The Integrative Graduate Education and Research Traineeship (IGERT) program in Bioinformatics at Boston University is a highly successful interdisciplinary training program that has served as a model for other universities. With this renewal award, it will shift research emphasis to focus on biological networks. Research in molecular biology is shifting fundamentally towards the study of complex, multi-component networks that underlie the living cell. These networks are modeled in terms of their component interactions, regulatory properties, sub-networks or pathways, and system dynamics. Important examples include 1) biochemical pathways of metabolism, 2) protein-DNA interactions that regulate gene transcription, and 3) signaling pathways for cellular response to hormones and other molecules. Training will continue to stress computational and mathematical sciences, biology, and biochemistry and will incorporate innovation in an initial year-long research experience to include intensive wet-lab training in high-throughput data generation techniques, a team oriented "grand challenge" bioinformatics research project, and laboratory validation of computational predictions. An international perspective will be fostered through student fellowships for extended visits with collaborating faculty at partner institutions in Germany, Japan, and Israel.
To disseminate successful training methodologies, the Program will sponsor a National Bioinformatics Education Workshop. It will provide undergraduate research opportunities in faculty labs through partnership with Boston University programs targeted to underrepresented groups and it will develop high school outreach activities, curricula and workshops, combining mathematics and biology. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries.
," was awarded to the Boston University Bioinformatics graduate program by the NSF Division of Graduate Education, grant number DGE-0654108, with a total budget of $3,200,000 from 7/2007 to 6/2014. The project partially funded training for 34 PhD students (10 with one year of support, 22 with two years of support, 2 with three years of support). The students included 11 women, and 5 from underrepresented minority groups. Ten of the students had graduated by the end of summer 2014. This was the second IGERT awarded to the BU Bioinformatics program and enabled implementation of major new, innovative training activities, including 1) the Summer Wet-Lab Experience, an extended experimental lab rotation for first-year students in the summer before their classes begin, 2) the Challenge Project, a two-semester, team-based project course for first-year students with open-ended projects involving analysis of high-throughput data derived from faculty mentor labs, 3) skills workshops in scientific communication, job talks, and research fellowship applications, 4) leadership opportunities through participation in the Student Organized Symposium, annual research poster sessions, and K-12 mentoring activities, 5) teaching opportunities through lead instruction in an undergraduate/Masters level bioinformatics applications course and in skills workshops and instruction assistance in several PhD level bioinformatics courses, and 5) international opportunities through annual research workshop participation in Japan and Germany, and extended collaborative research experiences in France, Germany, and Japan. The IGERT training has resulted in 49 publications in refereed journals and 109 conference presentations as of summer 2014. These have described the development of tools and databases to explore such topics as human-virus protein-protein interaction networks, fungal metabolic networks, compendia of functional RNAs (transcriptome) in sea anemones, the accuracy of genetic prediction, analysis of time series data to determine differential gene expression, gene expression profiling techniques for disease biomarker detection, design and experimental assembly of synthetic biology constructs, and discovery of signaling pathways responsible for regulating differentially expressed geness. The Challenge Project has been particularly successful, with three team projects culminating in journal articles, and one 2012-2013 team winning the Best Student Poster award at ISMB 2013, a top international bioinformatics conference. Broader impacts activities linking education and research have included: 1) participation by the PI, IGERT faculty, and IGERT trainees in the SACNAS and ABRCMS undergraduate research conferences (2010-2013) as poster session judges and in roundtable and one-to-one discussions with undergraduates of research and graduate school, 2) multi-year participation by IGERT trainees as elementary and middle school science club mentors and science night coordinators, community science festival volunteers, and undergraduate mentors, 3) participation by the PI in creation of high school bio-math lesson plans (high-throughput sequencing, genomic variation detection, and sequence sorting algorithms) in collaboration with Rutgers University DIMACS and COMAP of Bedford, MA, 4) participation by the PI as a National Judge at the finals of the Siemens Competition (2006, 2007, 2013) for high school STEM research projects related to bioinformatics, and 5) participation by the PI as an instructor to international graduate students, many from second and third world countries, as part of an annual Bioinformatics Short Course sponsored by the Institut Pasteur, Paris, and the European Molecular Biology Organization.
