CV

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Education · Experience · Memberships · Honors · Presentations · Publications

EDUCATION
PhD in Genome Science and Technology (GST) and Minor in Computational Science (IGMCS)
University of Tennessee, Knoxville (UTK) and Oak Ridge National Laboratory (ORNL)
May 2014 (3.88 GPA)

BS in Computer Science and BS in Mathematical Sciences
Florida Institute of Technology, Melbourne, FL
May 2009 (3.96 GPA – Summa Cum Laude)

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EXPERIENCE
University of Kentucky, Lexington, KY 3/2014-present

  • Assistant Professor, Division of Biomedical Informatics, UK College of Medicine
  • Manager, High Performance Computing, Markey Cancer Center, Cancer Research
    Informatics Shared Resource Facility

Graduate Research Assistant at Center for Molecular Biophysics (5/2009-2/2014)
University of Tennessee and Oak Ridge National Laboratory, TN (Supervisor: Jerome Baudry)

Technical Editor and Assistant in the Department of Mathematical Sciences (3/2005-5/2009)
Florida Institute of Technology, Melbourne, FL

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HONORS, FELLOWSHIPS, AWARDS

  • KL2 Career Development Award sponsored by Center for Clinical and Translational Sciences (CCTS) and College of Medicine, University of Kentucky
  • Travel grant to attend SIAM Computational Science and Engineering 2015
  • Best Graduate Poster for Translational and Clinical Research at Markey Cancer Center Research Day May 2014
  • Supercomputing 2013 Broader Engagement Participation Grant (Advanced)
  • Fall 2013 American Chemical Society Chemical Computing Group Research Excellence award
  • 2013 Science Alliance graduate student award for outstanding efforts
  • Co-PI High-throughput Docking in Undergraduate Curriculum (70,000 CPU hours on Kraken Supercomputer)
  • Supercomputing 2012 Broader Engagement Participation Grant (Advanced)
  • Grace Hopper Celebration 2012 Participation Grant (Neustar)
  • National Biomedical Computation Resource Summer Institute 2012 Participation Grant
  • 2012 EU-US Summer School on HPC Challenges Participation Grant (XSEDE/Prace)
  • Supercomputing 2011 Broader Engagement Participation Grant (Advanced)
  • Grace Hopper Celebration 2011 Participation Grant (NSF)
  • ACM Student Research Competition at GHC 2011
  • CRA-W Grad Cohort 2011 Participation Grant
  • Supercomputing 2010 Broader Engagement Participation Grant
  • SCALE-IT (IGERT/NSF) graduate student training program and fellowship
  • Outstanding Senior Award in Mathematical Sciences 2009 and Computer Science 2007

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CONFERENCE PRESENTATIONS
Organized Sessions

Posters

  • High Performance Computing at the Markey Cancer Center (Sustainable Research Pathways Fellows 2015)
  • Computational characterization of genomic analysis pipelines. (Woman in HPC workshop at Supercomputing)
  • Exome-Sequencing Pipeline for Genomic Characterization of Lung Cancer in Appalachian Kentucky (Markey Cancer Research Day 2015)
  • Convex-hull voting method on a large data set (SIAM CSE and Markey Cancer Center Research Day 2015)
  • Using large public data repositories to discover novel genetic mutations with prospective links to melanoma (KBRIN Bioinformatics Summit, Paris, TN and Markey Cancer Research Day 2015)
  • The Role Of Protein Dynamics In Computational Docking: Identifying Novel Binding Sites In The Cancer Drug Target Tyrosine-Protein Kinase Src (Markey Cancer Center Research Day and 3Dsig 2014)
  • High-throughput Docking in Undergraduate Curriculum (Broader Engagement and HPC Educators Networking SC13 Denver, CO)
  • Multi-Receptor High-Throughput Virtual Docking on Supercomputers with VinaMPI (2013 Smoky Mtn. Computational Sciences and Engineering Gatlinburg, TN and ACS National Meeting 2013 Indianapolis, IN)
  • Acceleration of High-Throughput Molecular Docking for Novel Drug Discovery on Supercomputers (ACS National Meeting 2013 New Orleans, LA)
  • Towards High-Throughput Virtual Docking with Multiple Receptor Conformations on High-Performance Computers (2012 Smoky Mtn. CS&Eng and Resource Fair Supercomputing ‘12)
  • High-throughput Virtual Molecular Docking on High-Performance Computers (CBSB12 and NBCR-SI 2012)
  • High-Throughput Virtual Molecular Docking within the MapReduce Framework of Hadoop (ACM-SRC GHC11 and Resource Fair Supercomputing ‘11)
  • Screening for potential novel drugs with the power of cloud computing (CRA-W Grad Cohort 2011 and TNWiC 2011)
  • Drug Discovery in a Cloud (Resource Fair Supercomputing ‘10)
  • The evolution and mechanics of uORF-mediated translation repression in plants (Gordon Research Conference on Post-Transcriptional Regulation 2010)
  • Functional analysis of NH3 and H2O transport of soybean nodulin 26 and regulation under conditions of flooding and hypoxia (NA Symbiotic Nitrogen Fixation Conference 2010).
  • Development of Tools for the Automated Analysis of Spectra Generated by Tandem Mass Spec. (Bioinfo. Summit ‘10, published BMC Bioinfo.)
  • Serendipitous discoveries in microarray analysis (Bioinfo. Summit ‘10, NSF IGERT Project Meeting ‘10, published BMC Bioinfo.).

