What is Bioinformatics?

Bio molecular biology Informatics computer science Bioinformatics solving problems arising from biology using methodology from computer science

Human Genome Project

Identify the approximate 20,000-25,000 genes in human DNA. Store this information in databases..

Some Facts
97% of DNA in the human genome has no known functions Over 2.000 article on endocrine per month

Bio- & Medical Informatics Differences - Gaps

Medicine Genomics

Medicine + Informatics = Medical Informatics

Informatics

Genomics + Informatics = Bioinformatics

What is Biomedical Informatics (BMI) ?

Medicine

Genomics

Medical Informatics + Bioinformatics = Biomedical Informatics

Informatics

Gene Bank Med Reference Drug Activities

REACTOME
Pathway : diseases mechanism drug data bases chemical data bases

SNP data bases

Mutant Data bases Metabolomic

Structure search in SciFinder

Retrieved 4000 papers

(refine search only MS and MALDI)

Applications of Bioinformatics
Medical science
Drug design Gene therapy Sequence analysis of proteins and DNA Analysis of microarrays Proteomics Genomics Molecular structure Analysis and simulation of metabolic networks

Applications of Bioinformatics : DRUG VACCINE DIAGNOSTIC DESIGN

Drug target Identification Virtual Screening Epitope Mapping

Applications of Bioinformatics : Gene Therapy

RNAi Target Prediction Antisense Target Prediction Specific Target for Gene Insertion

Applications of Bioinformatics :
Sequence analysis of proteins and DNA
Mutation analysis Structure analysis 3D Aligment: Structural change due to Mutation

Applications of Bioinformatics :
Analysis of microarrays
Gene expression level

analysis Sequencing by hybridization Mutation detection

Systems Biology

Genomics, Proteomics & Systems Biology

Genomics Proteomics

Systems Biology 1990 1995 2000 2005 2010 2015 2020

What is Systems Biology?

Systems Biology - Systems biology is the

study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions. The integration of genomics, proteomics, metabolomics & modeling

The Goal: Predictive, Preventative and

Personalized Medicine -- Leroy Hood

Whats it good for?

Basic Science/Understanding Life Predicting Phenotype from Genotype Understanding/Predicting Metabolism Understanding Cellular Networks Predicting Disease Outcome/Prognosis Understanding Pathogenicity/Toxicity Predicting Adverse Drug Reactions Improving Medical Efficiency/Efficacy

Systems Biology is Multidisciplinary

Going From Omics to Metrics

Genomics Genometrics Proteomics Proteometrics Metabolomics Metabometrics Phenomics Phenometrics Bioinformatics Biosimulation

Quantify, quantify, quantify

Going From Networks in vivo to Networks in silico

Going From Model Systems to Medicine

Systems Biology in Medicine

Still in its infancy Ethnopharmacology & traditional meds Integrated biodiagnostics (combined microarray, ICATMS and metabolite profiles multicomponent biomarkers) Adverse drug response prediction and monitoring (personalized medicine) Understanding complex metabolic diseases (cachexia, obesity, diabetes)

Clinical Lab Medicine Leads the Way

The Pyramid of Life

Metabolomics
1400 Chemicals

Proteomics
2500 Enzymes

Genomics

25,000 Genes

Limitation of Genome Project

Genomic theory : 1) Discovery of the gene related with a specific disease 2) Discovery of the protein related with the gene

Unsuccessful !!!! Reason : fundamental failure to understand biological complexity

Why ?
Problem 1 : the function of a gene is NOT specified in the DNA language Problem 2 : each gene plays roles in MULTIPLE functions Problem 3 : each function arises from co-operation of MANY genes

Problem 4 : function also depends on important properties NOT specified by

genes - properties of water, lipids, self-assembly etc

Problem 5 : nature has built-in fail-safe redundancy - this ONLY emerges at

the functional level

Pre-Genomic
Reductionist (DNA or RNA or Protein) Observational/ phenomenological Generally qualitative and non-numeric Hypothesis driven Cellular Molecular Organism

Post-Genomic
Global/ holistic Systems approach (DNA and RNA and Protein) Quantitative and highly numeric Cellular Organism Molecular

Not only hypothesis driven but also data driven