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 Functional Bioinformatics, Örebro University

2 Vad är bioinformatik och varför behöver vi det i vården? a bioinformatician's perspectives Dirk.Repsilber@oru.se Functional Bioinformatics, Örebro University

3 BIG wave of data...

4 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

5

6 Vad är bioinformatik? bioinformatics molecular data integration systems biology regulatory systems modeling biostatistics classical analysis of clinical trials medical informatics clinical data management

7 Vad är bioinformatik? Sequence analysis Structure analysis Function analysis

8 Vad är bioinformatik? Sequence analysis genome sequencing & assembly & annotation genome comparison phylogeny gene & promoter prediction motif discovery sequence database searching sequence alignment

9 Vad är bioinformatik? Sequence analysis Structure analysis nucleic acid structure prediction protein structure prediction protein structure classification protein structure comparison

10 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

11 metabolic pathways

12 regulatory networks

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

14 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,

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

16

17 databases: Ensembl

18 databases: NCBI

19 Protein 3-D Structure

20 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)!

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 precision medicine understanding: integration, models, mechanisms therapy, drug targets 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 precision medicine understanding: integration, models, mechanisms therapy, drug targets systems medicine

23 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

24 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

25 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

26 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

27 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

28 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

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 precision medicine understanding: integration, models, mechanisms therapy, drug targets systems medicine

30 precision medicine O. Wolkenhauer, Systems biology, University of Rostock

31 clinics and medical research diseases signs and symptoms drugs clinical laboratory measurements clinical images

32 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

33 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

34 Bioinformatics is the ideal tool to integrate data at all levels from molecule to man. Nijmegen Centre for Molecular Life Sciences, Netherlands:

35 "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."

36 "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."

38

39 biomedical data of various sources integrated data visualized data modeled data

40 "A lot of times it's through comparisons and comparisons and comparisons that researchers see an interesting trend..." David Butler

41 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:

42 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.

43 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.

44 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

45 BIA the Bioinformatics Intelligence Agency when should we meet?

46 integrative functional bioinformatics integrative part of future medicine!

47 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

48 Vad är bioinformatik och varför behöver vi det i vården? a bioinformatician's perspectives Dirk.Repsilber@oru.se Functional Bioinformatics, Örebro University

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