Neale DB,  Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA,  Lin BY, Zieve JJ,  Dougherty WM,  Fuentes-Soriano S, Wu L-S, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM,  Smith KE, Dean JFD, Lorenz WW, Whetten RW, Sederoff R, Wheeler N,  McGuire PM, Main D, Loopstra CA, Mockaitis K, deJong PJ,  Yorke JA, Salzberg SL, Langley CH. 2014. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategiesGenome Biology 15:R59.

Humann JL, Wildung M, Pouchnik D, Bates AA, Drew JC, Zipperer UN, Triplett EW, Main D, Schroeder BK. 2014. Complete genome of the switchgrass endophyteEnterobacter clocace P101Standards in Genomic Sciences 9(3):726-734.

Evans K, Jung S, Lee T, Brutcher L, Cho, I, Peace C, Main D. 2013. Addition of a breeding database in the Genome Database for Rosaceae. Database (Oxford) bat078. 

Sanderson LA, Ficklin SP, Cheng C-H, Jung S, Feltus FA, Bett KE, Main D. 2013. Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database (Oxford) bat075. 

Jung S, Ficklin SP, Lee T, Cheng C-H, Blenda A, Zheng P, Yu J, Bombarely A, Cho I, Ru S, Evans K, Peace C, Abbott AG, Mueller LA, Olmstead MA, Main D. 2014. The Genome Database for Rosaceae (GDR): year 10 update. Nucleic Acids Research. DOI 10.1093/nar/gkt1012

Yu J, Jung S, Cheng C-H, Ficklin SP, Lee T, Zheng P, Jones D, Percy R, Main D. 2014. CottonGen: A genomics, genetics and breeding database for cotton research. Nucleic Acids Research. DOI 10.1093/nar/gkt1064

Motamayor JC, K Mockaitis, J Schmutz, N Haiminen, D Livingstone, O Cornejo, SD Findley, P Zheng, F Utro, S Royaert, C Saski, J Jenkins, R Podicheti, M Zhao, BE Scheffler, JC Stack, FA Feltus, GM Mustiga, F Amores, W Phillips, JP Marelli, GD May, H Shapiro, J Ma, CD Bustamante, RJ Schnell, D Main, D Gilbert, L Parida and DN Kuhn. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology 14:R53 

Salazar JA, Ruiz D, Campoy JA, Sánchez-Pérez R, Crisosto CH, Martínez-García PJ, Blenda A, Jung S, Main D, Martínez-Gómez P, Rubio M. 2013. Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) analysis in Prunus: A breeding perspective and beyond. Plant Molecular Biology Reporter. DOI 10.1007/s11105-013-0643-7

Jiwan D, EH Roalson, D Main and A Dhingra. 2013. Antisense expression of peach mildew resistance locus O (PpMlo1) gene confers cross-species resistance to powdery mildew in Fragaria ananassa. Transgenic Research 22:1119-1131. 

Jung S and D Main. 2014. Genomics and bioinformatics resources for translational science in Rosaceae. Plant Biotechnology Reports May 2013.