Bioinformatics Research and Resources at the University of ...

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2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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JM
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http://folding.chmcc.org

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Introduction to Bioinformatics: Lecture I


An Overview of the Course



Jarek Meller


Division of Biomedical Informatics,

Children’s Hospital Research Foundation

& Department of Biomedical Engineering, UC

JM
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http://folding.chmcc.org

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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

& 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
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http://folding.chmcc.org

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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
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http://folding.chmcc.org

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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



JM
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http://folding.chmcc.org

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Other “definitions”




Subject or body of research


e.g. google
bioinformatics and simply digest the
2
ML (
1
ML=
10
6

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
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http://folding.chmcc.org

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Bioinformatics at the UC and CHRF:


Research and Resources


JM
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http://folding.chmcc.org

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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




JM
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http://folding.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

JM
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http://folding.chmcc.org

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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)

JM
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http://folding.chmcc.org

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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

JM
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http://folding.chmcc.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


JM
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http://folding.chmcc.org

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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


JM
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http://folding.chmcc.org

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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


JM
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http://folding.chmcc.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

JM
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http://folding.chmcc.org

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Genomic fingerprints of disease states

JM
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http://folding.chmcc.org

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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

JM
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http://folding.chmcc.org

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Summary of current resources

http://genome.uc.edu

http://info.chmcc.org

http://folding.chmcc.org

http://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
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http://folding.chmcc.org

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Web resources and materials for the course


http://folding.chmcc.org

http://folding.chmcc.org/protlab/protlab.html

http://folding.chmcc.org/intro
2
bioinfo/intro
2
bioinfo.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