Publications from Stuart K. Kim


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Kim SK (2018) Identification of 613 new loci associated with heel bone mineral density and a polygenic risk score for bone mineral density, osteoporosis and fracture. PLoS One. 2018 Jul 26;13(7):e0200785. doi: 10.1371/journal.pone.0200785. eCollection 2018.


Stuart K. Kim, Marwa A. Ahmed, Andrew L. Avins and John P. A. Ioannidis.(2017) A Genetic Marker Associated with De Quervain’s Tenosynovitis. Int. J. Sports Med. 38(12):942-948. doi: 10.1055/s-0043-116669.

Kim SK, Kleimeyer JP, Ahmed MA, Avins AL, Fredericson M, Dragoo JL, et al. (2017) Two genetic loci associated with ankle injury. PLoS ONE 12(9): e0185355.

Stuart K. Kim, John P. Kleimeyer, Marwa A. Ahmed, Andrew L. Avins, Michael Fredericson, Jason L. Dragoo and John P. A. Ioannidis. (2017) A Genetic Marker Associated with Shoulder Dislocation. Int J Sports Med. 2017 Jul;38(7):508-514. doi: 10.1055/s-0043-106190. [PDF]

Stuart K. Kim, Andrew L. Avins, John P. Kleimeyer, Michael Fredericson, John P. A. Ioannidis, Jason L. Dragoo, Marwa A. Ahmed.(2017) Genome-wide Association Study Reveals Two Genetic Variants Associated with Plantar Fasciitis or Fibromatosis. Int. J. Sports Med. in press.

Andrew K. Roos, Andrew L. Avins, Marwa A. Ahmed, John P. Kleimeyer, Thomas R. Roos, Michael Fredericson, John P. A. Ioannidis, Jason L. Dragoo, Stuart K. Kim. (2017) Two Genetic Loci Associated with Medial Collateral Ligament Injury. Int J Sports Med. 2017 Jul;38(7):501-507. doi: 10.1055/s-0043-104853. [PDF]

Thomas R. Roos, Andrew K. Roos, Andrew L. Avins, Marwa A. Ahmed, John P. Kleimeyer, Michael Fredericson, John P. A. Ioannidis, Jason L. Dragoo, Stuart K. Kim. Genome-Wide Association Study Identifies a Locus Near Cadherin8 Associated With Rotator Cuff Injury. PLoS One 12: e0189317.

Stephanie Tzouanas Schmidt, Stephanie M. Zimmerman, Jianbin Wang, Stuart K. Kim, and Stephen R. Quake. (2017) Quantitative Analysis of Synthetic Cell Lineage Tracing Using 2 Nuclease Barcoding. ACS Synth Biol. DOI: 10.1021/acssynbio.6b00309

Stuart K. Kim, Thomas R. Roos, Andrew K. Roos, John P. Kleimeyer, Marwa A. Ahmed, Gabrielle T. Goodlin, Michael Fredericson, John P. A. Ioannidis, Andrew L. Avins, Jason L. Dragoo.(2017) Genome-wide Association Screens for Achilles Tendon and ACL Tears and Tendinopathy. PLoS ONE 12(3): e0170422. doi:10.1371/journal.pone.0170422


Zimmerman SM, Kim SK. New insights into old worm proteomes. Worm 2016; 5: e1184391

Sánchez-Blanco A, Rodríguez-Matellán A, González-Paramás A, González-Manzano S, Kim SK, Mollinedo F. Dietary and microbiome factors determine longevity in Caenorhabditis elegans. Aging (Albany NY). 2016 Jul;8(7):1513-39. doi: 10.18632/aging.101008. PubMed PMID: 27510225; PubMed Central PMCID: PMC4993345.

Ehret GB, Ferreira T, Chasman DI, Jackson AU, Schmidt EM, Johnson T, Thorleifsson G, Luan J, Donnelly LA, Kanoni S, et al. The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals. Nat Genet. 2016 Sep 12. doi: 10.1038/ng.3667. [Epub ahead of print] PubMed PMID: 27618452.

Mann FG, Van Nostrand EL, Friedland AE, Liu X, Kim SK. Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans. PLoS Genet. 2016 Apr 12;12(4):e1005956. doi: 10.1371/journal.pgen.1005956. eCollection 2016 Apr. PubMed PMID: 27070429; PubMed Central PMCID: PMC4829211.

Frøkjær-Jensen C, Jain N, Hansen L, Davis MW, Li Y, Zhao D, Rebora K, Millet JR, Liu X, Kim SK, et al. An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline. Cell. 2016 Jul 14;166(2):343-57. doi: 10.1016/j.cell.2016.05.072. Epub 2016 Jun 30. PubMed PMID: 27374334; PubMed Central PMCID: PMC4947018.


S. K. Kim G. T. Goodlin, T. R. Roos, A. K. Roos, S. K. Kim. (2015) The Dawning Age of Genetic Testing for Sports Injuries. Clin J Sport Med. 2015 Jan;25(1):1-5. doi: 10.1097/JSM.0000000000000158.

Kim, S.K. and J. Higgins, Renal Aging and Transplantation, in Advances in Geroscience, F. Sierra and R. Kohanski, Editors. 2016, Springer. p. 377-396.

Eva Gomez-Orte, María Iñiguez, Eric Cornes, Rosario Lopez, Eric L. Van Nostrand, David G. Knowles, Juan-Félix San-Juan, Stuart K. Kim, Julián Cerón, Juan Cabello. Impact of temperature, food, and laboratory conditions on C. elegans transcriptomic analyses. Submitted.

Many authors including Kim, S. K., Gierman, H. J. New genetic loci link adipose and insulin biology to body fat distribution. Nature. 2015 Feb 12;518(7538):187-96. doi: 10.1038/nature14132. PubMed PMID: 25673412; PubMed Central PMCID: PMC4338562.

Many authors including Kim, S. K., Gierman, H. J. Genetic studies of body mass index yield new insights for obesity biology.Nature. 2015 Feb 12;518(7538):197-206. doi: 10.1038/nature14177. PubMed PMID: 25673413; PubMed Central PMCID: PMC4382211.

Dobriban E, Fortney K, Kim SK, Owen AB. Optimal multiple testing under a Gaussian prior on the effect sizes. Biometrika. 2015 Dec;102(4):753-766. Epub 2015 Nov 4. PubMed PMID: 27046938; PubMed Central PMCID: PMC4813057.

Zimmerman SM, Hinkson IV, Elias JE, Kim SK. Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans. PLoS Genet. 2015 Dec 11;11(12):e1005725. doi: 10.1371/journal.pgen.1005725. eCollection 2015 Dec. PubMed PMID: 26656270; PubMed Central PMCID: PMC4676719.

O'Brown ZK, Van Nostrand EL, Higgins JP, Kim SK. The Inflammatory Transcription Factors NFκB, STAT1 and STAT3 Drive Age-Associated Transcriptional Changes in the Human Kidney. PLoS Genet. 2015 Dec 17;11(12):e1005734. doi: 10.1371/journal.pgen.1005734. eCollection 2015 Dec. PubMed PMID: 26678048; PubMed Central PMCID: PMC4682820.

Fortney K, Dobriban E, Garagnani P, Pirazzini C, Monti D, Mari D, Atzmon G, Barzilai N, Franceschi C, Owen AB, Kim SK.Genome-Wide Scan Informed by Age-Related Disease Identifies Loci for Exceptional Human Longevity. PLoS Genet. 2015 Dec 17;11(12):e1005728. doi: 10.1371/journal.pgen.1005728. eCollection 2015 Dec. PubMed PMID: 26677855; PubMed Central PMCID: PMC4683064.

Goodlin, G. T., Roos, A. K., Roos, T. R., Hawkins, C., Beache, S., Baur, S. and Kim, S. K. (2015) Applying personal genetic data to injury risk assessment in athletes. PLOS ONE DOI: 10.1371/journal.pone.0122676


Zhang, X., Gierman, H. J., Levy, D., Plump, A., Dobrin, R., Goring, H. H. H., Curran, J. E., Johnson, M. P., Blangero, J., Kim, S. K., O'Donnell, C. J., Emilsson, V., Johnson, A. D. (2013) Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs.  2014 Jun 27;15:532. doi: 10.1186/1471-2164-15-532.

Gierman, H. J., Fortney, K., Roach, J. C., Coles, N. S., Li, H., Glusman, G., Markov, G. J., Smith, J. D., Hood, L., Coles, L. S., Kim, S. K. (2014) Whole-Genome Sequencing of the World's Oldest People. PLoS One. DOI: 10.1371/journal.pone.011243.


Zimmerman, S. M. and Kim, S. K. (2013), The GATA transcription factor/MTA-1 homolog egr-1promotes longevity and stress resistance in Caenorhabditis elegans. Aging Cell. doi: 10.1111/acel.12179.

Van Nostrand, E. L. and Kim, S. K. (2013) Integrative analysis of C. elegans modENCODE ChIP-seq datasets to infer transcription factor-responsive targets and upstream regulators of differentially-expressed genes from expression profiling experiments. Genome Research Jun;23(6):941-53. doi: 10.1101/gr.152876.112.

Van Nostrand EL, Sánchez-Blanco A, Wu B, Nguyen A, Kim SK (2013) Roles of the Developmental Regulator unc-62/Homothorax in Limiting Longevity in Caenorhabditis elegans. PLoS Genet 9(2): e1003325. doi:10.1371/journal.pgen.1003325.

Cho, U., Zimmerman, S. M., Chen, L.-C., Owen, E., Kim, J. V., Kim, S. K., and Wandless, T. J., (2013) Rapid and Tunable Control of Protein Stability in Caenorhabditis elegans Using a Small Molecule. PLOS One, 8(8): e72393. doi:10.1371/journal.pone.0072393.

Kim, S. K., Budovskaya, Y. V., Johnson, T. E. (2012) Reconciliation of daf-2 suppression by elt-3 in C. elegans from Tonsaker et al., 2012 and Kim et al., 2012. Mechanisms of Ageing and Development. 134, 64-65. [pdf]

Aerni, S. J., Liu, X., Gross, S. S., Do, C., Long, F., Peng, H., Myers, E., Kim, S. K., Batzoglou, S. (2012) Automated Cellular Annotation for High Resolution Images of Adult C. elegans. Bioinformatics. 2013 Jul 1;29(13):i18-i26.


Xu X, Kim SK (2012) The GATA Transcription Factor egl-27 Delays Aging by Promoting Stress Resistance in Caenorhabditis elegans. PLoS Genet 8(12): e1003108. doi:10.1371/journal.pgen.1003108.

D. Sagi and Stuart K. Kim. (2012) An Engineering Approach to Extending Lifespan in C. elegans. PLOS Genet. doi/pgen.1002780. Comment in Nature Methods (pdf) and Nature Reviews Genetics.

Kim SK, Budovskaya YV, Johnson TE. Response to Tonsaker et al. Mech Ageing Dev. 2012;133(1):54-6

Karczewski KJ, Tirrell RP, Cordero P, Tatonetti NP, Dudley JT, Salari K, et al. Interpretome: a freely available, modular, and secure personal genome interpretation engine. Pac Symp Biocomput. 2012:339-50

M. Sarov, J. Murray, K. Schanze, A. Pozniakovski, W. Niu, K. Angermann, S Hasse, M. Rupprecht, E. Vinis, M. Tinney, E. Preston, A. Zinke, S. Enst, T, Teichgraber, J. Janette, K. Reis, S. Janosch, S. Schlossnig, R. K. Ejsmont, C. Slightam, X. Xu, S. K. Kim, V. Reinke, A. F. Stewart, M. P. Snyder, R. Waterson, A. A. Hyman. (2012). The TransgeneOme of C. elegans: a platform for protein centric systems biology. Cell. 2012;150:855-66.

Chasman, D.I., Fuchsberger, C., Pattaro, C., Teumer, A., Boger, C.A., Endlich, K., Olden, M., Chen, M.H., Tin, A., Taliun, D., et al. (2012). Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function. Hum Mol Genet 21, 5329-5343.

Pattaro, C., Kottgen, A., Teumer, A., Garnaas, M., Boger, C.A., Fuchsberger, C., Olden, M., Chen, M.H., Tin, A., Taliun, D., et al. (2012). Genome-wide association and functional follow-up reveals new Loci for kidney function. PLoS Genet 8, e1002584.


Qu, L., Long, F., Liu, X., Kim, S., Myers, E., and Peng, H. (2011). Simultaneous recognition and segmentation of cells: application in C.elegans. Bioinformatics 27, 2895-2902.

X. Xu and Stuart K. Kim. (2011) The early bird catches the worm: new technologies for the C. elegans toolkit. Nat Rev Genet. 12(11):793-801. doi: 10.1038/nrg3050.

E. L. Van Nostrand and Stuart K. Kim. (2011) Seeing elegance in the gene regulatory networks of the worm. Current Opinion in Genetics and Development. (in press).

A. Sanchez-Blanco and Stuart K. Kim, (2011) Pathogenicity Determines Individual Lifespan in C. elegans. PLOS Genet. doi/pgen.1002047

Wei Niu, Zhi John Lu, Mei Zhong, Mihail Sarov, John I Murray, Cathleen M Brdlik, Judith Janette, Chao Chen, Pedro Alves, Elicia Preston, Cindie Slightham, Lixia Jiang, Anthony A Hyman, Stuart Kim, Robert H Waterston, Mark Gerstein, Michael P Snyder, and Valerie Reinke. Diverse Transcription Factor Binding Features Revealed by Genome-Wide ChIP-seq in C. elegans. (2011)
Genome Research 21(2).  DOI: 10.1101/gr.114587.11


ModENCODE consortium (~100 authors including Van Nostrand, E. L., Wu, B., Slightam, C., Kim, S. K.). (2010)  Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science. 330(6012):1775-87.

H. E. Wheeler and S. K. Kim Genetics and Genomics of Human Ageing. Royal Society New Science of Ageing. Phil. Trans. R. Soc. B 2011 366, 43-50. doi: 10.1098/rstb.2010.0259

M. Zhong, W. Niu, Z. J. Lu, M. S., J. I. Murray, J. Janette, K. L. Sheaffer, H. Y.K. Lam, E. Preston, C. Slightham, L. W. Hillier, T. Brock, A. Agarwal, D. Raha, R. Auerbach, A. A. Hyman, M. Gerstein, S. E. Mango, S. K. Kim, R. H. Waterston, V. Reinke, M. Snyder. (2010) Genome-wide identification of binding sites defines distinct functions for C. elegans PHA-4/FOXA in development and environmental response. PLoS Genet 6(2): e1000848.doi:10.1371/journal.pgen.1000848.


Budovskaya, Y.V., Wu, K., Southworth, L.K., Jiang, M., Tedesco, P., Johnson, T.E., and Kim, S.K. (2008). An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell 134, 291-303.

Graham E. J. Rodwell, Rebecca Sonu, Jacob M. Zahn, James Lund, Julie Wilhelmy, Lingli Wang, Wenzhong Xiao, Michael Mindrinos, Emily Crane, Eran Segal, Bryan D. Myers, Ronald W. Davis, John Higgins, Art B. Owen and Stuart K. Kim. A Transcriptional Profile of Aging in the Human Kidney. PLoS Biology, Dec 2004

Stuart, J. M.*, Segal, E.*, Koller, D#, and Kim, S. K#. A gene co-expression network for global discovery of conserved genetic modules, Science, 302, 249-255, 2003. *co first authors, #co-last authors

Kim et al., A gene expression map for C. elegans. Science 293: 2087-2092, 2001.


Publication Archives (2000 - 2009)


Last modified 1/2013

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