Graduate Opportunities Graduate Opportunities in Bioinformaticsin Bioinformatics

By Tristan ButterfieldBy Tristan ButterfieldAlternative Career PresentationAlternative Career Presentation

Senior Seminar, 25.10.2005Senior Seminar, 25.10.2005

Biowhat?Biowhat?

Bioinformatics is a sub-field of the Biological Bioinformatics is a sub-field of the Biological SciencesSciences

Bioinformatics is highly interdisciplinary and Bioinformatics is highly interdisciplinary and draws upon the following areas of study to draws upon the following areas of study to solve biological problems:solve biological problems:Applied MathematicsApplied MathematicsStatisticsStatisticsComputer ScienceComputer Science

Also referred to as Computational BiologyAlso referred to as Computational Biology

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

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

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

Current Problems in BioinformaticsCurrent Problems in Bioinformatics

Sequence alignmentSequence alignmentGene findingGene findingGenome assemblyGenome assemblyProtein structure alignmentProtein structure alignmentPrediction of Gene Prediction of Gene expressionexpressionProtein-protein interactionsProtein-protein interactionsModeling of evolutionModeling of evolution

Example Problem: Gene ExpressionExample Problem: Gene Expression

DNA Microarray: ~57,000 Sites

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

Bioinformaticians @ NDBioinformaticians @ NDFrank H. Collins (Professor of Biology)Frank H. Collins (Professor of Biology)

Research focuses on the genetics of arthropod Research focuses on the genetics of arthropod (mosquitoes) vectors of human pathogens(mosquitoes) vectors of human pathogens

Robert Bruggner, Graduate Student for CollinsRobert Bruggner, Graduate Student for CollinsND Undergraduate, Computer ScienceND Undergraduate, Computer ScienceHad no prior Biology educationHad no prior Biology educationEnrolled in the molecular biology curriculumEnrolled in the molecular biology curriculumCurrent research: Current research: 1. Write programs for gene prediction1. Write programs for gene prediction2. Create computer system to manage online 2. Create computer system to manage online

biological data librarybiological data libraryContact: Contact: Collins, 313 GalvinCollins, 313 Galvin

Bruggner, 325 GalvinBruggner, 325 Galvin

Graduate Study ElsewhereGraduate Study ElsewhereMolecular Biology Rankings:Molecular Biology Rankings:

1.1. HarvardHarvard2.2. StanfordStanford3.3. MITMIT4.4. BerkeleyBerkeley5.5. Johns HopkinsJohns Hopkins

6. Princeton, UC San Fransisco8. Cal Tech9. Yale10.Texas SW, Medcenter-Dallas,

Wisconsin, Washington University

Full List of Programs: Full List of Programs: http://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_12-14-04.htmhttp://ils.unc.edu/bmh/bioinfo/Bioinformatics_Programs_Brief_12-14-04.htm

Useful Site Provided by UCSC: Useful Site Provided by UCSC: http://www.soe.ucsc.edu/programs/bioinformatics/graduate/faq.htmlhttp://www.soe.ucsc.edu/programs/bioinformatics/graduate/faq.html

Career OpportunitiesCareer OpportunitiesOpportunities not just limited to academia and Opportunities not just limited to academia and teaching; the biotech boom created a huge teaching; the biotech boom created a huge demand for computer science professionals demand for computer science professionals with an understanding of biological systemswith an understanding of biological systemsPotential employers include both large Potential employers include both large corporations and small bio-”boutiques”corporations and small bio-”boutiques”Online Employment Resources:Online Employment Resources:

International Society for Computational Biology, job listingsInternational Society for Computational Biology, job listings biotech findbiotech find bioplanet bioplanet BioSpace Career Center jobsearchtech bio.com career center Hire bio BioSpace Career Center jobsearchtech bio.com career center Hire bio Canadian bioinformatics jobs Canadian bioinformatics jobs

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

ReferencesReferences

Private CommunicationPrivate Communication. Sharon Graw, Asst. . Sharon Graw, Asst. Research Professor, Eleanor Roosevelt Institute Research Professor, Eleanor Roosevelt Institute and University of Denver, 23.10.2005.and University of Denver, 23.10.2005.

Private Communication.Private Communication. Robert Bruggner, Robert Bruggner, Graduate Student, University of Notre Dame, Graduate Student, University of Notre Dame, 24.10.2005.24.10.2005.

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