BIBM 2009 Education Workshop

Nov 2, 2009

Moderators: Sun Kim and Dong Xu

Srinivas AluruMehl Professor of Computer EngineeringIowa State UniversityBajaj Chair Professor of Computer Science and EngineeringIndian Institute of Technology BombayResearch: Computational genomics, systems biology,parallel methods for computational biologyEducation 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 TombManager, BioinformaticsDuPont 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 visualizationo Genome evolution under selective pressureo 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, 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

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

Jeffrey A. MartinGraduate StudentGeorgia 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 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)

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 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?

Thanks!

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