1. Graduate Opportunities in Bioinformatics By Tristan Butterfield Alternative Career Presentation Senior Seminar, 25.10.2005

2. Biowhat? Bioinformatics is a sub-field of the Biological Sciences Bioinformatics is highly interdisciplinary and draws upon the following areas of study to solve biological problems: Applied Mathematics Statistics Computer Science Also referred to as Computational Biology

3. The Emergence Of Bioinformatics With the discovery of DNA came a desire among biologists to understand how genetic structure affects the biological traits of organisms Sequencing is not sufficient (95% of human genome is “junk” DNA) Genes must be identified and correlated with the functions of their corresponding proteins Biological phenomena must then be linked to protein identity, structure, and genomic origin

4. The Human Genome Project (HGP) 15-year project started in 1986 to sequence the human genome and identify all relevant genes The human genome consists of 3 billion base pairs and roughly 25,000 genes (gene identification is still under progress) Obviously, the amount of data produced by the HGP is immense! As a result, powerful new data management and analysis methods were developed These methods were precursors to current research in bioinformatics

5. Recent progress in several sub-fields of biology is resulting in a boom in database size and complexity Consequently, there is a great need in many areas of biology for efficient database management and new computer-based analytical techniques In practice, bioinformaticians manage and analyze large biological databases using a combination of their knowledge of computer science, statistics, and biology

6. Current Problems in Bioinformatics Sequence alignment Gene finding Genome assembly Protein structure alignment Prediction of Gene expression Protein-protein interactions Modeling of evolution Example Problem: Gene Expression DNA Microarray: ~57,000 Sites

7. Graduate Studies Because bioinformatics requires knowledge of biology, statistics, and computer science, many graduate students must fill in the holes in their education during the first 1-2 years of grad school There are no departments of bioinformatics Research in bioinformatics typically takes place within the context of a group dedicated to molecular biology, genetics, or biochemistry Degree programs in bioinformatics are plentiful, but because we, as physics majors, are lacking academic preparation for graduate work in this area, the first step to becoming involved is to contact the bioinformatics group here at ND

8. Bioinformaticians @ ND Frank H. Collins (Professor of Biology) Research focuses on the genetics of arthropod (mosquitoes) vectors of human pathogens Robert Bruggner, Graduate Student for Collins ND Undergraduate, Computer Science Had no prior Biology education Enrolled in the molecular biology curriculum Current research: 1. Write programs for gene prediction 2. Create computer system to manage online biological data library Contact: Collins, 313 Galvin Bruggner, 325 Galvin

9. Graduate Study Elsewhere Molecular Biology Rankings: 1. Harvard 2. Stanford 3. MIT 4. Berkeley 5. Johns Hopkins 6.Princeton, UC San Fransisco 8.Cal Tech 9.Yale 10.Texas SW, Medcenter-Dallas, Wisconsin, Washington University Full List of Programs: http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_12-14-04.htm http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_12-14-04.htm Useful Site Provided by UCSC: http://www.soe.ucsc.edu/programs/bioinformatics/graduate/faq.html http://www.soe.ucsc.edu/programs/bioinformatics/graduate/faq.html

10. Career Opportunities Opportunities not just limited to academia and teaching; the biotech boom created a huge demand for computer science professionals with an understanding of biological systems Potential employers include both large corporations and small bio-”boutiques” Online Employment Resources: International Society for Computational Biology, job listingsInternational Society for Computational Biology, job listings biotech find bioplanet BioSpace Career Center jobsearchtech bio.com career center Hire bio Canadian bioinformatics jobs biotech findbioplanet BioSpace Career Centerjobsearchtechbio.com career centerHire bio Canadian bioinformatics jobs International Society for Computational Biology, job listingsbiotech findbioplanet BioSpace Career Centerjobsearchtechbio.com career centerHire bio Canadian bioinformatics jobs

11. Conclusions Bioinformatics is a multi-disciplinary, highly collaborative field of study which relies on knowledge of biology, statistics, applied mathematics, and computer science There are many degree programs but, as students with a background in physics, we should expect degree completion to take a bit longer than usual Job opportunities are more than plentiful for qualified applicants (extremely good salary)

12. References Private Communication. Sharon Graw, Asst. Research Professor, Eleanor Roosevelt Institute and University of Denver, 23.10.2005. Private Communication. Robert Bruggner, Graduate Student, University of Notre Dame, 24.10.2005. <www.wikipedia.org>