Keith Sheppard

Scientific Software Engineer III

Software Development, Machine Learning, Visualization and Image Processing. My goal is to leverage these technical interests to develop software tools that help advance behavioral and genomics research.

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Location

Bar Harbor, ME

Contact

207-288-6000

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My role within the Kumar Lab is to develop software tools that enable and accelerate research into addiction and other behavioral disorders. This often involves developing deep neural networks or employing other computational methods to extract and analyze behavioral metrics of mice observed under many different experimental conditions. I enjoy being challenged to find or develop computational methods that allow our researchers to extract and analize the data that they need to answer important biological questions.

Selected Publications

0 Krebs MP, Xiao M, Sheppard K, Hicks W, Nishina PM. Bright-Field Imaging and Optical Coherence Tomography of the Mouse Posterior Eye. Methods Mol Biol. 2016;1438:395-415.
0 Didion JP, Yang H, Sheppard K, et al. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics. 2012;13:34.
0 Himes BE, Sheppard K, Berndt A, et al. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene. PLoS ONE. 2013;8(2):e56179.
23 Raghupathy N, Choi K, Vincent MJ, Beane GL, Sheppard KS, Munger SC, Korstanje R, Pardo-Manual de Villena F, Churchill GA. Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression. Bioinformatics. 2018 Jul 1; 34(13):2177-2184
7 Sutphin GL, Mahoney JM, Sheppard K, Walton DO, Korstanje R. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PLoS Comput Biol. 2016 Nov; 12(11):e1005182
5 Krebs MP, Xiao M, Sheppard K, Hicks W, Nishina PM. Bright-Field Imaging and Optical Coherence Tomography of the Mouse Posterior Eye. Methods Mol Biol. 2016; 1438:395-415
16 Himes BE, Sheppard K, Berndt A, Leme AS, Myers RA, Gignoux CR, Levin AM, Gauderman WJ, Yang JJ, Mathias RA, Romieu I, Torgerson DG, Roth LA, Huntsman S, Eng C, Klanderman B, Ziniti J, Senter-Sylvia J, Szefler SJ, Lemanske RF Jr, Zeiger RS, Strunk RC, Martinez FD, Boushey H, Chinchilli VM, Israel E, Mauger D, Koppelman GH, Postma DS, Nieuwenhuis MA, Vonk JM, Lima JJ, Irvin CG, Peters SP, Kubo M, Tamari M, Nakamura Y, Litonjua AA, Tantisira KG, Raby BA, Bleecker ER, Meyers DA, London SJ, Barnes KC, Gilliland FD, Williams LK, Burchard EG, Nicolae DL, Ober C, DeMeo DL, Silverman EK, Paigen B, Churchill G, Shapiro SD, Weiss ST. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene. PLoS One. 2013; 8(2):e56179
45 Didion JP, Yang H, Sheppard K, Fu CP, McMillan L, de Villena FP, Churchill GA. Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias. BMC Genomics. 2012 Jan 19; 13:34
20 Smith R, Sheppard K, DiPetrillo K, Churchill G. Quantitative trait locus analysis using J/qtl. Methods Mol Biol. 2009; 573:175-88

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