jm - 1 introduction to bioinformatics: lecture i an overview of the course jarek meller jarek...
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JM - http://folding.chmcc.org 1
Introduction to Bioinformatics: Lecture I An Overview of the Course
Jarek MellerJarek Meller
Division of Biomedical Informatics, Division of Biomedical Informatics, Children’s Hospital Research Foundation Children’s Hospital Research Foundation & Department of Biomedical Engineering, UC& Department of Biomedical Engineering, UC
JM - http://folding.chmcc.org 2
Outline of the outline lecture
Bioinformatics as hypothesis generator for
biomedical research in the postgenomic era Bioinformatics at the University of Cincinnati
& Children’s Hospital Research Foundation: research and resources
Introduction to Bioinformatics course: problems and case studies, web and Protein Modeling Lab resources, syllabus and some practical issues
JM - http://folding.chmcc.org 3
Bioinformatics as hypotheses generator
Making sense of massive amounts of genomic, proteomic etc. information in order to facilitate further experiments by data mining and inference, modeling and computer simulations.
JM - http://folding.chmcc.org 4
Some more “precise” definitions
“Roughly, bioinformatics describes any use of
computers to handle biological information” “In practice the definition used by most people is
narrower; bioinformatics to them is a synonym for "computational molecular biology“ -- the use of computers to characterize the molecular components of living things.”
“The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.”
More: http://bioinfomatics.org
JM - http://folding.chmcc.org 5
Other “definitions”
Subject or body of research – e.g. google bioinformatics and simply digest the 2 ML (1 ML= 106 Links) or so …
Methods and approaches: computational paradigm in molecular biology and biomedical research
Institutional boundaries – take a body of research from all the scientific institutions having “bioinformatics” in their name
Let us have look at local bioinformatics resources
JM - http://folding.chmcc.org 7
Pneumocystis Genome Project
Sequencing the genome of a fungal pathogen causing Pneumocystis pneumonia: towards novel drug targets and therapies.
Melanie Cushion (VA/UC) George Smulian (VA/UC) JM
http://pneumocystis.cchmc.org
UC/CHRF sequencing core:
http://dna.chmcc.org
JM - http://folding.chmcc.org 8
Microarray-based gene expression studies
Numerous studies on genome-wide expression profiles to identify interesting targets and elucidate protein pathways.
Bruce Aronow (CHRF) Mario Medvedovic (UC/CHRF) Yizong Cheng (UC)
CHRF Affymetrix GeneChip core
UC Genomics and Microarray Lab
JM - http://folding.chmcc.org 9
Clustering algorithms for expression profiles
Medvedovic M and Sivaganesan S; Bayesian infinite mixture model based
clustering of gene expression profiles , Bioinformatics 2002
Medvedovic M, Yeung KY, Bumgarner RE; Bayesian mixture model based
clustering of replicated microarray data, to appear in Bioinformatics 2004
GIMM (Gaussian Infinite Mixture Models) Software (M. Medvedovic)
Controls
Poly-Articular JRA Course
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242genes
105 Genes withSignificantly Lower
Expression InPolyArticular
JRA
137 Genes withSignificantly
HigherExpression InPolyArticular
JRA
Individual:Individuals (33 patients + 12 controls)
JM - http://folding.chmcc.org 10
Computational studies of transcription regulation
Jegga AG, Sherwood SP, Carman JW, Pinski AT, Phillips JL, Pestian JP, Aronow BJ;
Detection and visualization of compositionally similar cis-regulatory element clusters in
orthologous and coordinately controlled genes, Genome Research 2002
Detection of TranscriptionFactors binding sites
TRAFAC serverhttp://trafac.cchmc.org
JM - http://folding.chmcc.org 11
Proteomics
Studying protein expression, structure, interactions, pathways etc.
Rashmi Hedge (CHRF) Mark Rance (UC) Patt Limbach (UC) Bruce Aronow (CHRF) Michael Wagner (CHRF)
JM
HIF - 1
Elongin B
Elongin C
V H L
JM - http://folding.chmcc.org 12
Protein expression profiling
Wagner M, Naik D, Pothen A; Protocols for disease classification from mass spectrometry data, Proteomics 9 (2003)
Wagner M, Naik D, Pothen A, Kasukurti S, Devineni R, Adam B, Semmes O and Wright Jr G; Computational Protein Biomarker Prediction: A Case Study for Prostate Cancer, to appear in BMC Bioinformatics (2004)
Searching for disease fingerprints in mass spec profiles
JM - http://folding.chmcc.org 13
Structural and functional annotations for proteins
R. Adamczak, A. Porollo and J. Meller; Accurate Prediction of Solvent Accessibility Using Neural Networks Based Regression, Proteins: Structure, Function and Bioinformatics, to appear (2004)
A. Porollo, R. Adamczak and J. Meller; Polyview: A Flexible Visualization Tool for Structural and Functional Annotations of Proteins, Bioinformatics, to appear (2004)
SABLE serverhttp://sable.cchmc.org
POLYVIEW serverhttp://polyview.cchmc.org
JM - http://folding.chmcc.org 14
Machine learning and pattern recognition
JM Michael Wagner Rafal Adamczak Mario
Medvedovic
Fishing for patterns and fingerprints that correlate with phenotypes andbiological processes
JM - http://folding.chmcc.org 16
Perspectives and future directions
Integration of individual projects and systems biology approach
Predictive medicine using multi-dimensional fingerprints of disease states, risks and optimal treatments
Infrastructure challenges: the Center for Computational Medicine as a regional hub for biomedical research
JM - http://folding.chmcc.org 17
Summary of current resources
http://genome.uc.eduhttp://info.chmcc.orghttp://folding.chmcc.orghttp://www.cincinnatichildrens.org/research/cores/default.htm
UC Center for Genomics and Bioinformatics
UC NMR Core
UC/CHRF Proteomics Core
UC and CHRF sequencing cores
UC and CHRF microarrays cores
CHRF computational infrastructure
JM - http://folding.chmcc.org 18
Web resources and materials for the course
http://folding.chmcc.orghttp://folding.chmcc.org/protlab/protlab.htmlhttp://folding.chmcc.org/intro2bioinfo/intro2bioinfo.html
Protein Modeling Lab
Remote access to PML and the Citrix software
All lectures and other materials available electronically from the PML servers
Electronic tests and homework, web submission interfaces
The web site for the Introduction to Bioinformatics course
Updates
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