Smith, Ortiz Offer Course in Bioinformatics Genome Sequencing

By Purnell T. Cropper | August 31, 2010

Dr. Sheryl T. Smith, Assistant Professor of Biology, is teaching a new course this fall called BI360.1 Bioinformatics. Smith notes that while the Human Genome Project was completed in 2003 and computer modeling is underway on other species, scientists called bioinformatists are increasingly important in accurately unraveling the genetic code of plants and animals.

“Bioinformatics is a relatively new field that has been necessitated by the overwhelming amount of biological data that has been generated through advances in biological techniques,” says Smith. “Technological advances in whole-genome sequencing have surpassed expectations, with nearly 1,000 genomes, including those model systems of S. cerevisiae (yeast), C. elegans (worm), D. melanogaster (fruit fly), and A. thaliana (plant) having been sequenced to date. It is estimated that the sequencing of nearly 5,000 genomes is currently under way.

“The Human Genome Project produced a draft sequence in 2000 and was ‘finished’ to high quality in April 2003. The technology used to produce these sequences has improved dramatically in terms of speed; however, accuracy has been compromised in the process. Computer modeling of predicted genes in newly finished sequences has also fallen short of expectations, being accurate only between 60 to 70 percent of the time. Human ‘finishers’ and ‘annotators’ are now being required in higher numbers each year. Biotech companies requiring trained professionals in bioinformatics now number in the thousands.”

To meet the growing demands for bioinformatists, Smith and Dr. Carlos Ortiz, Professor of Computer Science and Mathematics, developed an interdisciplinary bioinformatics course. The course will be supported through the Genomics Education Partnership founded by Dr. Sarah Elgin at Washington University in St. Louis and funded by the Howard Hughes Medical Institute.

The partnership is a collaborative effort that involves undergraduate students in large-scale, ongoing projects to verify and provide high-quality genome sequences of various species and to annotate those sequences by predicting position and structure of genes and related isoforms. Students will work closely with faculty in semester-long projects, and their data will be reported back to the partnership. Results will be compared to those from students at another university collaborating in the partnership in order to identify inconsistencies, and final data will be reported in future peer-reviewed publications as well as a publicly available database. Students completing high-quality research projects to faculty satisfaction will be included as co-authors on a future publication.

Since projects involve hypothesis formulation and testing, results may be considered as a laboratory-based project from which a Capstone thesis might be derived. Students will gain exposure to topics in Bioinformatics including genome structure, database searching, basics in programs used for gene model prediction and sequence finishing, instruction in Unix, and other related topics. Arcadia University is one of 77 colleges and universities currently collaborating in the Genomics Education Partnership.

“In support of the Bioinformatics course being offered this fall, Dr. Ortiz and I were awarded $19,500 for the establishment of an iMAC laboratory for the Bioinformatics course and other related courses in the future,” says Smith.

The Arcadia University Instructional Technology Committee, according to Dr. Joshua E. Blustein, Associate Professor of Psychology and Chair of the committee, indicated that all faculty on the committee were “very impressed with the interdisciplinary nature of the grant, the strong connection between technology and pedagogy, and the impact the grant will have on providing the foundation for establishing cutting-edge student-faculty collaborative research projects. “The partnership established with Washington University will increase the scholarly index of Arcadia University,” says Blustein.