Organisation-wide talk on extracting value sand insights from data in bioinformatics.

1. Bioinformatics
Extracting value from data
Jorge Bouças, PhD | Bioinformatics

2. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
2
6 % 9 %

3. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
3
5 years performance: 7.59 % / year (netto)

4. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
4

5. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
5

6. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
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5 years performance: 9.66 % / year (netto)

7. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
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5 years simulation, 10 000 EUR (netto values)
passive active active - passive
performance / year 7.59 % 9.66 % 2.07 %
earnings / year 759 EUR 966 EUR 207 EUR
5 years performance 37.95 % 48.30 % 10.35 %
5 years earnings 3 795 EUR 4 830 EUR 1 035 EUR
min. intrachange - 30 % -

8. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Value
• 3%
• liquidity
• infrastructure free
• no renters
Value
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6 % 9 %

9. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Methods
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- Web scraping
- Data wrangling
- Modeling

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Web scraping pubmed
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11. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Publications based social network of a German institution, 2008-2018
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node = author
edge = coauthorship
n (papers) >= 2
n (coauthorships) >= 2
node size = n papers
edge size = n papers
blue = low IF
red = high IF

12. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Scraping experimental data online
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13. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Gene expression atlas
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• human RNAseq data (Ensembl 79)
• 20 studies
• 2259 samples
• 65225 genes

14. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Gene expression atlas
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detection of stimulus
sensory perception of smell
ion transport
sexual reproduction
amino acid transport
regulation of RNA
biosynthetic process
chondrocyte
proliferation
chromatin assembly
synaptic signaling
neurogenesis
immune response
synapsis
epidermis development
cell surface receptor
signaling pathway
cell cycle
RNA processing
translation
behavior
keratinocyte differentiation
interferon-gamma
production

15. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Gene expression atlas
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2 related genes indentified
in-house through an
experimental screening
screenings sizes and
number of screenings can
be reduced by use of
publicly available data

16. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
From Biochemistry to Web Scraping
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*gliobastoma multiforme
Boucas J, PLoS One, 2015

17. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
The world of omics
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DNA RNA Protein Metabolite
Genomics Transcriptomics Proteomics Metabolomics
substrate
A
C
G
T
T
G
C
A
A
C
G
T
Thr
Thr

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Integrating Transcriptomics and Metabolomics data
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RNA
Transcriptomics
Metabolite
Metabolomics

19. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Connecting the parts
target
sequences
motif
building
transcript.
scanning
MEME
FIMO
p53 cancer mutant Y220C in
complex with compound MB84
(5O1B)
API
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20. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Automated systems
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Phenomaster, Phenotyping Facility
37 parameters
every 15 min
for 48h

21. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Performance
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22. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Infrastructure
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23. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Services short list
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24. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Training
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Worshops (2x/year):
The Unix Shell (introduction)
Help your self on a remote server
RNAseq with the Tuxedo suite
Introduction to R
Automation in R
RNAseq analysis in R with DESeq2
Introduction to Python
Data wrangling in Python
Multidimensional and lifespan darta with Python
Network analysis with Cytoscape

25. MAX PLANCK INSTITUTE FOR BIOLOGY OF AGEING | BIOINFORMATICS
Services short list
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Services short list
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Services short list
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Coming soon:
Shiny apps
Tercen

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Tercen
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Shiny
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Services short list
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People
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