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Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman Slides: bit.ly/carleton2019

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Page 1: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Opportunities inbiomedical data science

Karl Broman

Biostatistics & Medical Informatics, UW–Madison

kbroman.orggithub.com/kbroman

@kwbromanSlides: bit.ly/carleton2019

Page 2: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Biomedical data explosion

▶ Electronic health records (EHR)▶ Imaging▶ Genome/proteome/metabolome/microbiome data▶ Personal activity/health tracking devices

2

Page 3: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Biomedical data explosion

▶ Electronic health records (EHR)▶ Imaging▶ Genome/proteome/metabolome/microbiome data▶ Personal activity/health tracking devices▶ High-throughput measurements in agriculture and ecology

2

Page 4: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

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Page 5: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

daviddeen.com

4

Page 6: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Intercross

P1 P2

F1 F1

F2

5

Page 7: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Genome scan

0

2

4

6

8

Chromosome

LOD

sco

re

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X

BB BR RR

0.80.91.01.1

6

Page 8: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Genome scan

0

2

4

6

8

Chromosome

LOD

sco

re

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X

6

Page 9: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

High-throughput phenotypes

7

Page 10: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

High-throughput phenotypesislet

QTL position (cM)

Pro

be p

ositi

on (

cM)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X

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Page 11: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Multi-parent crossesG0

A B C D E F G H

G1

G2

G10

G15

G20

8

Page 12: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

The work

▶ Collaboration▶ Data exploration▶ Methods development▶ Software development

– R– C++– Coffeescript– Ruby

9

Page 13: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

The work

▶ Collaboration▶ Data exploration▶ Methods development▶ Software development

– R– C++– Coffeescript– Ruby

9

Page 14: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Qiongshi LuHuman genome-wide association studies

10

Page 15: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Sündüz KeleşFunctional mediation analysis

11

Page 16: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Christina KendziorskiClock genes in stem cells

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Page 17: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Tony GitterPathways disrupted by cancer

13

Page 18: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Vikas SinghAnalysis of brain images

14

Page 19: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Biomedical data science PhD at UW-Madison

▶ Faculty spanning biostatistics, bioinformatics, and computer science▶ Broad opportunities for scientific collaborations▶ Flexible course requirements▶ Research rotations▶ Literature and professional skills seminars

bit.ly/MadBDS

15

Page 20: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

16

Page 21: Opportunities in biomedical data science · Opportunities in biomedical data science Karl Broman Biostatistics & Medical Informatics, UW–Madison kbroman.org github.com/kbroman @kwbroman

Slides: bit.ly/carleton2019

kbroman.org

github.com/kbroman

@kwbroman

17