Publications
Publications:
2024~
Do, H., M.-Y. Chung, W. Cho, Sang-Tae Kim, S.-B. Lee, and J.-M. Lee. 2023. CRISPR/Cas9-edited SPL-CNR quantitatively control tomato fruit ripening. Scientia Horticulturae. 330: 113073 doi: 10.1016/j.scienta.2024.113073
2023
Geonha Hwang, Ui-Chan Jung, and Sang-Tae Kim. 2023. A survey of the genome-wide genetic variation of Hibiscus hamabo (Malvaceae). Korean Journal of Plant Taxonomy. 53(2): 148-156. https://doi.org/10.11110/kjpt.2023.53.2.148
Nie H, Kim M, Lee S, Lim S, Lee MS, Kim JH, Noh SJ, Park SW, Kim S-T, Shin A-Y, Lee Y and Kwon S-Y. 2023. High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus). Front. Plant Sci. 14:1142856. doi: 10.3389/fpls.2023.1142856
2022
Wai, A. H., M. Waseem, L.-H. Cho, S.-T. Kim, D. Lee, C.-K. Kim, and M.-Y. Chung. 2022. Comprehensive Genome-Wide Analysis and Expression Pattern Profiling of the SlHVA22 Gene Family Unravels Their Likely Involvement in the Abiotic Stress Adaptation of Tomato. Int. J. Mol. Sci. 23(20): 12222. https://doi.org/10.3390/ijms232012222
J. Park, X. Hong, Y. Kim, and S.-T. Kim. 2022. The complete chloroplast genome of Utricularia tenuicaulis Miki (Lentibulariaceae) isolated in Korea. Mitochondrial DNA Part B. 7(6): 1143-1145. https://doi.org/10.1080/23802359.2022.2080597
J. Park, Y. Kim, J. Min, and S.-T. Kim. 2022. The complete chloroplast genome of Atriplex gmelinii CA Mey. ex Bong. (Amaranthaceae). Mitochondrial DNA Part B. 7(3): 541-543. https://doi.org/10.1080/23802359.2022.2055501
L. Fan, K. Fröhlich, E. Melzer, R. N. Pruitt, I. Albert, L. Zhang, A. Joe, C. Hua, Y. Song, M. Albert, S.-T. Kim, D. Weigel, C. Zipfel, E. Chae, A. A. Gust & T. Nürnberger. 2022. Genotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1. Nature Communications. 13:1294. doi.org/10.1038/s41467-022-28887-4
N. V. Hoang, S. Park, C. Park, H. Suh, S.-T. Kim, E. Chae, B.-C. Kang and. J.-Y. Lee. 2022. Oxidative stress response and programmed cell death guided by NAC013 modulate pithiness in radish taproots. The plant journal. 109(1): 144-163. https://doi.org/10.1111/tpj.15561
2021
Kim, Sang-Tae, S.-H. Oh, & J. Park. 2021. The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia. Korean Journal of Plant Taxonomy. 51(4): 345-352. https://doi.org/10.11110/kjpt.2021.51.4.345
Verloove*, Filip, Rainer Otto, Steven Janssens, and Sang-Tae Kim*. 2021. "A Cryptic Invader of the Genus Persicaria (Polygonaceae) in La Palma and Gran Canaria (Spain, Canary Islands)" Diversity 13, no. 11: 551. https://doi.org/10.3390/d13110551 *corresponding author
Kim, Sang-Tae*, M. Choi, S.-J. Bae, & J.-S. Kim (2021) The Functional Association of ACQOS/VICTR with Salt Stress Resistance in Arabidopsis thaliana was confirmed by CRISPR-mediated Mutagenesis. Int. J. Mol. Sci., 22(21), 11389, doi: doi.org/10.3390/ijms222111389 *corresponding author
Choi, M, Yun, J-Y, Kim, J-H, Kim, J-S*, and Kim, S-T.* (2021) The efficacy of CRISPR-mediated cytosine base editing with the RPS5a promoter in Arabidopsis thaliana. Scientific Reports. 11(1):8087, doi: 10.1038/s41598-021-87669-y *corresponding author
