History of the BCB Program

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Jim Cornette, a faculty member in Iowa State University (ISU's) Department of Mathematics, worked for many years to stimulate interactions between mathematicians and biologists. In the fall of 1997, he arranged a seminar to explore DNA sequence analysis. This weekly seminar attracted about twenty mathematicians, computer scientists and biological scientists, and stimulated remarkable excitement. As a consequence, during the 1997-1998 academic year the Iowa Computational Biology Laboratory (ICBL) was founded to provide an organized focus and a vehicle for promoting these activities. Members of the ICBL initiated student training in computational molecular biology, including workshops, seminars and a new graduate course in the subject. Twenty-two students took the first offering of Math/Gen/ComS 594X Computational Molecular Biology in the spring of 1998.

The first step toward a graduate program in BCB was made in the spring of 1998, when three existing graduate majors - Computer Science, Genetics, and Mathematics - cooperatively agreed to offer complementary "Areas of Specialization" in Computational Molecular Biology. An important second step took place when an ad hoc committee submitted a comprehensive report outlining recommendations for Iowa State University to position itself as a premier research institution in the plant sciences. The number one priority was to hire several computational biologists to work with biological researchers on the various plant genome projects to enable better access to and use of the rapidly growing body of plant genomic data.

The momentum continued to build during 1998-1999. In February 1999, the Department of Physics and Astronomy offered a faculty position to a computational structural biologist and candidates were interviewed for a joint position in bioinformatics by the departments of Statistics and Zoology & Genetics. A Computational Molecular Biology Curriculum Committee, chaired by Stephen Willson (Mathematics), and including members of ICBL and other interested faculty, developed a suggested curriculum. This proposed curriculum served as the basis for the Bioinformatics and Computational Biology Curriculum and Training Plan. Several courses and seminars in bioinformatics were offered in Spring 1999. These included the second offering of Gen/Math/ComS 594 (taught by new hire, Volker Brendel, Zoology & Genetics), and two new seminar courses, Gen 590 Topics in Molecular Biology for Computational Scientists (Drena Dobbs, Zoology & Genetics) and ComS 610 Intelligent Systems in Molecular Biology (Vasant Honavar, Computer Science). The curriculum expanded to 16 interdisciplinary courses.  Currently, BCB teaches four core courses.  Other courses related to our curriculum include a growing list of interdisciplinary courses.

In the spring of 1999, a proposal was put before the Iowa Board of Regents to establish the Bioinformatics and Computational Biology interdepartmental graduate major. The stated objectives of the new major were to: provide broad and robust graduate student training in bioinformatics and computational biology; enhance the national and international reputation of Iowa State University in the field of bioinformatics and computational biology; foster further intellectual exchange and research collaborations among Iowa State bioinformatics and computational biology faculty, students and staff; and provide a formal entity for seeking broad-based resources for the support of lecture series, retreats, graduate assistantships, postdoctoral fellowships and various graduate student prizes for excellence in bioinformatics and computational biology research. The Board of Regents approved the proposal, effective spring 2000, and the BCB program enrolled its first students that semester.

To support the budding graduate program, bioinformatics faculty submitted several interdisciplinary grant proposals, including a successful $2.7 million National Science Foundation Integrative Graduate Education and Research Traineeship (NSF IGERT) proposal (Dan Voytas, P.I.) for graduate training in computational molecular biology. The IGERT grant provided research assistantships for four new graduate students and two postdoctoral fellows each year for a total of five years (beginning in July 1999). An additional source of funding for students majoring in BCB was obtained through the efforts of Jim Cornette and the ICBL. Pioneer Hi-Bred International committed up to $500,000 for graduate and postdoctoral fellowships in computational molecular biology over a five-year period (beginning in January 1999). In Spring 2002, a group of animal scientists were successful in obtaining $1.7 million in support from the USDA for graduate training in bioinformatics. In Fall 2002, this award supported seven two-year graduate fellowships for each of three years.

Whereas bioinformatics graduate education became formalized through the creation of the interdepartmental graduate program, bioinformatics research on campus was institutionalized under the auspices of the Plant Sciences Institute. This process began in 1999 when the University funded the establishment of the Iowa Genomic Frontier Center (IGF, Patrick Schnable, Director), which provided support facilities for high-throughput DNA sequencing, microarray expression analysis, high-throughput protein identification and analysis (proteomics), robotics components, and computational support. Both the IGF and the ICBL subsequently became organized into four of the nine research centers that constitute the Plant Sciences Institute. The ICBL was transformed into the Baker Center for Bioinformatics and Biological Statistics, which is supported by a gift from the trust of Laurence H. Baker. The Baker Center provides an organizational framework for bioinformatics research on campus, including the requisite computer equipment, software and support services.

Advances in genome sequencing and molecular genetics now enable scientists to explore complex biological problems using an integrated systems-wide genomics approach. Two additional Centers were created to expand research efforts in the bioinformatics and computational biology areas at ISU. The Center for Integrated Animal Genomics (CIAG) was dedicated to developing state of the art techniques in computational, molecular and cell biology to improve animal and human health. CIAG, one of the Presidential initiatives at ISU, builds on the strengths of world-class programs in animal and microbial genetics, bioinformatics, biotechnology and the life sciences.

The Center for Computational Intelligence, Learning and Discovery (CCILD) is devoted to the development of sophisticated distributed informatics infrastructure, databases, knowledge bases, ontologies and sophisticated data mining algorithms and software to support integrative collaborative research in bioinformatics and computational and systems biology. Collaborative research projects involved faculty of the CCILD, CIAG, the Baker Center and the Computational Molecular Biology (CMB) training group. Research projects focused on information integration, discovery of macromolecular sequence-structure-function relationships and discovery of biomolecular signaling pathways. These projects offered a broad range of research-based training opportunities for BCB Graduate Students. Genomic and Computational Systems Biology approaches became a leading area of emphasis in the program at that time and a Systems Biology symposium was held at Iowa State in June, 2009.

Beginning in 1999, the NSF-IGERT training grant provided research assistantships to 29 graduate students with 17 BCB fellows.  Another 5 year training grant was approved in 2005. Of the 21 IGERT research assistantships provided by it, 15 were BCB graduate students.

With our faculty's efforts to collaborate across discipline, our interdisciplinary graduate program has a bright future at Iowa State: 

  • The University's recent emphasis on faculty hires in Big Data brought our program more than 10 new individuals trained in BCB to our faculty membership.
  • Work to secure another training grant was successful and a $3 million NSF GRT in Predictive Plant Phenomics was obtained by several BCB faculty. 
  • A BCB cluster hire approved by Iowa State's College of Liberal Arts and Sciences, in Spring, 2014, is underway.  Currently a BCB faculty search in the area of mathematical biology is underway in the Math Department. Faculty searches in the Statistics and Computer Science Departments for new BCB faculty were unsuccessful.

Congratulations for all the great efforts of our chair and associate chair: Dennis Lavrov, EEOB, and Carolyn Lawrence, GDCB, and Supervisory Committee members:  Oliver Eulenstein, Computer Science; Sue Lamont, Animal Science, Matt Hufford, EEOB, Julie Dickerson, ECPE; Karin Dorman, Stat, and Bob Jernigan, BBMB.  Thank you !

 

Participating Departments

 

Cooperating Programs

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