Lee Y-k*, Kang S*, Lim JA*, Kim K, Kim S-M, Casel MAB, Choi I, Choi YK#, Kim HU#, Kim Y#. Rapid discovery of antiviral targets through dimensionality reduction of genome-scale metabolic models. bioRxiv. 

Jeon J, Kim Y. (2025). Toward Unraveling Molecular Grammars for dsRNA-binding Proteins: Substrate Recognition to Binding Mechanisms. BMB Rep (In press)

Ku D*, Kim H*, Lim J, Song J, Yoon J, Jun L, Min S-J, Cho R, Lee N, Hur K, Park J-E, Lee LP, Hong J, Kim Y#, Park HG#. (2025). Self-modulating therapeutic platform using engineered miRNA-responsive oligonucleotides. Nano Converg 12, 32.

Ku D, Yang Y, Kim Y. (2025). RNA-associated nuclear condensates: Where the nucleus keeps its RNAs in check. Mol Cells. 48, 100240.

Lim J*, Jung HD*, Park SY, Jeon M, Kim DS, Cho R, Han D, Ryu HS#, Kim Y#, Kim HU#. (2025). Genome-scale knockout simulation and clustering analysis of drug-resistant breast cancer cells reveal drug sensitization targets. Proc Natl Acad Sci U S A 122, e2425384122.  

Chung J*, Lee Y*, Yoon J, Kim Y. (2025). Deciphering the multifaceted role of double-stranded RNA sensor protein kinase R: pathophysiological function beyond the antiviral response. RNA Biol 22, 1-14.

Lee M, Jeon J, Kim Y. (2025). Global translational regulation by Prkra: Is PKR no longer needed? Mol Cell 85, 1889-1891.

Ha Y-J*, Choi YS*, Choi SR, Yoon J, Ku D, Kim Y, Kang EH, Kim K-S, Jeong W-J, Hyon JY, Cha S, Lee YJ. (2025). Association of mitochondrial RNA expression levels in saliva and plasma with interferon signature gene expression and disease activity in patients with Sjögren's disease. RMD Open 11, e005166.

Yoon J*, Jang D*, Kim M-C, Paek J, Miller R, Veronese B, Alvarado R, Thatayatikom A, Kim Y#, Cha S#. (2025). Diminished SUV3 expression and its functional implications in the IFN-enriched monocyte subset of childhood Sjögren's disease. Rheumatology 64, 4393-4403.

Ku D, Yang Y, Park Y, Jang D, Lee N, Lee Y-k, Lee K, Lee J, Han YB, Jang S, Choi SR, Ha Y-J, Choi YS, Jeong W-J, Lee YJ, Lee KJ, Cha S#, Kim Y#. (2025). SLIRP amplifies antiviral signaling via positive feedback regulation and contributes to autoimmune diseases. Cell Rep 44, 115588.

Lee K*, Ku J*, Park SY, Kim N, Widowati TA, Chung H, Kim MJ, Kim DS, Kim HY, Jang WD, Ryu HS#, Kim Y#. Nuclear Retention and RNA Editing Suppress the Recognition of Undegraded Intron Lariats as Non-Self. Sneak Peek. 

Lim J*, Lee N*, Ju S*, Kim J, Mun S, Jeon M, Lee Y-k, Lee S-H, Ku J, Kim S, Bae S, Kim J-S#, Kim Y#. (2025). Cellular dsRNA interactome captured by K1 antibody reveals the regulatory map of exogenous RNA sensing. Commun Biol. 8, 389.

Park JW*, Jeon J*, Kim Y#, Jeon MH#. (2025). Double-Stranded RNA-Based Method for Diagnosing Severe Fever with Thrombocytopenia. J. Clin. Med 14, 105.

Tan S, Kim S, Kim Y. (2024). Targeting mitochondrial RNAs enhances the efficacy of the DNA-demethylating agents. Sci Rep 14, 30767.

Kim S*, Tan S*, Ku J, Widowati TA, Ku D, Lee K, You K, Kim Y. (2024). RNA 5-Methylcytosine Marks Mitochondrial Double-stranded RNAs for Degradation and Cytosolic Release. Mol Cell  84, 2935-2948.

