Scott J. Emrich Assistant Professor Department of Computer Science and Engineering University of Notre Dame Email: semrich at nd.edu Phone: 574-631-0353

Brief Bio

Education

• Ph.D., Bioinformatics and Computational Biology, Iowa State University, 2007
• B.S., Biology and Computer Science, Loyola College in Maryland, 2002

Research

• Publications
• Vita (PDF)
• Interests
  • Algorithms for large-scale problems in computational molecular biology
  • Genome assembly, validation and analysis
  • Comparative and statistical genomics

Teaching

• CSE 40532 / CSE 60532 - Bioinformatics Computing (Fall 2008)
• CSE 20212 - Fundamentals of Computing II (Spring 2008)
• CSE 40833 / CSE 60833 - Intro to Parallel Algorithms and Programming (Fall 2007)

Students

• Allison Regier (coadvised with Kevin Bowyer)
• Michael Olson
• Benjamin Drda (undergraduate)

Recent Professional Activities

• Program committee, 1st International Conference on Bioinformatics and Computational Biology (BiCoB 2009)
• Program committee, Applications, Supercomputing 2008
• Program committee, HiCOMB 2008 held in conjunction with IPDPS
• Program committee, Algorithms and Applications, AICCSA08
• Tutorial, "Computational problems in maize genomics," CSB 2007

Selected awards

• Zaffrano Prize for Graduate Research (2008)
• Iowa State University Research Excellence Award (2007)
• Electrical and Computer Engineering Research Excellence, Iowa State University (2006)
• Best paper, IEEE International Parallel and Distributed Processing Symposium (2006)

Recent news

September 2008
- Allison Regier successfully defends her Master's thesis entitled "Challenges in working with draft genomes."

July 2008
- Group members Allison Regier and Mike Olson present their bioinformatics research at ISMB 2008. Congrats!

April 2008
- Multi-million dollar genomics and bioinformatics initiative including myself and other Computer Science and Engineering faculty funded by the University. ND news story

March 2008
- Accepted the Zaffrano Prize for Graduate Research, the most prestigious award given to graduating Iowa State University PhD students. Nominations are made by deparments and submitted to a committee that evaluates quantity and impact of journal papers authored as a graduate student. Only one award is given per year. Full details can be found here.

February 2008
- The first draft of the corn genome released at the Annual Maize Genetics meeting in Washington D.C. press release.

January 2008
- Became a member of the Eck Family Center for Global Health and Infectious Diseases at the University of Notre Dame.

August 2007
- "Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)," was published early by the Plant Journal
- Awarded the Iowa State University Research Excellence award, which is given to honor graduates whose research accomplishments place them in the top 10% of all ISU M.S. and Ph.D. students (combined)

July 2007
- Accepted an invitation to chair the "Parallelization" session at ISCA-PDCS-2007
- Accepted an offer to present a tutorial on computational plant genomics at CSB-2007
- My paper "SNP discovery via 454 transcriptome sequencing" was published by the Plant Journal as an "Early access" article

June 2007
- My paper "Assembling genomes on large-scale parallel computers" was made available online by the Journal of Parallel and Distributed Computing.
- My paper "Massively Parallel EST Clustering" was accepted for presentation at ISCA-PDCS-2007, Las Vegas
- I successfully defended my doctoral thesis entitled "Assembly and analysis of complex plant genomes"

May 2007
- Effort on maize genome assembly was named a Computerworld Honors Program Finalist in "Environment, Energy & Agriculture." ISU press release