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CENTER FOR DATA SCIENCE SCIENCE Strength in Numbers AND BIG D BIG DATA ANALYTICS Earth, genomes, and time: a big data approach to integrative evolutionary histories Fabia U. Battistuzzi Biological Sciences battistu@oakland.edu Dec.

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CENTER FOR

DATA SCIENCE SCIENCE

AND

BIG D BIG DATA

ANALYTICS

Strength in Numbers

Earth, genomes, and time: a big data approach to integrative evolutionary histories

Fabia U. Battistuzzi Biological Sciences battistu@oakland.edu

Dec. 1, 2016

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky

Evolution

Past Future Present

Past history of life is a predictor of current and

future changes

Medical field
Climate science
Astrobiology
Conservation biology
Sustainable energy
…

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky
Genomes are repositories of billions of data

points (DNA bases)

Human genome: 3 billion DNA base pairs
7 billion individuals on Earth
2.1 e+19 base pairs
Species estimates: 10 million to 1 trillion
Many will be much smaller than us (< 1

million base pairs)

Many are much larger than us (up to

~150 billion base pairs)

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky
Comparative genomics
How and where did life originate
And where should we look for other

life (Astrobiology)

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky
Comparative genomics
How did life survive on Earth through

major environmental changes

Microbes are the longest living

lineages on Earth (~4 billion years)

They survived and thrived during

planetary-scale climate changes (conservation and sustainability)

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Nothing in biology makes sense except in the light of evolution

T. Dobzhansky
Comparative genomics
How do pathogens escape our immune

system and drugs

What changes at the genomic level

allow them to adapt?

How do pathogens arise and spread?

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Evolution in the Blab

Early life evolution
How to accurately reconstruct the evolutionary

histories of microbes on Earth

Conditions for life to thrive
Adaptations that sustained microbial life through climate

changes

Rate of species diversification

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Evolution in the Blab

Evolution of malaria
How does it adapt to humans and other

hosts?

Are genomes evolving differently depending on the

host?

Are genes involved in antimalarial drug resistance

evolving faster?

AT-rich AT-balance

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Evolution in the Blab

Students involvement
Undergrads & grads (current size: 11+1 students)
Skills
Scripting/programming
Phylogenetics
Comparative genomics
Data mining
Statistics

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

New opportunities with CDaS

Explore new statistical applications for Big Data
Systematic bias
False discovery rates

Kumar et al 2012

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

New opportunities with CDaS

Connect comparative and functional genomics
Text mining of functional databases
Integration of multiple databases

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

New opportunities with CDaS

Explore new strategies to gain computational support
On-site high-performance computational cluster (working on it…)
Cloud-based and off-site clusters (exploring options…)
Programming, database architecture

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CENTER FOR DATA SC SCIENC IENCE AND BIG BIG DATA A ANALYTICS

Strength in Numbers

Contact info

battistu@oakland.edu 340 Dodge Hall Biological Sciences Oakland University