Scott J. Emrich

Assistant Professor
Department of Computer Science and Engineering
Director
Notre Dame Bioinformatics Lab
Co-Director
Notre Dame Genomics and Bioinformatics Core

University of Notre Dame

If you are interested in joining my research group, please read this.
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 Biological Sciences and Computer Science and Engineering.

Education

Research

Teaching

Research group

Group Alumni

Recent Professional Activities

Selected awards


Recent news

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 gene annotation on a distributed system/cloud accepted by BMC Genomics. Andrew Thrasher lead author.
- Journal paper on running bioinformatics applications on a heterogenous system accepted. Irena Lanc lead author.

June 2012
- Emrich and Lanc participate in the Daphnia magna genome jamboree in Bloomington, IN.

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 NDBL collaborator Stuart Jones but will also be a member of our group. Welcome Josh!

February 2012
- SAND assembly paper accepted by Transactions on Parallel and Distributed Systems. NDBL alum Michael Olson and current NDBL PhD student Andrew Thrasher led the assembly effort.
- Andrew Thrasher and Wei Zhang both have conference papers accepted by ICCABS 2012 to be held in Las Vegas at the end of the month.

November 2011
- Nucleic Acids Research update of VectorBase accepted. Karyn Megy (European Bioinformatics Institute) and Emrich lead authors.
- Shawn O'Neil receives "Best poster: student choice" at the annual CSE poster session. Congrats Shawn!

October 2011
- Journal version of Shawn O'Neil's Hapler paper accepted as part of a BMC Genomics special issue.
- Nucleic Acids Research update of VectorBase under review. Karyn Megy (European Bioinformatics Institute) and Emrich lead authors.

September 2011
- NDBL/DIAL student Andrew Rider receives best performance in the DREAM6 competition, promoter prediction. This effort is part of our collaboration with the Ferdig lab and the submission was led by Geoffrey Siwo. Great job all!

July 2011
- Allison Regier successfully defends her PhD thesis entitled "A flexible comparative genomics framework for integrating heterogeneous sequence data," and will be joining the Genome Institute at WashU (St. Louis) as a research scientist this August. Congrats Allison!!

January 2011
- Paper on 454 malaria genome sequencing accepted in principle to BMC Genomics. Allison Regier was the lead bioinformatician on the analysis.
- A paper on population haplotyping accepted at 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). Shawn O'Neil is lead author.

October 2010
- Our paper on the two incicipient species of the malaria mosquito Anopheles gambiae published in Science. News coverage here and here.
- Collaborative work led by Neil Lobo on Anopheles inversions published in the Malaria Journal. Allison Regier primary contributor from the NDBL.
- Workshop paper on bioinformatics paper accepted to WORKS'10. Andrew Thrasher is lead author and will present in New Orleans.

September 2010
- Andrew Rider's paper on a new way to find eQTL assocations accepted in BMC Bioinformatics.
- Two regular conference papers accepted to the 2010 IEEE International Conference on Bioinformatics & Biomedicine, one led by Andrew Rider and another led by Wei Zhang. Congrats both!

July 2010
- Allison Regier, Shawn O'Neil, and Andrew Thrasher present their research at the ISMB bioinformatics conference in Boston.
- Shawn O'Neil successfully defends his PhD proposal. Congrats Shawn!
- Thain makeflow paper published in Cluster Computing.

June 2010
- Was an invited panelist at the Emerging Computational Methods for the Life Sciences workshop held in conjunction with the ACM International Symposium on High Performance and Distributed Computing (HPDC).
- Gave an invited talk at the 4th annual Arthropod Genomics Symposium.

May 2010
- Allison Regier's work on a framework for comparative genomics was accepted for the PhD forum portion of the 2010 Grace Hopper Conference in Atlanta.
- Lauren Assour received the Notre Dame Naughton fellowship to work on arthropod comparative genomics in my group. She will join over the summer and spend at least one year abroad at Trinity College Dublin.

April 2010
- Work on butterfly transcriptome assembly and analysis accepted in principle to BMC Genomics. Shawn O'Neil is lead author.
- Workshop paper on the biocompute bioinformatics portal accepted at Emerging Computational Methods for the Life Sciences Workshop (ECMLS) held in conjuction with HPDC 2010. Rory Carmichael lead author.

March 2010
-SJ Emrich participates in the 2010 Indo-American Frontiers of Engineering Symposium on the invitation of the National Academy of Engineering. Recent work on ecoinformatics was presented as part of the symposium.