Wai, A. H., W. Muhammad, A.B.M.M.M. Khan, U. Kumar Nath, D.-j. Lee, S.-T. Kim, C.-K. Kim, and M.‑Y. Chung (2021) Genome-wide identification and expression profiling of the PDI gene family reveals their probable involvement in abiotic stress tolerance in tomato (Solanum lycopersicum L.) Genes, 12: 23, doi.org/10.3390/genes12010023
Kim, M.-S., R. Lozano, J. H. Kim, D. N. Bae, S.-T. Kim, J.-H. Park, M. S. Choi, J. Kim, H. C. Ok, S.-K. Park, M. Gore, J.-K. Moon and S.-C. Jeong (2021) The patterns of deleterious mutations during the domestication of soybean Nature Communications, 12: 97, doi.org/10.1038/s41467-020-20337-3
Kim, A., Lee, K.-G., Kwon, Y., Lee, K.-I., Yang, H.-M., Habib, O., Kim, J., Kim, S.-T., Kim, S. J., Kim, J.-S., Hwang, D.-Y. (2021) Off-the-Shelf, Immune-Compatible Human Embryonic Stem Cells Generated Via CRISPR-Mediated Genome Editing Stem Cell Reviews and Reports, 17(3): 1053-1067, https://doi.org/10.1007/s12015-020-10113-7
Wan, W.-L., S.-T. Kim, B. Castel, N. Chroennit, and E. Chae (2021) Genetics of autoimmunity in plants: an evolutionary genetics perspective New Phytologists, 229: 1215-1233, doi.org/10.1111/nph.16947
2019
Kang, B.-C., J. W. Woo, S.-T. Kim, S.-J. Bae, M. Choi, J.-S. Kim, S.-G. Kim (2019) Guidelines for C to T base editing in plants: base-editing window, guide RNA length, and efficient promoter Plant Biotech. Reports, 13: 533-541, doi.org/10.1007/s11816-019-00572-x
Yun*, J.-Y., S.-T. Kim*, S.-G. Kim, J.-S. Kim, (2019) A Zero-background CRISPR Binary Vector System for Construction of sgRNA Libraries in Plant Functional Genomics Applications, Plant Biotech. Reports, 13: 543-551, doi.org/0.1007/s11816-019-00567-8 *co-first author
Barragan, C. A., R. Wu, S.-T. Kim, W. Xi, A. Habring, J Hagmann, A.-L. Van de Weyer, M. Zaidem, W. W. H. Ho, G. Wang, I. Bezrukov, D. Weigel & E. Chae, (2019) RPW8/HR repeats control NLR activation in Arabidopsis thaliana PLoS Genet 15(7): e1008313. doi.org/10.1371/journal.pgen.1008313
2018
Hwang, G.-H., J. Park, K. Lim, S. Kim, J. Yu, E. Yu, S.-T. Kim, R. Eils, J.-S. Kim, & S. Bae, (2018) Web-based design and analysis tools for CRISPR base editing BMC Bioinformatics 19:542. doi.org/10.1186/s12859-018-2585-4
Zhu*, W., M. Zaidem*, A.-L. Van de Weyer, R. M. Vutaker, E. Chae, S.-T. Kim, F. Bemm, L. Li, M. Todesco, R. Schwab, F. Unger, M. J. Beha, M. Demar, D. Weigel (2018) Modulation of ACD6 dependent hyperimmunity by natural alleles of an Arabidopsis thaliana NLR resistance gene PLOS Genetics 14(9): e1007628. doi.org/10.1371/journal.pgen.1007628
Ma, H., N. Marti-Gutierrez, S.-W. Park, J. Wu, T. Hayama, H. Darby, C. Van Dyken, Y. Li, A. Koski, D. Liang, K. Suzuki, Y. Gu, J. Gong, X. Xu, R.Ahmed, Y. Lee, E. Kang, D. Ji, A-R. Park, D. Kim, S.-T. Kim, S. B. Heitner, D. Battaglia, S. A. Krieg, D. M. Lee, D. H. Wu, D. P. Wolf, P. Amato, S. Kaul, J. C. I. Belmonte, J.-S. Kim, S. Mitalipov (2018) Ma et al. reply Nature 560: E10 - E23, doi.org/10.1038/s41586-018-0381-y
