Fun and not-so-fun writings

Inter-relationship guide to computers and biology

Kim and Warnow ISMB phylogeny tutorial (pdf)

Selected Recent Publications

Miao, Z., Wang, J. Park, K., Kuang, D. and Kim, J. Model-based compound hypothesis testing for snATAC-seq data with PACS. bioRxiv. 2023.

Eberwine, J., Kim, J., Anafi, R.C., Brem, S., Bucan, M., Fisher, S.A., Grady, M.S., Herr, A.E., Issadore, D., Jeong, H. and Kim, H. et al. Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. Nature methods, 2023.

Jain, S., Pei, L., Spraggins, J.M., Angelo, M., Carson, J.P., Gehlenborg, N., Ginty, F., Gonçalves, J.P., Hagood, J.S., Hickey, J.W. and Kelleher, N.L. et al. Advances and prospects for the Human BioMolecular? Atlas Program (HuBMAP). Nature cell biology, 2023.

Miao, Z. and Kim, J. Is single nucleus ATAC-seq accessibility a qualitative or quantitative measurement? Nature Methods (accepted). 2023.

Xiong, L., Liu, J., Han, S.Y., Koppitch, K., Guo, J.J., Rommelfanger, M., Miao, Z., Gao, F., Hallgrimsdottir, I.B., Pachter, L., Kim, J., MacLean?, A.L., and McMahon? A.P. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. Developmental Cell. 2023

Kuang, D., Issakova, D., and Kim, J. Learning Proteome domain folding using LSTMs in an empirical kernel space. Journal of Molecular Biology. 2022.

Doke, T., Abedini, A., Aldridge, D.L., Yang, Y.W., Park, J., Hernandez, C.M., Balzer, M.S., Shrestra, R., Coppock, G., Rico, J.M.I., Han, S.Y. et al., Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nature Immunology. 2022.

Miao, Z., Humphreys, B. D., McMahon?, A. P. and Kim, J. Multi-omics integration in the age of million single-cell data. Nature Reviews Nephrology. 2021; 1-15.

Huang, A., and Kim, J. A subspace clustering method for satisfying stoimetric constraints in scRNA-seq. IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2021.

Miao, Z., Balzer, M.S., Ma, Z., Liu, H., Wu, J., Shrestha, R., Aranyi, T., Kwan, A., Kondo, A., Pontoglio, M., Kim, J., Li, M., Kaestner, K. H. and Susztak, K. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nature communications. 2021; 12(1), 1-17.

Kumon, T., Ma, J., Akins, R.B., Stefanik, D., Nordgren, C.E., Kim, J., Levine, M.T. and Lampson, M.A. Parallel pathways for recruiting effector proteins determine centromere drive and suppression. Cell, 2021, 184(19), pp.4904-4918.

Dhillon, P., Park, J., Del Pozo, C.H., Li, L., Doke, T., Huang, S., Zhao, J., Kang, H.M., Shrestra, R., Balzer, M.S., Chatterjee, S., Prado, P., Han, S.Y., Liu, H., Sheng, X., Dierickx, P., Batmanov, K., Romero, J.P., Prosper, F., Li, M., Pei, L., Kim, J., Montserrat, N. and Susztak, K. The nuclear receptor ESRRA protects from kidney disease by coupling metabolism and differentiation. Cell Metabolism, 2021., 33(2), pp.379-394.

Kuang, D., and Kim, J. Resistant Fit Regression Normalization for Single-cell RNA-seq Data. IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2020, pp. 236-240

Kim, H., Takegahara, N., Walsh, M.C., Middleton, S.A., Yu, J., Shirakawa, J., Ueda, J., Fujihara, Y., Ikawa, M., Ishii, M., Kim, J. and Choi, Y. IgSF?11 regulates osteoclast differentiation through association with the scaffold protein PSD-95. Bone research, 2020, 8(1), pp.1-10.

Lee, Y.G., Lee, J.Y., Kim, J. and Kim, Y.J. Insertion variants missing in the human reference genome are widespread among human populations. BMC biology, 2020, 18(1), pp.1-15.

Han, L.U., Choudhury, S., Mich-Basso, J.D., Ammanamanchi, N., Ganapathy, B., Suresh, S., Khaladkar, M., Singh, J., Maehr, R., Zuppo, D.A. and Kim, J. Lamin B2 levels regulate polyploidization of cardiomyocyte nuclei and myocardial regeneration. Developmental cell, 2020, 53(1), pp.42-59.

Han, S.H., Kim, J. and Lee, D. Static array of droplets and on-demand recovery for biological assays. Biomicrofluidics, 2020, 14(5), p.051302.

Packer, J.S., Zhu, Q., Huynh, C., Sivaramakrishnan, P., Preston, E., Dueck, H., Stefanik, D., Tan, K., Trapnell, C., Kim, J., Waterston, R.H., Murray, J.I. A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution. Science. 2019; 365(6459):eaax1971.

Park, J., Liu, C., Kim, J., and K. Susztak. Understanding the kidney one cell at a time. Kidney International. 2019; 96(4):862-870.

Ransick, A., Lindstrom, N.O., Liu, J., Zhu, Q., Guo, J.-J., Alvarado, G.F., Kim, A.D., Black, H.G., Kim, J., and McMahon?, A. P. Single cell profiling reveals sex, lineage, and regional diversity in the mouse kidney. Dev Cell. 2019; 51(3):399-413.

Middleton, S., Eberwine, J., and Kim, J. Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. BMC Biology. 2019; 17:5.

Zhu, Q., S.A. Fisher, H. Dueck, S. Middleton, M. Khaladkar and J. Kim. PIVOT: Platform for interactive analysis and visualization of transcriptomics data. BMC Bioinformatics. 2018. 1994-0.

Anafi, R.C., Francey, L.J., Hogenesch, J.B., and J. Kim. CYCLOPS reveals human transcriptional rhythms in health and disease. PNAS. 2017. doi: 10.1073/pnas.1619320114.

Morris, J., Na, Y.-J., Zhu, H., Lee, J.-H., Giang, H., Ulyanova, A., Baltuch, G.H., Brem, S., Kung, D.K., Lucas, T.H., Isaac-Chen, H., O’Rourke, D.M., Wolf, J.A., Grady, S., Sul, J.-Y., Kim, J. and J. Eberwine. Pervasive heteroplasmy load within single cells revealed by single mitochondrion sequencing. Cell Reports. 2017; 21(10):2706-2713.

Hannah R. Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian-Bing Fan, Stephen A. Fisher, Jennifer S. Herstein, Tae Kyung Kim, Jae Mun (Hugo) Kim, Ming-Yi Lin, Rui Liu, William J. Mack, Sean McGroty?, Joseph D. Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher P. Walker, Jinhui Wang, Kai Wang, Wei Wang, Andre Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim. Assessing characteristics of RNA amplification methods for single cell RNA sequencing BMC Genomics. 2016; 17: 966; doi:

Qin Zhu, Stephen A Fisher, Jamie Shallcross, Junhyong Kim VERSE: a versatile and efficient RNA-Seq read counting tool (Preprint) bioRxiv 053306; doi:

Spaethling, J.M., Na, Y.-J., Lee, J., Ulyanova, A., Baltuch, G.H., Bell, T.J., Brem, S., Chen, H.I., Dueck, H., Garcia, M.P., Khaladkar, M., Kung, D.K., Lucas Jr., T.H., O’Rourke, D.M., Stefani, D., Wang, J., Wolf, J.A., Bartfai, T., Grady,M.S., Sul, J.-Y., Kim, J. and J.H. Eberwine. Adult human brain cell single cell transcriptomics: model system, cell type specific markers and residual patient drug effects. Cell Reports. 2016; 18(3):791-803.

Jeong H, Na YJ, Lee K, Kim YH, Lee Y, Kang M, Jiang BC, Yeom YI, Wu LJ, Gao YJ, Kim J, Oh SB. High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury. Pain. 2016 Apr;157(4):964-76. doi: 10.1097/j.pain.0000000000000470.

