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

Education

Research

Recent Teaching

Research group

Group Alumni

Recent Professional Activities


Bioinformatics updates

Recent updates via @NDbioinform

News archive

August 2015
- New R21 arrive with Emrich as PI to look at genome structure in Culex mosquitoes. Will get some members of the community together to talk strains at the end of the semester.

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!