Public data as a�lab resource.

Casey Greene @GreeneScientist

Image: William R Shepherd

2,087,215 assays ~$2.1 billion

•  Pseudomonas aeruginosa compendium •  > 100 different experiments •  Many different labs

Image: Nathan Reading

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

If you showed 16,000 computers 10 million images from youtube, what would they see?

Le et al. 2012

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

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

eADAGE node 164 captures phosphate concentration in

media.

Georgia Doing and Jie Tan

Production of alkaline phosphatase indicates phosphate

limitation. Low Phosphate

PhoB (TF)

Alkaline phosphatase

BCIP Blue color

Kimberley Lewis

PhoR

The mechanism of PhoB regulation differs.

Kimberley Lewis

Our pathway requires another input to PhoB.

Low Phosphate

PhoB (TF)

Alkaline phosphatase

BCIP Blue color

PhoR ?

Public data suggests the alternative mechanism.

GSE48429 – PIA vs. PIA + ammonium metavanadate (July 2013)

GSE35248 – ΔKinB vs ΔKinB/ΔRpoN (March 2012)

kinB is necessary for activity on intermediate phosphate levels.

Where do we have (enough) data?

Greene et al. Pac Sym Bio. 2016

The worst thing that can be said about your grant is that it's a fishing expedition.

�- Tom Blumenthal (@ 2016 Gold Lab Symposium)

�- Tom Blumenthal (@ 2016 Gold Lab Symposium)

If you engage in a fishing expedition you can actually catch fish.�

Image by Peter (stockispicts)

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

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.

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: