Fun and not-so-fun writings

Inter-relationship guide to computers and biology

Kim and Warnow ISMB phylogeny tutorial (pdf)

Selected Publications from the last 6 years...

Sheng Guo, Junhyong Kim Molecular Evolution of Drosophila Odorant Receptor Genes Molecular Biology and Evolution 24(5):1198-207, 2007.

Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim. Efficient Enumeration of Phylogenetically Informative Substrings Journal of Computational Biology, 14(6):701-23, 2007.

Dexter Hadley, Tara Murphy, Otto Valladares, Sridhar Hannenhalli, Lyle Ungar, Junhyong Kim and Maja Bućan Patterns of sequence conservation in presynaptic neural genes Genome Biology 7(11): R105, 2006.

Fan Ge, Li-San Wang, and Junhyong Kim. The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. Public Library of Science (PLoS) Biology, 3(10):e316, 2005.

Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, and Li-San Wang. Phylogeny by Hybridization. Lecture Notes for Computer Science No. 3240: Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04), pp. 400-411.

Kerr, A., Janies, D., Clouse, R., and J. Kim. Molecular phylogeny of coral-reef sea cucumbers (Holothuriidae: Aspidochirotida) based on 16S mt rDNA sequence. Marine Biotechnology, in press.

P.M. Magwene and J. Kim. Estimating Genomic Co-expression Networks using First-Order Conditional Independence. Genome Biology, vol. 5 no. 12 (2004), pp. R100.

J. Kim and P.M. Magwene. Computational challenges for integrative genomics, Genomics and Informatics, vol. 2 no. 1 (2004), pp. 7-18.

Kirkup, B. and J. Kim. From rolling hills to jagged mountains: Scaling of heuristic searches for phylogenetic estimation. Mol. Biol. Evol. (In revision).    KirkupKim Abstract   PDF preprint

Magwene, P. M., Lizardi, P., and J. Kim. 2003. Reconstructing the temporal order of biological samples using microarray data. Bioinformatics. (In press) text (pdf)

Rifkin, S. A., J. Kim, and K. P. White. 2003. Evolution of gene-expression during metamorphosis in the Drosophila melanogaster subgroup. Nature Genetics 33(2):138-144. text (pdf)

Aspnes, J., M.-Y. Kao, J. Kim. J. Hartling, and G. Shah. 2002. A Combinatorial Toolbox for Protein Landscapes in the Grand Canonical Model. J. Comp. Biol. 9(5):721-742. text (pdf)

Kim, J. 2002. After the molecular evolutionary revolution: a review of Molecular Systematics. Evolution 55(12):2620-2622.

Kim, J. Computers are from Mars, Organisms are from Venus: An interrelationship guide to Biology and Computer Science. IEEE Computer, July 2002.

Rifkin, S.A. and J. Kim. 2002. Geometry of gene expression dynamics. Bioinformatics 18:1176-1183. text (pdf)

Kim, J. and J.R. Carlson. 2002. Gene discovery by e-Genetics:Drosophila odor and taste receptors. J. Cell Sci. 115:1107-1112. text (pdf)

Aspnes, J., M.-Y. Kao, J. Kim. J. Hartling, and G. Shah. A combinatorial toolbox for protein sequence design and landscape analysis in the grand canonical model. In P. Eades and T. Takaoka, editors, Lecture Notes in Computer Science: Proceedings of the 12th Annual International Symposium on Algorithms and Computation. Springer-Verlag, New York, NY, 2001. Abstract Preprint (pdf)

Kim, J. 2001 Macroevolution of the hairy enhancer in Drosophila species. J. Exp. Zool. (Mol. Dev. Evol.) 291:175-185. text (pdf)

Kerr, A. and J. Kim. 2001 Phylogeny of Holothuroidae (Echinodermata) inferred from morphology. Zool. J. Linn. Soc. 133:63-81. text (pdf)

Kim, J. and B. Salisbury. 2001. A tree obscured by vines: horizontal gene transfer and the median tree method of estimating species phylogeny. Pacific Symposium on Biocomputing. 6:571-582.    KimSalisbury01 Abstract   PDF preprint

Salisbury, B. and J. Kim. 2001. Ancestral state estimation and taxon sampling. Syst. Biol. 50(4):557-564

Warr, C., P. Clyne, J. Kim, and J. R. Carlson. 2001. Olfaction in Drosophila: Genetics and e-Genetics. Chemical Senses 26:201-206.

Bininda-Edmonds, O.R.P., S. Brady, J. Kim, and M. J. Sanderson, 2001. Scaling of accuracy in extremely large phylogenetic trees. Pacific Symposium on Biocomputing 6:547-558. text (pdf)

Kim, J. 2001. Descartes' fly: Geometry of genomic annotation. Functional and Integrated Genomics 1:241-249.    Kim01 Abstract   PDF preprint

Rifkin, S. A., K. Atteson, and J. Kim. 2000. Structural analysis of microarray data using singular value decomposition. Functional and Integrative Genomics 1:174-185.   PDF reprint. The original publication is available on

Sanderson, M. J. and J. Kim. 2000. Parametric phylogenetics?. Syst. Biol. 49:817-829.

J. Kim, E. N. Moriyama, C. G. Warr, P. J. Clyne, and J. R. Carlson. 2000. Identification of multi-transmembrane proteins from genomic databases using quasi-periodic structural properties. Bioinformatics 16:767-775. text (pdf)

Kim, J. 2000. Geometry of Phylogenetic Estimation. Mol. Phyl. Evol. 17:58-75.

Kim, J. and M. Kim. 2000. Evolution of characters and modularity. In "Characters", G. Wagner ed., Academic Press.   PDF preprint

Kim, J., J. Kerr, and G.S. Min. 1999. Heterochrony in the molecular developmental cascade of Drosophila. PNAS 97:212-216.

Kerr, A. and J. Kim. 1999. Bi-Penta-Bi-Deca Symmetry: Evolution and developmental trends in Holothuroidae. J. Exp. Zool. 285:93-103.

Clyne, P. J., C. G. Warr, M. R. Freeman, D. Lessing, J. Kim, and J. Carlson. 1999. A novel family of seven transmembrane proteins are candidate odorant receptors in Drosophila. Neuron. 22(2):327-338.

Kim, J., 1998. Large scale phylogenies and measuring the performance of phylogenetic estimators. Syst. Biol. 47:43-60.

Kim, J., 1998. What do we know about the performance of estimators for large phylogenies? TREE 13:25.

Bailey, W. J., J. Kim, G. Wagner, and F. H. Ruddle. 1997. Phylogenetic reconstruction of vertebrate Hox cluster duplications. Mol. Biol. Evol. 14:843-853.