Selected Genomics Publications from the Kim lab.

2009

L. K. Southworth, A. B. Owen and Stuart K. Kim. (2009) Aging Mice Show a Decreasing Correlation of Gene Expression within Genetic Modules. PLoS Genet 5(12): e1000776. doi:10.1371/journal.pgen.1000776.

Southworth, L.K., Kim, S.K., Owen, A.B. (2009) Properties of balanced permutations. J. Comp. Bio. 16, 625-638.

H. E. Wheeler, E. J. Metter, T. Tanaka, D. Absher, J. Higgins, J. M. Zahn, J. Wilhelmy, R. W. Davis, A. Singleton, R. M. Myers, L. Ferrucci, S. K. Kim. (2009) Genomic Convergence Reveals Common Variants Associated with Gene Expression and Aging in the Human Kidney. PLoS Genet 5(10): e1000685. doi:10.1371/journal.pgen.1000685.

Long, F., Peng, H., Liu, X., Kim, S. K., Myers, E. (2009) A 3D digital atlas of C. elegans and its application to single-cell expression analysis. (2009) Nature Methods 6. 667-672. [News and Views from Bill Mohler][cover photo].

Liu, X., Long, F., Peng. H., Aerni, S. J., Jiang, M., Sanchez-Blanco, A., Murray, J. I., Preston, E., Mericle, Batzoglou, S., Myers, E. W., Kim, S. K. (2009) Analysis of gene regulation and cell fate from single-cell gene expression profiles in C. elegans. Cell 139, 623-633 .

2008

Choi, J., Southworth, L.K., Sarin, K.Y., Venteicher, A.S., Ma, W., Chang, W., Cheung, P., Jun, S., Artandi, M.K., Shah, N., et al. (2008). TERT promotes epithelial proliferation through transcriptional control of a Myc- and Wnt-related developmental program. PLoS Genet 4, e10.

Long, F., Peng, H., Liu, X., Kim, S.K., and Myers, G. (2008). Automatic Recognition of Cells (ARC) for 3D images of C. elegans. Recomb.

Peng, H., Long, F., Liu, X., Kim, S.K., and Myers, E.W. (2008). Straightening Caenorhabditis elegans images. Bioinformatics (Oxford, England) 24, 234-24

2007

Zahn, J.M., Poosala, S., Owen, A.B., Ingram, D.K., Lustig, A., Carter, A., Weeraratna, A.T., Taub, D.D., Gorospe, M., Mazan-Mamczarz, K., Lakatta, E.G., Boheler, K.R., Xu, X., Mattson, M.P., Falco, G., Ko, M.S., Schlessinger, D., Firman, J., Kummerfeld, S.K., Wood, W.H. 3rd, Zonderman, A.B., Kim, S.K., Becker, K.G. (2007). AGEMAP: a gene expression database for aging in mice PLoS Genet 3, e201.

Kim, S.K. Genome-wide Views of Aging Gene Networks, (2007) Cold Spring Harbor (Cold Spring Harbor Press).

Kim, S.K. Common aging pathways in worms, flies, mice and humans. (2007) J Exp Biol. 2007 May 1;210(Pt 9):1607-12.

Warren, L.A., Rossi, D.J., Schiebinger, G.R., Weissman, I.L., Kim, S.K., and Quake, S.R. (2007). Transcriptional instability is not a universal attribute of aging. Aging Cell 6, 775-782.

J.M. Zahn and S.K. Kim. Systems biology of aging in four species, (2007) Current Opinion in Biotechnology, 18 (335-339)

2006

J.M. Zahn, R. Sonu, H. Vogel, E. Crane, K. Mazan-Mamczarz, R. Rabkin, R.W. Davis, K.G. Becker, A.B. Owen, S.K. Kim. Transcriptional Profiling in Human Muscle Reveals a Common Aging Signature. (2006) PLOS Genetics, 2(7): e115.

F. Pauli, Y. Liu, Y. A. Kim, P.-J. Chen and S. K. Kim. Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans. (2006) Development. 133(2):287-95.

Long Ago

Owen, Art B., Josh Stuart, Kathy Mach, Anne M. Villeneuve and Stuart K. Kim. A gene recommender algorithm to identify co-expressed genes in C. elegans. Genome Research, 8, 1828-37, 2003.

Wang, J. and Kim, S. K. Global Analysis of Gene Expression in the Dauer Larvae of Caenorhabditis elegans. Development 130: 1621-1634, 2003

Lund et al., Global Profile of Aging in Caenorhabditis elegans. Current Biology, 12, 1566, 2002.

Roy et al., Chromosomal clustering of muscle-expressed genes in C. elegans Nature, 418, 975-9, 2002.

Romagnolo et al., Downstream targets of let-60 Ras in C. elegans. Dev. Bio. 247, 127-136, 2002.

Kim, http://C.elegans: mining the functional genomic landscape. Nature Reviews Genetics 2, 681-689, 2001.

Jiang et al., Genome-wide analysis of developmental and sex-regulated gene expression profiles in C. elegans PNAS, 98, 218-233, 2001

Reinke et al., A global profile of germ line gene expression in C. elegans, Molecular Cell 6, 605-616, 2000.  

 

 

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Last modified 8/2012

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