1. August 19, 2002Slide 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

2. Slide 2 Some relevant biology New language of biology Bioinformatics research at Virginia Tech Getting into bioinformatics at Virginia Tech Overview

3. August 19, 2002Slide 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).

4. August 19, 2002Slide 4 Transcription and Translation DNAmRNAProtein TranscriptionTranslation

5. August 19, 2002Slide 5 DNA Strand A= adenine complements T= thymine C = cytosine complements G=guanine

6. August 19, 2002Slide 6 RNA Strand U=uracil replaces T= thymine

7. August 19, 2002Slide 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.

8. August 19, 2002Slide 8 Translation to a Protein Unlike DNA, proteins have three-dimensional structure Protein folds to a three-dimensional shape that minimizes energy

9. August 19, 2002Slide 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

10. August 19, 2002Slide 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

11. August 19, 2002Slide 11 The biological role of individual genes; Mechanisms underlying the regulation of their expression; Regulatory interactions among them. Functional Genomics

12. August 19, 2002Slide 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

13. August 19, 2002Slide 13 Gene Expression Varies

14. August 19, 2002Slide 14 Networks and Pathways: Glycolysis, Citric Acid Cycle, and Related Metabolic Processes

15. August 19, 2002Slide 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

16. August 19, 2002Slide 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

17. August 19, 2002Slide 17 NutriPotato Microarray technology used to investigate genes responsible for stress resistance and for the production of nutrients in Andean potato varieties.

18. August 19, 2002Slide 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.

19. August 19, 2002Slide 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

20. August 19, 2002Slide 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

21. August 19, 2002Slide 21 CS 5984: Algorithms in Bioinformatics Genetic and physical mapping Sequence comparison Sequence alignment Probabilistic models for molecular biology Fragment assembly Genome rearrangements Evolutionary tree (re-)construction