Applied Bioinformatics for Exploring College Freshmen and High School Students
Bioinformatics is a growing professional field characterized by the combination of skills required in the fields of biology, computer science, and information technology. Generally, bioinformatics programs offered at the undergraduate level and beyond focus on preparing their students to develop programs that will be used to analyze and organize data generated by biologists. There is an apparent disconnect between the programs being developed and biologists willing to use them. This paper describes the field of bioinformatics and attempts to establish a need for a course that teaches students how to use various tools and programs currently available for use in analyzing biological data, primarily in the form of genes and proteins. Additionally, a course design and a framework is presented that can be easily adopted by interested instructors.
Informatics, Bioinformatics, Undergraduate, Biotechnology, Bioengineering
US Department of Energy Human Genome Program. 2003. Genomics and Its Impact on Science and Society. http://web.ornl.gov/sci/techresources/Human_Genome/publicat/primer2001/primer11.pdf.
Sczyrba A., Konermann S., and Giegrach R. 2008. Two interactive Bioinformatics courses at the Bielefeld University Bioinformatics Server. Briefings in Bioinformatics. 9 (3), pp. 243-249.
Iratxeta-Perez, C., Andrade-Navarro, M. A., and Wren, J. D. 2006. Evolving research trends in bioinformatics. Briefings in Bioinformatics. 8 (2), pp. 88-95.
National Institute of Health. 2000. NIH Working Definition of Bioinformatics and Computational Biology.
Hogeweg, P. 2011. The Roots of Bioinformatics in Theoretical Biology. PLoS Computational Biology. 7 (3), e1002021.
Burhans, D. T., DeJongh, M., Doom, T. E., and LeBlanc, M. 2004. Bioinformatics in the Undergraduate Curriculum: Opportunities for Computer Science Educators. In Proceedings of the 35th SIGCSE technical symposium on Computer science education (SIGCSE '04). ACM, New York, NY, USA, 229-230. DOI=http://dx.doi.org/10.1145/971300.971381.
Pevzner, P. and Shamir R. 2009. Computing has Changed Biology – Biology Education Must Catch Up. Science. 325 pp. 541-542.
Bednarski, A. E., Elgin, S. C. R., and Pakrasi, H. B. 2005. An Inquiry into Protein Structure and Genetic Disease: Introducing Undergraduates to Bioinformatics in a Large Introductory Course. Cell Biology Education. 4 (3). pp. 207-220.
Crick, F. 1970. The Central Dogma of Molecular Biology. Nature. 227. pp. 561-563.
Reiger, J. C., Shultz, J. W., and Kambic, R. E. 2005. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Procedings of the Royal Society B. 272. pp. 395-401.
Sakamoto, M. and Ruta, M. 2012. Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity. PLoS ONE. 7 (7). e39752.
Offner, S. 2010. Using the NCBI Genome Databases to Compare the Genes for Human & Chimpanzee Beta Hemoglobin. The American Biology Teacher. 72 (4) pp. 252-256.
Hardison, R. C. 2012. Evolution of Hemoglobin and its Genes. Cold Spring Harbor Perspectives in Medicine. 2 (12) a011627.
Sundaresan, S. S., Ramesh, P., and Ponnuswamy, M. N. 2009. Crystal Structure of hemoglobin from mouse (Mus musculus) and 2.8. To be published. doi: 10.2210/pdb3hrw/pdb.
Oksenberg, D., Dufu, K., Patel, M. P., Chuang, C., Li, Z., Xu, Q., Silva-Garcia, A., Zhou, C., Hutchaleelaha, A., Patskovska, L., Patskovsky, Y., Almo, S. C., Sinha, U., Metcalf, B. W., Archer, D. R. 2016. GBT440 increases haemoglobin oxygen affinity, reduces sickling and prolongs RBS half-life in a murine model of sickle cell disease. British Journal of Haematology. 175 (1) pp. 141-153.
Khoshouei, M., Radjainia M., Baumeister, W., and Danev, R. 2016. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate. bioRxiv. Preprint.