
Alkaline
phosphatase
BCIP Blue color
Kimberley Lewis
PhoR

11. The mechanism of PhoB
regulation differs.
Kimberley Lewis

12. Our pathway requires another
input to PhoB.
Low Phosphate
PhoB (TF)
Alkaline
phosphatase
BCIP Blue color
PhoR
?

13. Public data suggests the
alternative mechanism.
GSE48429 – PIA vs. PIA + ammonium metavanadate (July 2013)
GSE35248 – ΔKinB vs ΔKinB/ΔRpoN (March 2012)

14. kinB is necessary for activity on
intermediate phosphate levels.

15. Where do we have (enough) data?
Greene et al. Pac Sym Bio. 2016

16. The worst thing that can be said about your
grant is that it's a fishing expedition.
- Tom Blumenthal (@ 2016 Gold Lab Symposium)

17. - Tom Blumenthal (@ 2016 Gold Lab Symposium)
If you engage in a fishing expedition you can
actually catch fish.
Image by Peter (stockispicts)

18. Greene Lab:
Jaclyn Taroni (Postdoc)
Daniel Himmelstein (Postdoc)
Jie Tan (Grad Student)
Gregory Way (Grad Student)
Brett Beaulieu-Jones (Grad Student)
Linda Zhou (Rotation Student)
Amy Campbell (Postbacc)
René Zelaya (Programmer)
Matt Huyck (Programmer)
Dongbo Hu (Programmer)
Kathy Chen (Undergrad)
Tim Chang (Undergrad)
Roshan Ravishankar (Undergrad)
Collaborators:
Deb Hogan + Jack Hammond, Georgia Doing,
Kimberley Lewis,
Data:
All investigators who publicly release their gene
expression data.
Images:
Artists who release their work under a Creative
Commons license.
Funding:
Gordon and Betty Moore Foundation
National Science Foundation
Cystic Fibrosis Foundation
National Institutes of Health
Find us online:
http://www.greenelab.com
Calvin and Hobbes. Bill Watterson

19. Research Parasite Awards
(The “Parasites”)
Selection criteria for the work in question:
• The awardee must not have been involved the design of the experiments
that generated the data.
• The awardee published independently of the original investigators, and the
original investigators are not authors of the secondary analyses but are
appropriately credited in the manuscripts.
• The awardee may have extended, replicated or disproved what the original
investigators had posited.
• The awardee has provided source code and intermediate or final results in a
manner that enhances reproducibility.

20. Details
• Submit by October 14, 2016 @ 5PM HST
• Instructions at http://researchparasite.com
• COI rules are strict! I can only talk about rules.
2017 Selection Committee: