Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
[email protected] – 2015-05-21
Functional Bioinformatics, Örebro University
Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
[email protected] – 2015-05-21
Functional Bioinformatics, Örebro University
BIG wave of data ...
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
precision medicine
understanding: integration, models, mechanisms
– therapy, drug targets
systems medicine
Vad är bioinformatik ?
●
bioinformatics – molecular data integration
●
systems biology – regulatory systems modeling
●
biostatistics – classical analysis of clinical trials
●
medical informatics – clinical data management
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
–
whole cell modeling
metabolic pathways
regulatory networks
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
databases: Ensembl
databases: NCBI
Protein 3-D Structure
http://upload.wikimedia.org/wikipedia/commons/8/80/Docking.jpg
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.
but we can in-silico predict (and then validate)!
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
precision medicine
understanding: integration, models, mechanisms
– therapy, drug targets
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
precision medicine
understanding: integration, models, mechanisms
– therapy, drug targets
systems medicine
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
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
precision medicine
understanding: integration, models, mechanisms
– therapy, drug targets
systems medicine
precision medicine
O. Wolkenhauer, Systems biology, University of Rostock
●
clinics and medical
research
–
diseases
–
signs and symptoms
–
drugs
–
clinical laboratory
measurements
–
clinical images
●
clinics and medical
research
–
–
–
–
–
●
molecular and cell
biology
diseases
–
biomolecules
signs and symptoms
–
signalling mechanisms
drugs
–
cellular organization
–
available in databases
clinical laboratory
measurements
clinical images
●
GeneBank, GEO, PDB,
KEGG, Rreactome
translational bioinformatics
●
clinics and medical
research
–
–
–
–
–
●
molecular and cell
biology
diseases
–
biomolecules
signs and symptoms
–
signalling mechanisms
–
cellular organization
–
available in databases
drugs
clinical laboratory
measurements
clinical images
?!
●
GeneBank, GEO, PDB,
KEGG, Rreactome
Bioinformatics is the ideal tool to integrate data at all
levels from molecule to man.
Nijmegen Centre for Molecular Life Sciences, Netherlands:
http://www2.cmbi.ru.nl/who-and-where/bioinformatics-and-medicine/
●
●
"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
integrated data
visualized data
modeled data
"A lot of times it's through comparisons and
comparisons and comparisons that researchers
see an interesting trend..."
David Butler
“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 inhouse bioinformatician
individual researcher, beyond a basic
acquisition and analysis of simple data, would
certainly need external bioinformatic advice for
any complex analysis.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1122955/
daily practise and needs
ever-increasing need for constant input from
bioinformatic experts
most biomedical laboratories have their own inhouse bioinformatician
individual researcher, beyond a basic
acquisition and analysis of simple data, would
certainly need external bioinformatic advice for
any complex analysis.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1122955/
daily practise and needs
ever-increasing need for constant input from
bioinformatic experts
most biomedical laboratories have their own inhouse bioinformatician
individual researcher, beyond a basic
acquisition and analysis of simple data, would
certainly need external bioinformatic advice for
any complex analysis.
Ardeshir Bayat
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1122955/
BIA
– the Bioinformatics Intelligence
Agency
when should we
meet?
integrative functional bioinformatics
integrative part of future 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
precision medicine
understanding: integration, models, mechanisms
– therapy, drug targets
systems medicine
Vad är bioinformatik
och
varför behöver vi det i vården?
– a bioinformatician's perspectives
[email protected] – 2015-05-21
Functional Bioinformatics, Örebro University