- Education
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B.S. in Biology, 1991 - 1997
- Hanyang University, Seoul, Korea
- (Army Service: 1993 - 1995)
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M.S. in Plant Molecular Biology, 1997 - 1999
- Pohang University of Science and Technology (POSTECH), Pohang, Korea
- Advisor: Dr. Gynheung An
- Thesis: Study on early fruit development in apple and rice
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Ph.D. in Molecular Evolutionary Genomics, 2000 - 2005
- The Pennsylvania State University (Penn State), University Park, PA
- Advisor: Dr. Masatoshi Nei
- Thesis: Evolution of two gene families controlling the fundamental processes of eukaryotic development: MADS-box gene family and homeobox gene family
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Postdoctoral training in Developmental Gene Regulatory Network Biology, 2005 - present
- California Institute of Technology (Caltech), Pasadena, CA
- Advisor: Dr. Eric H. Davidson
- Project: Functional cis-regulatory genomics for gene regulatory network analysis
- Research Interests
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- Molecular evolutionary genomics of developmental gene regulatory networks
- Development of experimental and statistical tools for functional and evolutionary genomics
- Positions
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Research Assistant and Graduate Researcher (Plant Molecular Biology), 1997 - 2000
- Dr. Gynheung An's Laboratory, POSTECH
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Research Assistant, 2000 - 2005
- Dr. Masatoshi Nei's Laboratory, Penn State
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Postdoctoral Scholar, 2005 - 2010
- Dr. Eric Davidson’s Laboratory, Caltech
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Scientific Research Associate, 2011 - present
- Dr. Eric Davidson’s Laboratory, Caltech
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Graduate Teaching Assistant, 2003-2004
- Biol230W, Molecules and Cells Lab.
- Biol220W, Populations and Communities Lab.
- Biol110, Basic Concepts and Biodiversity Lab.
- Department of Biology, Penn State
- Awards and Scholarships
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- Genentech Postdoctoral Award, Society for Developmental Biology, 2010
- Biology Department Outstanding Teaching Assistant Award, 2003
- Ambassadorial Scholarship from the Rotary Foundation, 2000 - 2003
- Travel Grant, Institute of Molecular Evolutionary Genetics, Penn State, 2001 - 2004
- Braddock Scholarship from the Eberly College of Science, Penn State, 2000 - 2001
- Presentations
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- Quantitative analysis of cis-regulatory genes and cis-trans gene regulatory networks. School of Life Science, Arizona State University, Tempe, AZ. 2011
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- Quantitative analysis of cis-regulatory genes and cis-trans gene regulatory networks. Department of Biology, University of Rochester, Rochester, NY. 2011
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- Quantitative analysis of cis-regulatory genes and networks. Program in Systems Immunology and Infectious Disease Modeling, NIAID (NIH), Bethesda, MD. 2010
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- Cis-regulatory genes and cis-trans gene regulatory networks. Department of Biological Sciences, University of Southern California, Los Angeles, CA. 2010
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- Quantitative analysis of cis-regulatory genes and networks. Hilde Mangold Postdoctoral Symposium, Society for Developmental Biology 69th Annual Meeting, Albuquerque, NM. 2010
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- DNA-tags for regulatory genomics in development and evolution. Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL. 2010
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- A novel experimental method for the multiplex and quantitative measurement of cis-regulatory module activity in vivo. Developmental Biology of the Sea Urchin XIX, Marine Biological Laboratory, Woods Hole, MA. 2009
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- A novel experimental method for the multiplex and quantitative measurement of cis-regulatory module activity in vivo. Society for Molecular Biology and Evolution Meeting, Univ. of Iowa, Iowa City, IA. 2009
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- New experimental approaches for cis-regulatory analysis: ideas and realization. Developmental Biology of the Sea Urchin XVIII, Marine Biological Laboratory, Woods Hole, MA. 2008
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- Cis-regulatory control of the nodal gene, initiator of the sea urchin oral ectoderm gene network. Experimental Biology 2008, Invited Talk, San Diego, CA. 2008
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- On the correlation of the two ways of functional differentiation of duplicate genes. The Third Rice Genome Annotation Meeting (RAP3), Invited Talk, Tsukuba, Japan. 2006
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- The ectoderm GRN: nodal cis-regulatory control. Developmental Biology of the Sea Urchin XVII, Marine Biological Laboratory, Woods Hole, MA. 2006
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- Evolutionary change of the numbers of homeobox genes in animals. Society for Molecular Biology and Evolution Meeting, Arizona State Univ. Tempe, AZ. 2006
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- Birth, death, and differentiation of MADS-box genes in plants. The First Rice Genome Annotation Meeting (RAP1), Invited Talk, Tsukuba, Japan. 2004
