Vad är bioinformatik och varför behöver vi det i vården? a bioinformatician's perspectives

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(1)

Vad är bioinformatik

och

varför behöver vi det i vården?

– a bioinformatician's perspectives

Dirk.Repsilber@oru.se – 2015-05-21

(2)

Vad är bioinformatik

och

varför behöver vi det i vården?

– a bioinformatician's perspectives

Dirk.Repsilber@oru.se – 2015-05-21

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Vad är bioinformatik … ?

… for large & complex bio-medical data, computer aided

● data management,

● data analysis and modeling,

● data interpretation.

… och varför behöver vi det i vården?

● patterns: biomarkers, biosignatures

– diagnosis, prognosis

● understanding: integration, models, mechanisms

– therapy, drug targets

precision medicine systems medicine

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Vad är bioinformatik ?

bioinformatics – molecular data integration

● systems biology – regulatory systems modeling

● biostatistics – classical analysis of clinical trials

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Vad är bioinformatik ?

● Sequence analysis ● Structure analysis ● Function analysis

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Vad är bioinformatik ?

● Sequence analysis

– genome sequencing & assembly & annotation – genome comparison

– phylogeny

– gene & promoter prediction – motif discovery

– sequence database searching – sequence alignment

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Vad är bioinformatik ?

● Sequence analysis ● Structure analysis

– nucleic acid structure prediction – protein structure prediction

– protein structure classification – protein structure comparison

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Vad är bioinformatik ?

● Sequence analysis ● Structure analysis ● Function analysis

– metabolic pathway modeling – gene expression profiling

– protein interaction prediction

– reverse engineering of regulatory networks, network biology – biosignature mining

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complex patterns

biosignature for classifying human Alzheimer diseased brain tissue from healthy tissue Scheubert et al. BMC Bioinformatics 2012, 13:266

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complex patterns

miRNA decision tree to classify two kinds of leukemia, and healthy lymph nodes Roehle, Höfig, Repsilber, et al. 2008, British Journal of Haematology, 142, 732–744

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complex patterns

Classification of TB-infected and healthy controls by 3D-discrimination gene expression signature. Jacobsen et al., J Mol Med, 2007

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Protein 3-D Structure

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Structure = Function

● proteins function by 3-D interactions with other

molecules

for a protein, 3-D structure is function.

we cannot accurately determine 3-D structure from gene sequence.

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Vad är bioinformatik … ?

… for large & complex bio-medical data, computer aided

● data management,

● data analysis and modeling,

● data interpretation.

… och varför behöver vi det i vården?

● patterns: biomarkers, biosignatures

– diagnosis, prognosis

● understanding: integration, models, mechanisms

– therapy, drug targets

precision medicine systems medicine

(22)

Vad är bioinformatik … ?

… for large & complex bio-medical data, computer aided

● data management,

● data analysis and modeling,

● data interpretation.

… och varför behöver vi det i vården?

● patterns: biomarkers, biosignatures

– diagnosis, prognosis

● understanding: integration, models, mechanisms

– therapy, drug targets

precision medicine systems medicine

(23)

precision medicine

(24)

precision medicine

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precision medicine

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precision medicine

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precision medicine

(28)

precision medicine

(29)

Vad är bioinformatik … ?

… for large & complex bio-medical data, computer aided

● data management,

● data analysis and modeling,

● data interpretation.

… och varför behöver vi det i vården?

● patterns: biomarkers, biosignatures

– diagnosis, prognosis

● understanding: integration, models, mechanisms

– therapy, drug targets

precision medicine systems medicine

(30)

precision medicine

(31)

● clinics and medical

research

– diseases

– signs and symptoms – drugs

– clinical laboratory

measurements

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● molecular and cell biology – biomolecules – signalling mechanisms – cellular organization – available in databases ● GeneBank, GEO, PDB, KEGG, Rreactome ● clinics and medical

research

– diseases

– signs and symptoms – drugs

– clinical laboratory

measurements

(33)

● molecular and cell biology – biomolecules – signalling mechanisms – cellular organization – available in databases ● GeneBank, GEO, PDB, KEGG, Rreactome ● clinics and medical

research

– diseases

– signs and symptoms – drugs – clinical laboratory measurements – clinical images ?!

translational bioinformatics

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Bioinformatics is the ideal tool to integrate data at all levels from molecule to man.

Nijmegen Centre for Molecular Life Sciences, Netherlands:

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● "The key to bioinformatics is integration, integration,

integration."

Jim Golden, Connecticut

● "To answer most interesting biological problems, you

need to combine data from many data sources."

Russ Altman, Stanford University

"However, creating seamless access to multiple data sources is extremely difficult."

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● "The key to bioinformatics is integration, integration,

integration."

Jim Golden, Connecticut

● "To answer most interesting biological problems, you

need to combine data from many data sources."

Russ Altman, Stanford University

"However, creating seamless access to multiple data sources is extremely difficult."

(37)

● "The key to bioinformatics is integration, integration,

integration."

Jim Golden, Connecticut

● "To answer most interesting biological problems, you

need to combine data from many data sources."

Russ Altman, Stanford University

"However, creating seamless access to multiple data sources is extremely difficult."

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biomedical data of various sources

visualized data

modeled data integrated data

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"A lot of times it's through comparisons and

comparisons and comparisons that researchers see an interesting trend..."

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“As a result of comparative genomic and

proteomic research, we will soon be able to not only locate each human gene but also fully

understand its function.”

Subramanian G, Adams MD, Venter JC, Broder S. JAMA. 2001;286:2296–2306.

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daily practise and needs

ever-increasing need for constant input from bioinformatic experts

most biomedical laboratories have their own in-house bioinformatician

individual researcher, beyond a basic

acquisition and analysis of simple data, would certainly need external bioinformatic advice for any complex analysis.

(43)

daily practise and needs

ever-increasing need for constant input from bioinformatic experts

most biomedical laboratories have their own in-house bioinformatician

individual researcher, beyond a basic

acquisition and analysis of simple data, would certainly need external bioinformatic advice for any complex analysis.

(44)

daily practise and needs

ever-increasing need for constant input from bioinformatic experts

most biomedical laboratories have their own in-house bioinformatician

individual researcher, beyond a basic

acquisition and analysis of simple data, would certainly need external bioinformatic advice for any complex analysis.

Ardeshir Bayat

(45)

BIA

– the Bioinformatics Intelligence

Agency

when should we meet?

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integrative

functional bioinformatics

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Vad är bioinformatik … ?

… for large & complex bio-medical data, computer aided

● data management,

● data analysis and modeling,

● data interpretation.

… och varför behöver vi det i vården?

● patterns: biomarkers, biosignatures

– diagnosis, prognosis

● understanding: integration, models, mechanisms

– therapy, drug targets

precision medicine systems medicine

(48)

Vad är bioinformatik

och

varför behöver vi det i vården?

– a bioinformatician's perspectives

Dirk.Repsilber@oru.se – 2015-05-21

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