Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
Dirk.Repsilber@oru.se – 2015-05-21
Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
Dirk.Repsilber@oru.se – 2015-05-21
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
Vad är bioinformatik ?
● bioinformatics – molecular data integration
● systems biology – regulatory systems modeling
● biostatistics – classical analysis of clinical trials
Vad är bioinformatik ?
● Sequence analysis ● Structure analysis ● Function analysis
Vad är bioinformatik ?
● Sequence analysis
– genome sequencing & assembly & annotation – genome comparison
– phylogeny
– gene & promoter prediction – motif discovery
– sequence database searching – sequence alignment
Vad är bioinformatik ?
● Sequence analysis ● Structure analysis
– nucleic acid structure prediction – protein structure prediction
– protein structure classification – protein structure comparison
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
complex patterns
biosignature for classifying human Alzheimer diseased brain tissue from healthy tissue Scheubert et al. BMC Bioinformatics 2012, 13:266
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
complex patterns
Classification of TB-infected and healthy controls by 3D-discrimination gene expression signature. Jacobsen et al., J Mol Med, 2007
Protein 3-D Structure
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.
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
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
precision medicine
precision medicine
precision medicine
precision medicine
precision medicine
precision medicine
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
precision medicine
● clinics and medical
research
– diseases
– signs and symptoms – drugs
– clinical laboratory
measurements
● 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
● 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
Bioinformatics is the ideal tool to integrate data at all levels from molecule to man.
Nijmegen Centre for Molecular Life Sciences, Netherlands:
● "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."
● "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."
● "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."
biomedical data of various sources
visualized data
modeled data integrated data
"A lot of times it's through comparisons and
comparisons and comparisons that researchers see an interesting trend..."
“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.
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.
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.
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
BIA
– the Bioinformatics Intelligence
Agency
when should we meet?
integrative
functional bioinformatics
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
Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
Dirk.Repsilber@oru.se – 2015-05-21
