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 received a BS in Biology and Computer Science from Loyola College in Maryland and a PhD in Bioinformatics and Computational Biology from Iowa State University (ISU). 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 (ND). My research interests include genome-focused bioinformatics, parallel computing, and arthropod genomics (VectorBase and Arthropod Genomics Consortium). Specifically, my group is focusing on non-model genome assembly and analysis with applications to global health and ecology. This is collaborative work with multiple faculty members in the Department of Biological Sciences at ND. We also collaborate with ND Profs. Chawla (DIAL) and Thain (CCL) on systems biology and distributed bioinformatics tools, respectively.

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

Research group

Allison Regier (fourth-year PhD)
Shawn O'Neil (fourth-year PhD)
Andrew Rider (second year PhD, coadvised by Nitesh Chawla)
Wei Zhang (first year PhD, coadvised by Erliang Zeng)
Irena Lanc (first year MS/PhD)
Andrew Thrasher (first year MS/PhD)
Benjamin Drda (undergraduate)
Rory Carmichael (Senior analyst, Bioinformatics Core)
Erliang Zeng (Managing directior, Bioinformatics Core)
Group picture outside Fitz

Recent Professional Activities

Steering committee, 4th Annual Arthropod Genomics Symposium
Program committee, 2nd Workshop on using Emerging Parallel Architectures (WEPA 2010)
Program committee, Applications, Supercomputing 2008, 2009
Program committee, International Conference on Bioinformatics and Computational Biology (BiCoB), 2008, 2009
Program committee, HiCOMB 2008 held in conjunction with IPDPS

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

November 2009
- Gave an invited talk at the 1st International Workshop on Information Systems for Insect Pests organized by INRIA Rennes-Bretagne-Atlantique. VectorBase and new tools developed by the NDBL were presented.

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."