Guay, C.L.*, McQuade, S.T.*, Nam, J. (2017) Single embryo-resolution quantitative analysis of reporters permits multiplex spatial cis-regulatory analysis. Dev. Biol. In press. (*co-first authors)


Nam*, J., Davidson*, E.H. (2012) Barcoded DNA-tag reporters for multiplex cis-regulatory analysis. PLoS ONE. 7(4): e35934. doi:10.1371/journal.pone.0035934

Materna, S.C., Nam, J., Davidson, E.H. (2010) High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development. Gene Expr. Patterns. 10(4-5):177-184.

Nam, J., Dong, P., Tarpine, R., Istrail, S., Davidson, E.H. (2010) Functional cis-regulatory
genomics for systems biology. Proc. Natl. Acad. Sci. USA. 107(8):3930-3935.

Lee, P.Y., Nam, J., Davidson, E.H. (2007) Exclusive developmental functions of gatae cis-regulatory modules in the Strongylocentrorus purpuratus embryo. Dev. Biol. 307(2):434-445.

Nam, J., Su, Y.H., Lee, P.Y., Robertson, A.J., Coffman, J.A., Davidson, E.H. (2007) Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Dev. Biol. 306(2):860-869.

The Rice Annotation Project (2007) Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thalianaGenome Research. 17(2):175-183.

Sea Urchin Genome Sequencing Consortium (2006) The genome of the sea urchin Strongylocentrotus purpuratusScience. 314(5801):941-952.

Nam*, J., and Nei, M. (2005) Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol. Biol. Evol. 22:2386-2394.

Nam*, J., Kaufmann, K., Theissen, G., and Nei, M. (2005) A simple method for predicting the functional differentiation of duplicate genes and its application to MIKC-type MADS-box genes. Nucleic Acids Res. 33:e12.

Nam*, J., Kim, J., Lee, S., An, G., Ma, H., and Nei, M. (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. USA. 101:1910-1915.

Nam, J., dePamphilis, C.W., Ma, H., and Nei, M. (2003) Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol. Biol. Evol. 20:1435-1447.

Lee, S., Kim, J., Son, J.S., NamJ., Jeong, D.H., Lee, K., Jang, S., Yoo, J., Lee, J., Lee, D.Y., Kang, H.G., and An, G. (2003) Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case. Plant Cell Physiol. 44:1403-1411.

An, S., Park, S., Jeong, D.H., Lee, D.Y., Kang, H.G., Yu, J.H., Hur, J., Kim, S.R., Kim, Y.H., Lee, M., Han, S., Kim, S.J., Yang, J., Kim, E., Wi, S.J., Chung, H.S., Hong, J.P., Choe, V., Lee, H.K., Choi, J.-H., NamJ., Kim, S.R., Park, P.B., Park, K.Y., Kim, W.T., Choe, S., Lee, C.B., and An, G. (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol. 133:2040-2047.

Jeon, J.S., Lee, S., Jung, K.H., Jun, S.H., Jeong, D.H., Lee, J., Kim, C., Jang, S., Yang, K., NamJ., An, K., Han, M.J., Sung, R.J., Choi, H.S., Yu, J.H., Choi, J.H., Cho, S.Y., Cha, S.S., Kim, S.I., An, G. (2000) T-DNA insertional mutagenesis for functional genomics in rice. Plant J. 22:561-70.

Jeon, J.S., Jang, S., Lee, S., NamJ., Kim, C., Lee, S.H., Chung, Y.Y., Kim, S.R., Lee, Y.H., Cho, Y.G., and An, G. (2000) leafy hull sterile1 is a homeotic mutation in a rice MADS box gene affecting rice flower development. Plant Cell. 12:871-884.

Sung S.K., Yu, G.H., NamJ., Jeong, D.H., and An, G. (2000) Developmentally regulated expression of two MADS-box genes, MdMADS3 and MdMADS4, in the morphogenesis of flower buds and fruits in apple. Planta. 210:519-828.

Sung S.K., Jeong, D.H., NamJ., Kim, S.H., Kim, S.R., and An, G. (1998) Expressed sequence tags of fruits, peels, and carpels and analysis of mRNA expression levels of the tagged cDNAs of fruits from the Fuji apple. Mol. Cells. 8:565-877.