Scott Emrich's Home Page

Scott J. Emrich

Assistant Professor
Department of Computer Science and Engineering
Director
Notre Dame Bioinformatics Core

University of Notre Dame

Email: semrich at nd.edu
Phone: 574-631-0353

Brief Bio

I have received the BS in Biology and Computer Science from Loyola College in Maryland and the PhD in Bioinformatics and Computational Biology from Iowa State University under the direction of Drs. Aluru and Schnable. Upon graduation, I received a ISU Research Excellence award and the university-wide Zaffrano Prize for Graduate Research. In August 2007, I joined the faculty of the University of Notre Dame. My research interests include computational biology, bioinformatics and parallel computing. Currently, my group is focusing on arthropod and malaria genome analysis with applications to global health and ecology. This is collaborative work with multiple faculty members in the Department of Biological Sciences at Notre Dame.

Education

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

Research

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

Teaching

CSE 40833/60833 - Intro to Parallel Algorithms and Programming (Fall 2009)
CSE 20212 - Fundamentals of Computing II (Spring 2009)
CSE 40532/60532 - Bioinformatics Computing (Fall 2008)

Research group

Allison Regier (PhD)
Shawn O'Neil (PhD)
Michael Olson (MS/PhD)
Andrew Rider (MS/PhD, coadvised by Nitesh Chawla)
Irena Lanc (new MS/PhD student)
Andrew Thrasher (new MS/PhD student)
Benjamin Drda (undergraduate)
Rory Carmichael (Senior analyst, Bioinformatics Core)
Erliang Zeng (Managing directior, Bioinformatics Core)
Group picture outside Fitz

Recent Professional Activities

Program committee, Applications, Supercomputing 2008, 2009
Program committee, International Conference on Bioinformatics and Computational Biology (BiCoB), 2008, 2009
Program committee, International Conference on Contemporary Computing, 2009
Program committee, HiCOMB 2008 held in conjunction with IPDPS
Program committee, Algorithms and Applications, AICCSA08

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

October 2009
- Conference paper on improved inversion prediction in A. gambiae accepted by ISCB Africa ASBCB Joint Conference, Bamako, Mail. Allison Regier is lead author.

- NIAID/NIH renewed VectorBase for another 5 years ($12.2 million total). SJ Emrich is scientific manager and a co-PI. Details here.

- Work on scalable genome assembly on campus grids w/ Doug Thain accepted for presentation at the 2nd Workshop on Many-Task Computing on Grids and Supercomputers, Portland, Oregon. Mike Olson is a primary author.

March 2009
- Conference paper on distributed large-scale sequence alignment w/ Doug Thain accepted for presentation at the 18th International Symposium on High Performance Distributed Computing (HPDC2009)

Janurary 2009
- Became director of the ND Bioinformatics Core

December 2008
- Conference paper on comparing similar genomes motivated by A. gambiae research accepted by BiCoB 2009. Allison Regier is lead author.

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 funded by the University. ND news story