Kang*, B.-C., J.-Y. Yun*, S.-T. Kim, Y. Shin, J. Ryu, M. Choi, J. W. Woo, J.-S. Kim (2018) Precision Genome Engineering through Adenine Base Editing in Plants Nature Plants 4: 427-431. doi:10.1038/s41477-018-0178-x
Ryu*, S.-M., T. Koo*, K. Kim*, K. Lim, G. Baek, S.-T. Kim, H. S. Kim, D.-E. Kim, H. Lee, E. Chung, J.-S. Kim (2018) Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy Nature Biotechnology 36: 536-539. doi:10.1038/nbt.4148
Kim, Sang-Tae*, J. Park*, D. Kim, K. Kim, S. Bae, M. Schlesner, J.-S. Kim (2018) Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo” Nature Methods 15(4): 239-240. doi:10.1038/nmeth.4554 *co-first author
2017
Ma*, H., N. Marti-Gutierrez*, S.-W. Park*, J. Wu*, Y. Lee, K. Suzuki, A. Koski, D. Ji, T. Hayama, R. Ahmed, H. Darby, C. Van Dyken, Y. Li, E. Kang, A-R. Park, D. Kim, S.-T. Kim, J. Gong, Y. Gu, X. Xu, D. Battaglia, S. A. Krieg, D. M. Lee, Di. H. Wu, D. P. Wolf, S. B. Heitner, J. C. I. Belmonte,#, P. Amato#, J.-S. Kim#, S. Kaul#, S. Mitalipov# (2017) Correction of a Pathogenic Gene Mutation in Human Embryos Nature 548: 413-419. doi:10.1038/nature23305
Kim, Sang-Tae*, M. J. Donoghue, S. E. Sultan (2017) On the resurrection of Persicaria puritanorum (Polygonaceae) Phytotaxa 308 (1): 20–36. doi:10.11646/phytotaxa.308.1.2 *corresponding author
Park, J., L. Childs, D. Kim, G.-H. Hwang, S. Kim, S.-T. Kim, J.-S. Kim, S. Bae (2017) Digenome-seq web tool for profiling CRISPR specificity Nature Methods 14: 548-549. doi:10.1038/nmeth.4262
D. Kim, K. Lim, S.-T. Kim, S.-h. Yoon, J.-S. Kim (2017) Genome-wide target specificities of CRISPR RNA-guided programmable deaminases Nature Biotechnology 35: 475-480. doi:10.1038/nbt.3852
Kim, K., S.-M. Ryu, S.-T. Kim, G. Baek, D. Kim, K. Lim, E. Chung, S. Kim, J.-S. Kim (2017) Highly efficient RNA-guided base editing in mouse embryos Nature Biotechnology 35: 435-437. doi:10.1038/nbt.3816
H. Kim, S.-T. Kim, J. Ryu, B.-C. Kang, J.-S. Kim, S.-G. Kim (2017) CRISPR/Cpf1-Mediated DNA-Free Plant Genome Editing Nature Communications 14406. doi:10.1038/ncomms14406
B. K. Mable, J. Hagmann, S.-T. Kim, A. Adam, E. Kilbride, D. Weigel, M. Stift (2017) What causes mating system shifts in plants? Arabidopsis lyrata as a case study Heredity 118: 52-63. doi:10.1038/hdy.2016.99
M. Świadek, S. Proost, D. Sieh, J. Yu, M. Todesco, C. Jorzig, A. E. R. Cubillos, B. Plötner, Z. Nikoloski, E. Chae, P. Giavalisco, A. Fischer, F. Schröder, S.-T. Kim, D. Weigel, R. Laitinen, (2017) Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana New Phytologist 213(2): 900-915. DOI:10.1111/nph.14155
2016
H. Kim*, S.-T. Kim*, J. Ryu, M.-K. Choi, J. Kweon, B.-C. Kang, H.-M. Ahn, S. Bae, J. Kim, J.-S. Kim, S.-G. Kim, (2016) A simple, flexible and high-throughput cloning system for plant genome editing via CRISPR-Cas system Journal of Integrative Plant Biology 58(8): 705-712. DOI: 10.1111/jipb.12474 *co-first author.
