Sally Rose Ellingson, PhD

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sel228@uky.edu
859-218-3197 (o)
865-405-3659 (c)
800 Rose St, CC405
Lexington, KY 40536-0093
Personal site
sallyrose0425

Position(s):

Assistant Professor, Biomedical Informatics

Other Affiliation(s):

Markey Cancer Center

Interests / Specialties:

Computational Biology

High-performance computing

Bio / Education:

PhD in Genome Science and Technology (GST)
Interdisciplinary Graduate Minor in Computational Science (IGMCS)
University of Tennessee, Knoxville (UTK) and Oak Ridge National Laboratory (ORNL)

BS in Computer Science
BS in Mathematical Sciences
Florida Institute of Technology, Melbourne, FL

PubMed Publications:

Jones, D.;Bopaiah, J.;Alghamedy, F.;Jacobs, N.;Weiss, H.L.;Jong, W.A.;Ellingson, S.R. "Polypharmacology Within the Full Kinome: a Machine Learning Approach." AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2017, (2018): 98-107. [PubMed Link] |
Alghamedy, F.;Bopaiah, J.;Jones, D.;Zhang, X.;Weiss, H.L.;Ellingson, S.R. "Incorporating Protein Dynamics Through Ensemble Docking in Machine Learning Models to Predict Drug Binding." AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science 2017, (2018): 26-34. [PubMed Link] |
Katsumata, Y.;Nelson, P.T.;Ellingson, S.R.;Fardo, D.W. "Gene-based association study of genes linked to hippocampal sclerosis of aging neuropathology: GRN, TMEM106B, ABCC9, and KCNMB2." Neurobiology of aging 53, (2017): 193.e17-193.e25. [PubMed Link] | [ Full text ]
Monsell, S.E.;Mock, C.;Fardo, D.W.;Bertelsen, S.;Cairns, N.J.;Roe, C.M.;Ellingson, S.R.;Morris, J.C.;Goate, A.M.;Kukull, W.A. "Genetic Comparison of Symptomatic and Asymptomatic Persons With Alzheimer Disease Neuropathology." Alzheimer disease and associated disorders 31, 3 (2017): 232-238. [PubMed Link] | [ Full text ]
Evangelista, W.;Weir, R.L.;Ellingson, S.R.;Harris, J.B.;Kapoor, K.;Smith, J.C.;Baudry, J. "Ensemble-based docking: From hit discovery to metabolism and toxicity predictions." Bioorganic & medicinal chemistry 24, 20 (2016): 4928-4935. [PubMed Link] | [ Full text ]
Ellingson, S.R.;Fardo, D.W. "Automated quality control for genome wide association studies." F1000Research 5, (2016): 1889. [PubMed Link] | [ Full text ]
Ellingson, S.R.;Miao, Y.;Baudry, J.;Smith, J.C. "Multi-conformer ensemble docking to difficult protein targets." The journal of physical chemistry. B 119, 3 (2015): 1026-34. [PubMed Link] | [ Full text ]
Nelson, P.T.;Wang, W.X.;Partch, A.B.;Monsell, S.E.;Valladares, O.;Ellingson, S.R.;Wilfred, B.R.;Naj, A.C.;Wang, L.S.;Kukull, W.A.;Fardo, D.W. "Reassessment of risk genotypes (GRN, TMEM106B, and ABCC9 variants) associated with hippocampal sclerosis of aging pathology." Journal of neuropathology and experimental neurology 74, 1 (2015): 75-84. [PubMed Link] | [ Full text ]
Ellingson, S.R.;Dakshanamurthy, S.;Brown, M.;Smith, J.C.;Baudry, J. "Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer." Concurrency and computation : practice & experience 26, 6 (2014): 1268-1277. [PubMed Link] |
Ellingson, S.R.;Smith, J.C.;Baudry, J. "VinaMPI: facilitating multiple receptor high-throughput virtual docking on high-performance computers." Journal of computational chemistry 34, 25 (2013): 2212-21. [PubMed Link] | [ Full text ]
Be, N.A.;Thissen, J.B.;Gardner, S.N.;McLoughlin, K.S.;Fofanov, V.Y.;Koshinsky, H.;Ellingson, S.R.;Brettin, T.S.;Jackson, P.J.;Jaing, C.J. "Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing." PloS one 8, 9 (2013): e73455. [PubMed Link] | [ Full text ]
Vaughn, J.N.;Ellingson, S.R.;Mignone, F.;Arnim, A. "Known and novel post-transcriptional regulatory sequences are conserved across plant families." RNA (New York, N.Y.) 18, 3 (2012): 368-84. [PubMed Link] | [ Full text ]
Hwang, J.H.;Ellingson, S.R.;Roberts, D.M. "Ammonia permeability of the soybean nodulin 26 channel." FEBS letters 584, 20 (2010): 4339-43. [PubMed Link] | [ Full text ]

About

I am a Research Faculty at The University of Kentucky (UK) through the Division of Biomedical Informatics, UK College of Medicine and a KL2 scholar through the UK Center for Clinical and Translational Sciences. I am working with the Markey Cancer Center (MCC) Cancer Research Informatics Shared Resource Facility (CRI) to manage their high-performance computing services. My research interests include the testing and validation of genomic sequence analysis tools and biological simulations for drug discovery and development.

I obtained my PhD in Genome Science and Technology (GST) at the University of Tennessee (UT) where I was also a member of the SCALE-IT program. SCALE-IT (Scalable Computing and Leading Edge Innovative Technologies) is an NSF-IGERT funded program that aims to integrate the fields of computer science and quantitative biology in order to reach new insights on biological questions of high societal value. In addition to my training through GST and SCALE-IT, I obtained a minor in computational science through the IGMCS (Interdisciplinary Graduate Minor in Computational Science) program at the University of Tennessee.

Full CV