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 | Due to advances in molecular biology over the past fifteen years, biological questions can now be approached at new levels of complexity. Rather than dissecting individual components of a biological system, system-wide analytical approaches can be pursued. A critical factor in this paradigm shift has been the availability of vast amounts of genomic sequence data. Studies of gene evolution, for example, are no longer restricted by incomplete or fragmentary data sets. Access to complete genomic sequences, coupled with rapidly accumulating data related to RNA and protein expression patterns, has also made it possible to envision new ways to understand how genes contribute to complex phenotypes. With this broader focus, it is now possible to begin to address how entire biochemical and developmental pathways are organized and regulated. Implicit in the understanding of complex phenotypes is the ability to discern and predict function from sequence information. At Iowa State University (ISU), we have established a Computational Molecular Biology (CMB) Training Group. The goal of the training group is to provide Ph.D. and postdoctoral students with the necessary tools and expertise to approach biological questions from a systems-wide perspective. This training is largely focused on preparing students to appreciate and utilize the richness of biological information in the accumulating sequence and expression databases. Such preparation requires a multidisciplinary approach, involving not only diverse expertise in the biological sciences - from evolutionary to structural biology - but also expertise from disciplines in which biologists typically have only rudimentary training. For example, a solid understanding of aspects of mathematics, computer science, and statistics will be required for systems-wide approaches, particularly to develop novel and better computational tools for research under this new paradigm. This CMB training group consists of a diverse group of highly interactive scientists who are enthusiastic about the challenges and opportunities presented by modern biology. As illustrated in the diagram, these scientists have expertise in four interdependent research areas. The top triangle represents the ISU faculty involved in genomics initiatives with plants, animals and microbes. These scientists, along with their colleagues and collaborators from around the world, are producing the prodigious quantities of sequence and expression data that make the systems-wide approaches possible. The bottom two triangles represent ISU faculty with expertise in genome evolution - understanding patterns and processes of change that occur among genes and genomes over time - and macromolecular structure and function - discerning structural and functional meaning from DNA, RNA and protein sequences. Integrating these two different biological perspectives will make it possible to obtain new insights about biological systems from genomics data. The triangles representing the three disciplines overlap to form the fourth keyresearch area - bioinformatics. Bioinformatics provides the tools and methods of analysis necessary to integrate genomics data to understand biological systems at new levels of complexity. The strength of the CMB Training Group is its multidisciplinary research environment. Members of the training group include mathematicians, physicists, biochemists, structural, evolutionary and molecular biologists, statisticians and computer scientists. The CMB training program is structured to ensure that our students are exposed to the CMB faculty's diverse talents and perspectives. During the first year, laboratory rotations with three CMB faculty provide Ph.D. trainees with first-hand experience in both "wet" and "dry" lab environments. To provide exposure to computational biology in an industrial setting, fellows also have the opportunity to work as interns with industrial partners (such as Pioneer Hi-Bred International) during the summer semester, either prior to or after the first academic year. In the second year, fellows initiate a multidisciplinary research project under the guidance of a team of two mentors: one a biologist and one a computational scientist/mathematician. This intensive emphasis on collaborative research training is balanced by a core group of courses in biological and computational sciences and several newly developed specialized courses at the interface of these disciplines. Among the latter are courses designed to provide either biologists with accelerated training in mathematics or computer scientists/mathematicians with accelerated training in molecular biology. Postdoctoral fellowships will further enable cross-disciplinary training. For example, a student with a Ph.D. in molecular biology would be required to select a postdoctoral mentorin computer science/mathematics. The CMB Training Group has grown out of a variety of faculty andstudent initiatives that have taken place at ISU over the past several years. In the fall of 1997, collaborating faculty from mathematics, computer science and life sciences departments formed the Iowa Computational Biology Laboratory (ICBL). Members of the ICBL met weekly during the 1997-98 academic year and initiated student training in computational molecular biology. In the spring of 1998, ICBL faculty members coordinated a workshop: "Advances and Challengesin Computational Biology". That spring, ICBL members also developed and staffed a new graduate course in Computational Molecular Biology. A new Ph.D. Area of Specialization in Computational Molecular Biology was created and adopted by three departments and graduate programs (Mathematics, Computer Science, Genetics), and in 1999-00, a new interdepartmental Ph.D. program was launched in Bioinformatics. Four departments (Zoology & Genetics, Mathematics, Computer Science and Agronomy) pooled resources and hired three new computational biologists. A structural biologist with computational interests was also hired by the Dept. of Biochemistry and Biophysics. These hires were supported by the State Legislature, which added new funds to the University budget specifically for these appointments ($200K per year). In 2000, an additional hire in bioinformatics was made jointly by the Zoology & Genetics and Statistics Departments. Interest in Computational Biology is also high among ISU students. Computer science courses are taken by about one third of Genetics graduate students, and several have initiated double majorsin Genetics and Computer Science. Three faculty (two biologists and one computer scientist) have taken advantage of University on-campus sabbatical opportunities to train in Computational Biology as a second discipline. The CMB Training Group builds on these initiatives and provides a mechanism to formalize student training, to strengthen newly forged collaborations among faculty, and to bring new faculty and new expertise into the fold. | |
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