Bioinformatics at Virginia Tech
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Transcript of Bioinformatics at Virginia Tech
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August 19, 2002 Slide 1
Bioinformatics at Virginia Tech
David Bevan (BCHM)Lenwood S. Heath (CS)
Ruth Grene (PPWS)Layne Watson (CS)
Chris North (CS)Naren Ramakrishnan (CS)
August 19, 2002
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August 19, 2002 Slide 2
• Some relevant biology
• New language of biology
• Bioinformatics research at Virginia Tech
• Getting into bioinformatics at Virginia Tech
Overview
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August 19, 2002 Slide 3
Some Molecular Biology
•The encoded instruction set for an organism is kept in DNA molecules.
• Each DNA molecule contains 100s or 1000s of genes.
•A gene is transcribed to an mRNA molecule.
• An mRNA molecule is translated to a protein (molecule).
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August 19, 2002 Slide 4
Transcription and Translation
DNA mRNA ProteinTranscription Translation
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August 19, 2002 Slide 5
DNA Strand
A= adenine complements T= thymine
C = cytosine complements G=guanine
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August 19, 2002 Slide 6
RNA Strand
U=uracil replaces T= thymine
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August 19, 2002 Slide 7
Amino Acids
• Protein is a large molecule that is a chain of amino acids (100 to 5000).
• There are 20 common amino acids
(Alanine, Cysteine, …, Tyrosine)
• Three bases --- a codon --- suffice to encode an amino acid, according to the genetic code.
• There are also START and STOP codons.
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August 19, 2002 Slide 8
Translation to a Protein
Unlike DNA, proteins have three-dimensional structure
Protein folds to a three-dimensional shape thatminimizes energy
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August 19, 2002 Slide 9
A new language has been created. Words in the language that are useful today.
Genomics
Functional Genomics
Proteomics
Global Gene Expression Patterns
Networks and Pathways
The Language of the New Biology
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August 19, 2002 Slide 10
• Genome sequencing projects: Drosophila, yeast, human, mouse, Arabidopsis, microbes, …
• Identification of genetic sequences:• Sequences that code for proteins; • Sequences that act as regulatory elements.
Genomics
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August 19, 2002 Slide 11
• The biological role of individual genes;
• Mechanisms underlying the regulation of their expression;
• Regulatory interactions among them.
Functional Genomics
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August 19, 2002 Slide 12
• When a gene is transcribed (copied to mRNA), it is said to be expressed.
• The mRNA in a cell can be isolated and examined using microarrays. Its contents give a snapshot of the genes currently being expressed.
• Correlating gene expression with conditions gives hints into the dynamic functioning of the cell.
Gene Expression
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August 19, 2002 Slide 13
Gene Expression Varies
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August 19, 2002 Slide 14
Networks and Pathways:Glycolysis, Citric Acid Cycle, and Related
Metabolic Processes
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August 19, 2002 Slide 15
Computer Science interacts with the life sciences.
Bioinformatics at Virginia Tech
• Joint research with: plant biologists, microbial biologists, biochemists, cell-cycle biologists, animal scientists, crop scientists, statisticians.• Projects: Expresso; NutriPotato; MURI; Multimodal Networks; Barista; Fusion;
Arabidopsis Genome; Cell-Cycle Modeling• Graduate option in bioinformatics
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August 19, 2002 Slide 16
• Integration of design, experimentation, and analysis
• Data mining; inductive logic programming (ILP)
• Closing the loop
• Drought stress experiments with pine trees and Arabidopsis
Expresso: A Problem Solving Environment (PSE) for Microarray Experiment Design and Analysis
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August 19, 2002 Slide 17
NutriPotato
Microarray technology used to investigate genes responsible for stress resistance and for the production of nutrients in Andean potato varieties.
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August 19, 2002 Slide 18
MURI• Some microorganisms have the ability to
survive drying out or intense radiation.
• Using microarrays and proteomics, we are attempting to correlate computationally the genes in the genomes with the special traits of the microorganisms.
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August 19, 2002 Slide 19
Other Projects
• Multimodal Networks: represent, manipulate, and identify biological networks
• Barista: serves software for Expresso, et al.
• Fusion: visualization via redescription
• Arabidopsis Genome Project: mine the Arabidopsis genome for regulatory sequences
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August 19, 2002 Slide 20
Getting Into Bioinformatics at VT
• Learn some biology: genetics, molecular biology, cell biology, biochemistry (2 courses)
• Study computational biology: CS 5984• Get involved with bioinformatics research
in interdisciplinary teams• Work with biologists to solve their
problems
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August 19, 2002 Slide 21
CS 5984: Algorithms in Bioinformatics
• Genetic and physical mapping• Sequence comparison• Sequence alignment• Sequence alignment• Probabilistic models for molecular biology• Fragment assembly• Genome rearrangements• Evolutionary tree (re-)construction