Introduction to Bioinformatics: Lecture I An Overview of the Course

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Introduction to Bioinformatics Lecture I
An Overview of the Course

• Jarek Meller
• Division of Biomedical Informatics,
• Childrens Hospital Research Foundation
• Department of Biomedical Engineering, UC

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Outline of the outline lecture

• Bioinformatics as hypothesis generator for
  biomedical research in the postgenomic era
• Bioinformatics at the University of Cincinnati
  Childrens 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

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Bioinformatics as hypotheses generator
0111010010110001101
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.
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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

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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

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Bioinformatics at the UC and CHRF
Research and Resources
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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

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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

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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)
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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 Transcription Factors binding sites
? TRAFAC server http//trafac.cchmc.org
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Proteomics

• Studying protein expression, structure,
  interactions, pathways etc.
• Rashmi Hedge (CHRF)
• Mark Rance (UC)
• Patt Limbach (UC)
• Bruce Aronow (CHRF)
• Michael Wagner (CHRF)
• JM

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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 ?
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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 server http//sable.cchmc.org POLYVIEW
server http//polyview.cchmc.org
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Machine learning and pattern recognition

• JM
• Michael Wagner
• Rafal Adamczak
• Mario Medvedovic

Fishing for patterns and fingerprints that
correlate with phenotypes and biological processes
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Genomic fingerprints of disease states
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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

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Summary of current resources
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
http//genome.uc.edu http//info.chmcc.org http//
folding.chmcc.org http//www.cincinnatichildrens.o
rg/research/cores/default.htm
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Web resources and materials for the course

• 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

http//folding.chmcc.org http//folding.chmcc.org
/protlab/protlab.html http//folding.chmcc.org/int
ro2bioinfo/intro2bioinfo.html