Justin Vaughn, Ph.D.

Computational biologist
Genomics and Bioinformatics Research Unit, USDA-ARS
Rm. 125 USDA Russell Research Center
950 College Station Rd, Athens, GA 30605
justin.vaughn@ars.usda.gov
(706) 546-3185
genemachine.net

Ph.D., Genetics and Bioinformatics, 2011, University of Tennessee, Knoxville, Tennessee, USA

B.S., Biology, 2003, Samford University, Birmingham, Alabama, USA

Dr. Justin Vaughn studied general biology as an undergraduate at Samford University. He received his doctoral degree from the University of Tennessee, Knoxville, working with Albecht von Arnim to develop computational pipelines for comparative transcriptomics in plants. As a postdoctoral researcher in Jeff Bennetzen’s lab at the University of Georgia, Athens, Dr. Vaughn characterized structural variation in rice populations and used this data to develop new models of tandem duplication formation. He also assisted on numerous genome sequencing projects ranging from orphan grains to culinary herbs. He moved to Zenglu Li’s group at the University of Georgia as a postdoctoral researcher and then research scientist. There, he helped in efforts to characterize the global soybean germplasm as well as dissect the genetic architecture of key agronomic traits such as seed composition. He has additionally consulted on the design of the Alfalfa Breeder’s Toolbox, which aims to enhance the usefulness of genomic and phenotypic information in cultivar development. He is currently a computational biologist with the Genomics and Bioinformatics Research Unit at USDA-ARS.

Publications

Vaughn JN and Li Z. Genomic signatures of North American soybean improvement inform diversity enrichment strategies and clarify the impact of hybridization. G3. 2016; 6(9), 2693-2705

Clevenger J, . . ., Vaughn JN, . . . Hovav R. Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut. Molecular Plant. 2017; 10(2), 309-322.

Vaughn JN, Nelson RL, Song Q, Perry PB, and Li Z. The genetic architecture of seed composition in soybean is re_ned by genome-wide association scans across multiple populations. G3. 2014; 4(11):2283-94. Selected as one of fourteen G3 spotlight articles for 2014.

Shin JH, Vaughn JN, Abdel-Haleem H, Chavarro C, Abernathy B, Kim KD, Jackson SA, and Li Z. Transcriptomic changes due to water de_cit de_ne a general soybean response and accession-specific pathways of drought avoidance. BMC Plant Biology. 2015; 15(1):26. *equal contribution

Ladics, GS, . . ., Vaughn JN, . . . Parrott W. Genetic basis and detection of unintended effects in genetically modified crop plants. Transgenic research. 2015; 24(4), 587-603.

Vaughn JN and Bennetzen JL. Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair. Proc Natl Acad Sci USA. 2014; 111(18):6684-9.

Vaughn JN, Chaluvadi SR, Tushar, Rangan L, and Bennetzen JL. Whole plastome sequences from five ginger species facilitate marker development and define limits to barcode methodology. PLoS One. 2014; 9(10):e108581.

von Arnim AG, Qidong J, and Vaughn JN. Regulation of plant translation by upstream open reading frames. Plant Science. 2013; 214:1-12.

Bennetzen JL, . . ., Vaughn JN, . . ., Devos KM. Reference genome sequence of the model plant Setaria. Nature Biotechnology. 2012; 30(6):555-61

Vaughn JN, Ellingson SR, Mignone F, von Arnim AG. Known and novel post-transcriptional regulatory sequences are conserved across plant families. RNA. 2012; 18(3):368-84.

von Arnim AG and Vaughn JN. Upstream Open Reading Frames. Encyclopedia of Systems Biology, 1st edition. (eds. Dubitzky W, Wolkenhauer O, Cho K, Yokota H). Springer. 2012

Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, von Arnim AG. The h subunit of eIF3 promotes reinitiation on mRNAs harboring upstream open reading frames. RNA. 2010; 16(4): 748-61

Kim BH, Cai X, Vaughn JN, von Arnim AG. On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biology. 2007; 8(4):R60