Talks

  • Computational Prediction of Adverse Drug Reactions at Systems Biology and Omics Integration seminar series at University of Kentucky, March 2016
  • Detecting genomic structural variations using NGS data at Systems Biology and Omics Integration seminar series at University of Kentucky, August 2015
  • Big Data Analytics: Parallelization of Algorithms for Precision Medicine at CCTS Spring Conference March 2015, Lexington, KY
  • Scientific Workflow Solutions: Facilitating Bioinformatics Research at Systems Biology and Omics Integration seminar series at University of Kentucky, April 2014
  • Adventures in Computational Biology at Markey Cancer Center, University of Kentucky, December 2013 (invited seminar)
  • Leveraging the Power of the Fastest Supercomputers to Advance Drug Discovery at University of Tennessee Exhibitor Booth Supercomputing 2013
  • Multi-Receptor High-Throughput Virtual Docking on Supercomputers with VinaMPI at Supercomputing 2013 Doctoral Showcase
  • The future of drug discovery: Supercomputers as virtual laboratories at Using Bioinformatics Data and Tools to Engage Students in Problem Solving: A Curriculum Development Workshop at NIMBioS, Knoxville, TN (invited talk)
  • Accelerating Virtual High-Throughput Ligand Docking: Screening One Million Compounds Using a Petascale Supercomputer at HPDC12 ECMLS workshop
  • Discovering Next Generation Pharmaceuticals: Acceleration of Virtual High-Throughput Molecular Docking at NSF IGERT Meeting 2012 (by Dr. Cynthia Peterson, PI SCALE-IT)
  • Virtual high-throughput molecular docking at JICS/GRS Joint Workshop on Large Scale Computer Simulation April 2012
  • High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud at HPDC11 ECMLS workshop
  • Using Digital Technologies in Research and Education at NSF IGERT Meeting 2010
  • Homology modeling and molecular dynamics using MOE of Nodulin-like intrinsic protein 6 (NIP6;1) at GST colloquium 2010

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PUBLICATIONS

  • Reassessment of risk genotypes (GRN, TMEM106B, and ABCC9 variants) associated with hippocampal sclerosis of aging pathology. Journal of Neuropathology and Experimental Neurology, January 2015, Volume 74, Issue 1, p 75-84. doi: 10.1097/NEN.0000000000000151.
  • Multi-Conformer Ensemble Docking to Difficult Protein Targets. S Ellingson, Y Miao, J Baudry, J Smith. J. Physical Chemistry Part B. J. Phys. Chem. B, 2015, 119 (3), pp 1026–1034. DOI: 10.1021/jp506511p
  • Polypharmacology and supercomputer-based docking: opportunities and challenges. *S Ellingson, J C. Smith, and J Baudry. Molecular Simulations. Volume 40, Issue 10-11, 2014. Special Issue: Recent Advances in Molecular Biology
  • Accelerating virtual high-throughput ligand docking: current technology and case study on a petascale supercomputer. S Ellingson, S Dakshanamurthy, M Brown, J C. Smith, and J Baudry. (2014) Concurrency Computat.: Pract. Exper., 26: 1268–1277. doi: 10.1002/cpe.3070
  • VinaMPI: Facilitating Multiple Receptor High-Throughput Virtual Docking on High Performance Computers. Sally R. Ellingson, Jeremy C. Smith, and Jerome Baudry. (2013) Computers. J. Comp. Chem. Volume 34, Issue 25, pages 2212–2221, DOI: 10.1002/jcc.23367.
  • Accelerating Virtual High-Throughput Ligand Docking S Ellingson, S Dakshanamurthy, M Brown, J Smith, and J Baudry. Concurrency and Computation: Practice and Experience. doi: 10.1002/cpe.3070
  • Limit of detection of Bacillus anthracis in complex soil and air samples using next-generation sequencing. PLoS ONE 8(9): e73455. doi:10.1371/journal.pone.0073455
  • Accelerating Virtual High-Throughput Ligand Docking: Screening One Million Compounds Using a Petascale Supercomputer. S Ellingson, J Baudry. Et al. In Proceedings of the 3rd international workshop on Emerging computational methods for the life sciences (ECMLS ’12). ACM, New York, NY, USA, 33-38. http://doi.acm.org/10.1145/2483954.2483961
  • High-Throughput Virtual Molecular Docking with AutoDockCloud. S Ellingson and J Baudry. Concurrency and Computation: Practice and Experience DOI: 10.1002/cpe.2926.
  • Known and novel post-transcriptional regulatory sequences are conserved across highly diverged plant lineages. JVaughn, SEllingson, and A vonArnim. RNA. Mar 2012 18: 368-84.
  • High-Throughput Virtual Molecular Docking: Hadoop Implementation of AutoDock4 on a Private Cloud. S Ellingson and J Baudry. ECMLS proceedings at HPDC11.
  • Ammonia Permeability of the Soybean Nodulin 26 Channel. JH Hwang, S Ellingson, D Roberts. FEBS Letters 22 October 2010 (Vol. 584, Issue 20, Pages 4339-4343.

(*Co-Corresponding Author)
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