M. T. Agler, J. Ruhe, C. Morhenn, S.-T. Kim, D. Weigel, E. M. Kemen (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation PLoS Biology 14(1): e1002352. DOI: 10.1371/journal.pbio.1002352
2015
H. Kim*, S.-T. Kim*, S.-G. Kim, and J.-S. Kim (2015) Targeted Genome Editing for Crop Improvement Plant Breed. Biotech. 3(4): 283-290. doi:10.9787/PBB.2015.3.4.283 *co-first author
J. W. Woo, J. Kim, S. I. Kwon, C. Corvalan, S. W. Cho, H. Kim, S.-G. Kim, S.-T. Kim, S. Choe, and J.-S. Kim (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins Nature Biotechnology 33: 1162 – 1164. doi:10.1038/nbt.3389
B. Arnold, S.-T. Kim, and K. Bomblies (2015) Single geographic origin of a widespread autotetraploid Arabidopsis arenosa lineage followed by interploidy admixture Molecular Biology and Evolution 32(6): 1382-95. doi: 10.1093/molbev/msv089
2014
E. Chae, K. Bomblies, S.-T. Kim, D. Karelina, M. Zaidem, S. Ossowski, C.M. Pizarro, R.A.Laitinen, B.A. Rowan, H. Tenemboim, S. Lechner, M. Demar, A. Habring-Muller, C. Lanz, G. Rätsch and D. Weigel (2014) A Species-wide Analysis of Genetic Incompatibilities Identifies NLR Loci as Hotspots of Deleterious Epistasis CELL 159(6): 1341 – 1351. doi: 10.1016/j.cell.2014.10.049
E.-C. Lim, J. Müller, J. Hagmann, S. R. Heny, S.-T. Kim, and D. Weigel (2014) Trowel: a fast and accurate error correction module for Illumina sequencing reads Bioinformatics 30(22): 3264 – 3265. doi: 10.1093/bioinformatics/btu513
Todesco M, S.-T. Kim, E. Chae, K. Bomblies, M. Zaidem, L. Smith, D. Weigel, and RAE Laitinen (2014) Activation of the Arabidopsis thaliana immune system by combinations of common ACD6 alleles PLoS Genet. 10(7): e1004459. Doi: 10.1371/journal.pgen.1004459
2010
Bomblies, K., L.Yant, R. A Laitinen, S.-T. Kim, J. D Hollister, N. Warthmann, J. Fitz, and D. Weigel (2010) Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana PLoS Genet. 6(3): e1000890. Doi: 10.1371/journal.pgen.1000890
Yasmin, G., S. R. Pearce, M. A. Khan, S.-T. Kim, N. Shaheen, and M. Q. Hayat (2010) Taxonomic implication of AFLP fingerprinting in selected Polygonaceous species Pak. J. Bot. 42(2): 739-750.
2009
Haberle, R. C., A. Dang, T. Lee, C. Penaflor, H. Cortes-Burns, A. Oestreich, L. Raubeson, N. Cellinese, E. J. Edwards, S.-T. Kim, W. M. Eddie, and R. K. Jansen (2009) Taxonomic and biogeographic implications of a phylogenetic analysis of the Campanulaceae based on three chloroplast genes Taxon 58(3): 715-734. http://www.jstor.org/stable/27756940
Cellinese, N., S. A. Smith, E. J. Edwards, S.-T. Kim, R. C. Haberle, M. Avramakis, and M. J. Donoghue (2009) Historical biogeography of the endemic Campanulaceae of Crete Journal of Biogeography 36: 1253-1269. Doi:10.1111/j.1365-2699.2008.02077.x
2008
Kim, Sang-Tae* and Michael J. Donoghue (2008) Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae) American Journal of Botany 95(9): 1122-1135. doi: 10.3732/ajb.0700008 *Corresponding author.
Kim, Sang-Tae, Sonia E. Sultan, and Michael J. Donoghue (2008) Allopolyploid speciation in Persicaria (Polygonaceae): Insights from a low-copy nuclear region Proc Natl Acad Sci USA 105(34): 12370-12375. doi: 10.1073/pnas.0805141105
Kim, Sang-Tae* and Michael J. Donoghue (2008) Molecular phylogeny of Persicaria (Persicarieae, Polygonaceae) Systematic Botany 33:77-86. Doi:10.1600/036364408783887302 *Corresponding author.
~ 2001
Bell, C. D., E. J. Edwards, S.-T. Kim, and M. J. Donoghue (2001) Dipsacales phylogeny based on chloroplast DNA sequences Harvard Papers in Botany 6:2 481-499. http://www.jstor.org/stable/41761758
Kim, Sang-Tae, M.-H. Kim and C.-W. Park (2000) A systematic study on Fallopia section Fallopia (Polygonaceae) Korean Journal of Plant Taxonomy 30:1 1-20 (Abstract in English)
Patents:
J.-Y. Yun, J.-S. Kim, S.-T. Kim, Y. Shin (22 Apr 2019) Ref-No: P2018-0053USKR Gene Construct for Base Editing in Plant, Vector Comprising the Same and Method for Base Editing Using the Same, Filed application no.: 10-2019-0046807
Book chapters:
C.-W. Park, M. Kwak, S.-P. Hong, M.-H. Kim, H. Won, S.-T. Kim, G. S. Bhandari (2018) Polygonaceae. In Flora of Korea Editorial Committee (eds) Flora of Korea vol. 3: 62-115. Incheon, National Institute of Biological Resources Environmental Research Complex