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. Starting after graduation in 2007 I spent the first ten
years of my career as a faculty member at the University of Notre Dame, and now am an Associate Professor at the University of
Tennessee (Knoxville). My research interests include genome-focused bioinformatics,
parallel and distributed computing, and the intersection of biological applications
and second and
third-gen sequencing. Most of my research has been funded by the
National Institute of Health (NIH). We have received recent funding from USDA, DOE, and the state of Tennessee.
Education
Research
Recent Teaching
Research group
- Ashley Babjac (fourth year PhD; NSF GFRP fellow)
- Mengling He (first year PhD; Bredescen Data Science)
- Shawn-Patrick Barhorst (EECS sophomore)
Group Alumni (largely Notre Dame students)
- Owen Queen (undergraduate Goldwater scholar; researcher at Harvard Medical)
- Zhixiu Lu (EECS PhD; also a bioinformatics specialist at Cincinatti Children's)
- Cai John (Bredescen PhD; industry position in Boston. Cco-advised by Wellington Muchero)
- Katrina Schlum (UT-ORII GST PhD; now a bioinformatics specialist at Cincinatti Children's)
- Gabe Wright (CS PhD, co-advised by Tijana Milenkovic; now an Asst. Prof at MSOE)
- David Molik (IBMS PhD, advised by Mike Pfrender; now a postdoc with USDA ARS)
- Shenglong Zhu (CSE PhD, co-advised by
Danny Chen; now works at Amazon)
- Abigal Prosice (2018-2019; UTK undergraduate)
- Will Markley (2015-2018; undergraduate)
- Mara Staines (2016-2017; undergraduate)
- Olivia Choudhury (2012-2017; PhD now postdoctoral
researcher at IBM)
- Caleb Reinking (CRC); now CRC development lead,
former programmer and lead programmer for VectorBase
- Xuanli (Lexi) Li (2013-2016; undergraduate)
- Chris Ray (2014-2016; undergraduate)
- RJ Nowling (2014-2016 PhD; co-advised by Mary Ann McDowell)
- Kim Ngo (2013-2015; undergraduate co-advised by Patricia Clark)
- Lauren Assour (2009-2015; PhD Computer Science and Engineering, Naughton Fellow)
- Colin Teberg (2013-2015; MS Computer Science and Engineering)
- Irena Lanc (2008-2014; PhD Computer Science and Engineering)
- Erliang Zeng
(former Managing directior, Bioinformatics Core; now at University
of Iowa)
- Wei Zhang (2009-2014; PhD Computer Science and Engineering)
- Andrew Thrasher (2008-2013; PhD Computer Science and Engineering)
- Rory Carmichael (2009-2012; former analyst; 2013 MS)
- Andrew Rider (2008-2013; PhD Computer Science and Engineering, coadvised by Nitesh Chawla)
- Brian Kachmarck (2009-2012; undergraduate)
- Paul Baranay (2011-2012; BS undergraduate; NSF graduate fellow)
- Shawn O'Neil (2009-2012; PhD Computer Science and Engineering)
- Allison Regier (2007-2011; PhD Computer Science and Engineering)
- Michael Olson (2008-2009; MS Computer Science and Engineering)
- Benjamin Drda (2008-2010; undergraduate honors thesis)
Recent Professional Activities
Bioinformatics updates
News archive (pre twitter 2014 and after)
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.
