Scott J. Emrich

Director of Bioinformatics
University of Notre Dame

Research Associate Professor
Department of Computer Science and Engineering
Department of Biological Sciences

Research groups:
Notre Dame Bioinformatics Lab
Notre Dame Genomics and Bioinformatics Core

If you are interested in joining my research group, please read this.

See my most recent updates on Twitter via @ScottEmrich

Email: semrich at           Phone: 574-631-0353
Office: 211B Cushing Hall        Notre Dame, IN

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/i5K). Specifically, my group is focusing on non-model genome assembly and analysis with applications to global health and ecology.



Recent Teaching

Research group

Group Alumni

Recent Professional Activities

Bioinformatics updates

Recent updates via @NDbioinform

News archive (pre twitter)

August 2015
- New R21 arrives with Emrich as PI to look at genome structure in Culex mosquitoes.

November 2015
- Rhodnius genome (kissing bug) published in PNAS. Continues to be one of the most read papers at UND according to ResearchGate.

August 2015
- Lauren Assour successfully defends her PhD thesis. Congrats Lauren!!

June 2015
- Paper on incipient speciation in Rhagaletis published in Ecology Letters

November 2014
- Two flagship papers from the Anopheles genome consortium published in Science. Aaron Steele (introgression) and Lauren Assour (synteny) key contributors. Emrich co-led the second paper on the gambiae complex with Matt Hahn and Nora Besansky.

June 2014
- Emrich and Besansky receive an NIH R21 to improve the genome of a neglected malaria vector.
- Aaron Steele received a ISMB travel award to present work related to R21. Congrats Aaron!
- Olivia Choudary and Nick Hazekamp present their work at CCGrid. Congrats!

May 2014
- Emrich and others receive an internal $100K grant (inc. cost share) to purchase 6 high memory machines for bioinformatics.

March 2014
- Novel virus discovered by Emrich and characterized by collaborators published in PLoS ONE.
- Shanw O'Neil's paper on expression differences under climate change published in Molecular Ecology.

August 2013
- Shawn O'Neil publishes on assessing de novo transcriptome assembly metrics in BMC Genomics.
- Josh Livermore published collaborative work on infering bacterial life styles from fresh water bacteria genomes in Environmental Microbiology.
- i5K marker paper published in Journal of Heredity.

May 2013
- Anopheles 16 genome marker paper published. Link here
- Andrew Rider (PhD) and Rory Carmichael (MS) successfully defend their theses. Congrats both!

January 2013
- Assemblethon2 preprint made available online. Metaassembler used for the fish was primarily designed by former undergrad Paul Baranay (now in the PhD program at Yale).
- Conference paper looking at elasticity of NDBL bioinformatiacs applications in a heterogenous cloud environment accepted by CCGrid 2013. Andrew Thrasher is the key NDBL contributor.

December 2012
- Journal paper on trait-based genomics accepted by BMC Genomics. Wei Zhang lead author.

August 2012
- Emrich gives invited talk at the International Congress of Entomology held in Daegu, Korea.
- Journal paper on running bioinformatics applications on a heterogenous system accepted. Irena Lanc lead author.

April 2012
- Emrich and new NDBL collaborator Patricia Clark awarded a special supplement to Clark's current NIH R01 grant intended to connect a NIH-funded computational PI with a NIH-funded experimental PI. Support is for two years and will involve Rory Carmichael from the NDBL.
- Shawn O'Neil successfully defends his PhD thesis entitled "Non-model Transcriptomics: Applications, Assessments, and Algorithms." Congrats Shawn!
- Josh Livermore joins the Environmental Change Initiative as a postdoctoral fellow working primarily with us and NDBL. Welcome Josh!