Dueck H, Eberwine J, Kim J. Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. Bioessays. 2016 Feb;38(2):172-80. doi: 10.1002/bies.201500124. Epub 2015 Dec 2.

Eberwine J, Kim J. Cellular Deconstruction: Finding Meaning in Individual Cell Variation. Trends Cell Biol. 2015 Oct;25(10):569-78. doi: 10.1016/j.tcb.2015.07.004. Review.

Spaethling JM, Sanchez-Alavez M, Lee J, Xia FC, Dueck H, Wang W, Fisher SA, Sul JY, Seale P, Kim J, Bartfai T, Eberwine J. Single-cell transcriptomics and functional target validation of brown adipocytes show their complex roles in metabolic homeostasis. FASEB J. 2016 Jan;30(1):81-92. doi: 10.1096/fj.15-273797.

Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM, Park WY. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol. 2015 Jun 19;16:127. doi: 10.1186/s13059-015-0692-3.

Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J. Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. Genome Biol. 2015 Jun 9;16:122. doi: 10.1186/s13059-015-0683-4.

Feltzin VL, Khaladkar M, Abe M, Parisi M, Hendriks GJ, Kim J, Bonini NM. The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila. Aging Cell. 2015 Jun;14(3):443-52. doi: 10.1111/acel.12323.

Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J Comput Biol. 2015 May;22(5):377-86. doi: 10.1089/cmb.2014.0156.

Kim J, Mossel E, Rácz MZ, Ross N. Can one hear the shape of a population history? Theor Popul Biol. 2014 Dec 11;100C:26-38. doi: 10.1016/j.tpb.2014.12.002.

Francis C, Natarajan S, Lee MT, Khaladkar M, Buckley PT, Sul JY, Eberwine J, Kim J. Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution. BMC Genomics. 2014 Oct 9;15:883. doi: 10.1186/1471-2164-15-883.

Middleton SA, Kim J. NoFold?: RNA structure clustering without folding or alignment. RNA. 2014 Nov;20(11):1671-83. doi: 10.1261/rna.041913.113.

Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30;15(6):R86. doi: 10.1186/gb-2014-15-6-r86.

Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe J, Liu AC, Kim J, Hogenesch JB. Machine learning helps identify CHRONO as a circadian clock component. PLoS Biol. 2014 Apr 15;12(4):e1001840. doi: 10.1371/journal.pbio.1001840.

Eberwine J, Sul JY, Bartfai T, Kim J. The promise of single-cell sequencing. Nat Methods. 2014 Jan;11(1):25-7.

Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, Sul JY, Dmochowski IJ, Eberwine J. Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat Methods. 2014 Feb;11(2):190-6. doi: 10.1038/nmeth.2804.

Spaethling JM, Piel D, Dueck H, Buckley PT, Morris JF, Fisher SA, Lee J, Sul JY, Kim J, Bartfai T, Beck SG, Eberwine JH. Serotonergic neuron regulation informed by in vivo single-cell transcriptomics. FASEB J. 2014 Feb;28(2):771-80. doi: 10.1096/fj.13-240267.

Buckley PT, Khaladkar M, Kim J, Eberwine J. Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis. Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):223-30. doi: 10.1002/wrna.1203.

Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. PLoS One. 2013 Oct 3;8(10):e76194. doi: 10.1371/journal.pone.0076194.

Kim TK, Sul JY, Helmfors H, Langel U, Kim J, Eberwine J. Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics. Cell Rep. 2013 Oct 17;5(1):114-25. doi: 10.1016/j.celrep.2013.08.029.

Goodman AJ, Daugharthy ER, Kim J. Pervasive antisense transcription is evolutionarily conserved in budding yeast. Mol Biol Evol. 2013 Feb;30(2):409-21. doi: 10.1093/molbev/mss240.

Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. J R Soc Interface. 2012 Dec 7;9(77):3165-83. doi: 10.1098/rsif.2012.0417.

Turner PE, McBride? RC, Duffy S, Montville R, Wang LS, Yang YW, Lee SJ, Kim J. Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6. BMC Evol Biol. 2012 Aug 22;12:153. doi: 10.1186/1471-2148-12-153.

Selected Older Publications

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.