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- Evolution of homeobox genes controlling the fundamental processes of animal development. Institute of Molecular Evolutionary Genetics Seminar, Penn State. 2004
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- Evolution of MADS-box gene family in plants: birth-and-death evolution. Institute of Molecular Evolutionary Genetics Seminar, Penn State. 2003
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- Floral MADS-box gene evolution in plants. Society for Molecular Biology and Evolution Meeting, Univ. of Georgia, Athens, GA. 2001
- Professional Services
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- Reviewer for BMC Plant Biology, Developmental Biology, Gene, Genetica, Genome Research, Genomics, Journal of Biology, Molecular Biology and Evolution, Molecular & Cellular Proteomics, New Phytologist, Nucleic Acids Research, Plant Systematics and Evolution, PLoS One, Proceedings of the National Academy of Sciences of the USA, Trends in Genetics
- Professional Memberships
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- Member of the Society for Molecular Biology and Evolution since 2001
- Member of the Society for Developmental Biology
- Publications (Click here to view PubMed
listing)
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- 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.
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- 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.
- ##News in brief, Nature Methods
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- 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.
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- 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.
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- The Rice Annotation Project (2007) Curated Genome Annotation of Oryza sativa ssp. Japonica and Comparative Genome Analysis with Arabidopsis thaliana. Genome Research. 17(2):175-183.
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- Sea Urchin Genome Sequencing Consortium (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science. 314(5801):941-952.
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- Nam*, J., and Nei, M. (2005) Evolutionary change of the numbers of homeobox genes in bilateral animals. Mol. Biol. Evol. 22(12):2386-94.
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- 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.
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- 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.
- ##Faculty of 1000 comment
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- 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.
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- Lee, S., Kim, J., Son, J.S., Nam, J., 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.
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- 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., Nam, J., 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.
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- Jeon, J.S., Lee, S., Jung, K.H., Jun, S.H., Jeong, D.H., Lee, J., Kim, C., Jang, S., Yang, K., Nam, J., 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.
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- Jeon, J.S., Jang, S., Lee, S., Nam, J., 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. 12:871-84.
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- Sung S.K., Yu, G.H., Nam, J., 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. 210:519-28.
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- Sung S.K., Jeong, D.H., Nam, J., 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. 8:565-77.
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- * - as corresponding author
- Manuscripts in Preparation
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- Nam*, J., Davidson*, E.H. (submitted) Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.
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- Nam, J. (manuscript in preparation) On the prevalence of combinatorial gene expression control by cis-regulatory modules.
- References
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- Dr. Eric H. Davidson (Postdoctoral advisor)
- Norman Chandler Professor of Cell Biology
Division of Biology, California Institute of Technology, Pasadena, CA 91125
Email: davidson AT caltech.edu
Phone: 1-626-395-4937
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- Dr. Masatoshi Nei (Ph.D. advisor)
- Evan Pugh Professor of Biology and Director of the Institute of Molecular Evolutionary Genetics
Department of Biology, Pennsylvania State University, University Park, PA 16802
Email: nxm2 AT psu.edu
Phone: 1-814-863-7334
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- Dr. David R. McClay
- Professor
Department of Biology, Duke University, Durham, NC 27708
Email: dmcclay AT duke.edu
Phone: 1-919-613-8188
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- Dr. Sorin Istrail
- Julie Nguyen Brown Professor of Computational and Mathematical Sciences
Department of Computer Science, Brown University, Providence, RI 02912
Email: sorin AT cs.brown.edu
Phone: 1-401-863-6196
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- Dr. Jianzhi George Zhang
- Professor
Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048
Email: jianzhi AT umich.edu
Phone (office): 1-734-763-0527
Phone (lab): 1-734-763-0514
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