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
Technical Editor and Assistant in the Department of Mathematical Sciences (3/2005-5/2009)
Florida Institute of Technology, Melbourne, FL
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
- Poster preparation and presentation tips, Poster Session Activity for Broader Engagement Participants at SIAM Computational Science and Engineering 2015
- Creating an Open Environment for Interdisciplinary Research, BoF at GHC12.
- Challenges and Advantages of Interdisciplinary Research, BoF at TNWiC 2011.
- 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.).
- 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
- 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.
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