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BIBM 2009 Education Workshop

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

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BIBM 2009 Education Workshop

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  1. BIBM 2009 Education Workshop Nov 2, 2009 Moderators: Sun Kim and Dong Xu

  2. 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)

  3. 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) • Genome annotation, Metabolic reconstruction, Flux analysis, Network visualization • Genome evolution under selective pressure • Protein engineering • Lecturer on genomics and bioinformatics at UPenn (>5 years) • Mentor to members of the bioinformatics group, summer interns and experimental biologists

  4. 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

  5. Jake Y. Chen, PhDAssistant 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

  6. Majid MassoPostdoctoral Fellow, Laboratory for Structural BioinformaticsDepartment of Bioinformatics and Computational BiologyGeorge 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

  7. 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.

  8. Three Discussion Topics • Bioinformatics education and curriculum • Bioinformatics from industry perspective • Women in Bioinformatics

  9. Discussion topic 1Bioinformatics 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)

  10. Discussion Topic 2 Bioinformatics from industry perspective • Impact of bioinformatics research on industry • How does bioinformatics education meet the need of industrial research?

  11. Discussion Topic 3Women 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?

  12. Thanks! • Everyone’s experience and opinion matter to better educate the next generation bioinformaticians, which may be our biggest contribution to science.

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