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BIBM 2009 Education Workshop Nov 2, 2009 Moderators: Sun Kim and Dong Xu Srinivas Aluru Mehl Professor of Computer Engineering Iowa State University Bajaj Chair Professor of Computer Science and Engineering Indian Institute of Technology Bombay Research: Computational genomics, systems biology, parallel methods for computational biology Education and Mentoring: Chair (2005-2007) & Assoc. chair (2003-2005), Bioinformatics and Computational Biology Ph.D. program at Iowa State Involved in two NSF IGERT Grants in Bioinformatics Taught at NSF/NIH funded summer school at Iowa State Produced a comprehensive handbook 4 Ph.D.s in last 3 years (2 working as faculty) Jean-Francois Tomb Manager, Bioinformatics DuPont CR&D 14 years of research and development in Genomics and Bioinformatics Current focus on microbial engineering in the context of Industrial Biotechnology (Biofuels) o Genome annotation, Metabolic reconstruction, Flux analysis, Network visualization o Genome evolution under selective pressure o Protein engineering Lecturer on genomics and bioinformatics at UPenn (>5 years) Mentor to members of the bioinformatics group, summer interns and experimental biologists Jean Gao, PhD • Associate Professor, Computer Science Department University of Texas at Arlington • Bioinformatics Expertise and Research – High-throughput data analysis (mass spectrometry, protein/gene microarray) – Molecular/Cellular Image Processing • Bioinformatics Education and Mentoring – Graduated Students: PhD: 3; MS: 3 – Current Students: PhD: 4; MS: 2; Undergraduates: 2 – GirlEngineering Summer Camp Jake Y. Chen, PhD Assistant Professor of Informatics and Computer Science (2004-present) Indiana University – Purdue University Indianapolis • Educational/Professional Background – Founding Director, Indiana Center for Systems Biology and Personalized Medicine, Indianapolis, IN (2007-present) – Head of Computational Proteomics, Myriad Proteomics, Inc., Salt Lake City, UT (2002-3) – Bioinformatics Computer Scientist, Affymetrix, Inc., Santa Clara, CA (1998-2002) – MS/PhD in Computer Science & Engineering, BS in Biochemistry and Molecular Biology • Bioinformatics mentorship experience: – Led a department of 7 bioinformaticians to map the human proteome (2002-3) – Supervised 6 postdocs, >20 MS as thesis committee chair/advisors, >8 PhD candidates, 4 undergrads summer interns – Participated in training of bioinformatics students internationally (China) – Students/postdoc employed at Harvard Medical School, Eli Lilly, Dow Agrosciences, and biotech companies Majid Masso Postdoctoral Fellow, Laboratory for Structural Bioinformatics Department of Bioinformatics and Computational Biology George Mason University, Manassas, Virginia • Training: mathematician turned computational biologist • Protein structure analysis / structure – function relationships • Computational mutagenesis (modeling structural changes) • Machine learning (predicting mutant functional changes) • Teaching: university and community college faculty • Courses: math at both levels, bioinf. at graduate level • Mentoring: upper-level undergraduate bioinf. research projects • Co-mentoring: bioinf. student theses / dissertation research Jeffrey A. Martin Graduate Student Georgia Institute of Technology Bioinformatics Experience • First began studying Bioinformatics in 2004. • Completed Bachelor of Science in Bioinformatics in 2006. • Currently in second-year of graduate Bioinformatics program at Georgia Tech. • Current research (Advisor – Mark Borodovsky, Ph.D.): – Analysis of next-generation RNA-Seq sequencing data from the SOLiD platform. – Application of machine-learning algorithms to infer gene expression levels and operon structures. Experience in Education and Mentoring • Teaching Assistant for the graduate-level Bioinformatics course at Georgia Tech. Three Discussion Topics 1. Bioinformatics education and curriculum 2. Bioinformatics from industry perspective 3. Women in Bioinformatics Discussion topic 1 Bioinformatics education and curriculum: • Student educational background (CS vs. Biology) and recruitment • Training tailored for career goals • Teaching exploratory vs. rigorous approaches • Problem-based learning (Jianlin Cheng, University of Missouri) • Bioinformatics as an interdisciplinary science: a synergistic but independent science. • Increasing the impact of bioinformatics research (eg., translational bioinformatics) Discussion Topic 2 Bioinformatics from industry perspective • Impact of bioinformatics research on industry • How does bioinformatics education meet the need of industrial research? Discussion Topic 3 Women in Bioinformatics • Recruiting women in bioinformatics is better than in computer science and electrical engineering, but lags behind science (biology) area. How can we increase participation of women? Thanks! • Everyone’s experience and opinion matter to better educate the next generation bioinformaticians, which may be our biggest contribution to science.