Na H, Koo BI, Park JC, Lim J, Kim Y, Chung HJ, Nam YS. (2024). Live-cell Imaging of MicroRNA Expression via Photoinduced Electron Transfer Controlled by Catalytic Hairpin Assembly. Adv Healthc Mater  13, e2401483

Lim J*, Lee N*, Ju S*, Kim J, Mun S, Jeon M, Lee Y-k, Lee S-H, Ku J, Kim S, Bae S, Kim J-S#, Kim Y#. Cellular dsRNA interactome reveals the regulatory map of exogenous RNA sensing. bioRxiv.  (Published as Lim et al. Commun Biol, 2025)

Ku D, Yang Y, Park Y, Jang D, Lee K, Lee N, Lee Y-k, Lee J, Han YB, Jang S, Choi SR, Ha Y-J, Choi YS, Jeong W-J, Lee YJ, Lee KJ, Cha S#, Kim Y#. SLIRP mediates nuclear-mitochondrial communication during antiviral signaling to promote robust interferon response. bioRxiv.  (Published as Ku et al. Cell Rep, 2025)

Ku J*, Lee K*, Ku D, Kim S, Lee J, Bang H, Kim N, Do H, Lee H, Lim C, Han J, Lee Y-s#, Kim Y#. (2024). Alternative Polyadenylation Determines the Functional Landscape of Inverted Alu Repeats. Mol Cell 84, 1062-1077.

Lee K*, Ku J*, Ku D, Kim Y. (2024). Inverted Alu Repeats: Friends or Foes in the Human Transcriptome. Exp Mol Med 56, 1250-1262.

Yoon J*, Kim S*, Lee M#, Kim Y#. (2023). Mitochondrial Nucleic Acids in Innate Immunity and Beyond. Exp Mol Med 55, 2508-2518.

Ku J, Kim S, Lee K, Ku D, Kim N, Do H, Lee H, Han J, Lee Y-s#, Kim Y#. Alternative Polyadenylation Determines the Functional Landscape of Inverted Alu Repeats. bioRxiv  (published as Ku J et al., Mol Cell 2024)

Kim S*, Tan S*, Ku J, Widowati TA, Ku D, Lee K, You K, Kim Y. RNA 5-Methylcytosine Marks Mitochondrial Double-stranded RNAs for Degradation and Export. Sneak Peek  (published as Kim S et al., Mol Cell 2024)

Song Y*, Lee Y-k*, Lee Y*, Hwang W-T, Lee J, Park S, Kim H, Lee KG, Kim I-D#, Kim Y#, Im SG#. (2023). Anti-viral, Anti-bacterial, but Non-cytotoxic Nanocoating for Reusable Face Mask with High Filtration, Breathability, and Robustness in Humid Environment. Chem Eng J 470, 144224.

Yoon J*, Ku D*, Lee M, Lee N, Im SG, Kim Y. (2023). Resveratrol attenuates the mitochondrial RNA-mediated cellular response to immunogenic stress. Int J Mol Sci 24, 7403.

Aldonza MBD*, Cha J*, Yong I, Ku J, Sinitcyn P, Lee D, Sinitcyn P, Cho R, Delos Reyes RD, Kim D, Kim S, Kang M, Ku Y, Park G, Sung H-J,Ryu HS, Cho S, Kim TM, Kim P#, Cho JY#, Kim Y#. (2023). Multi-targeted therapy resistance via drug-induced secretome fucosylation. eLife 12, e75191.

Kim S*, Yoon J*, Lee K, Kim Y. (2023). Analysis of mitochondrial double-stranded RNAs in human cells. STAR Protoc 4, 102007.

Lee K*, O'Neill KM*, Ku J, Shvartsman SY, Kim Y. (2023). Patterning potential of the terminal system in the Drosophila embryo. Korean J Chem Eng 40, 436-444.

Yoon J*, Lee M*, Ali AA, Oh YR, Choi YS, Kim S, Lee N, Jang SG, Park S, Chung J-H, Kwok S-K, Hyon JY, Cha S#, Lee YJ#, Im SG#, Kim Y#. (2022). Mitochondrial double-stranded RNAs as a pivotal mediator in the pathogenesis of Sjögren's syndrome. Mol Ther Nucleic Acids 30,257-269.

Kim S*,Lee K*, Choi YS,Ku J, Kim H, Kharbash R, Yoon J, Lee YS, Kim JH, Lee YJ#, Kim Y#. (2022). Mitochondrial double-stranded RNAs govern the stress response in chondrocytes to promote osteoarthritis development. Cell Rep 40, 111178

Kang M*, Kharbash R*, Byun JM*, Jeon J*, Ali AA, Ku D, Yoon J, Ku Y, Sohn J, Lee S-JV, Shin D-Y, Koh Y, Yoon S-S, Hong J#, Kim Y#. Double-stranded RNA induction as a potential dynamic biomarker for DNA-demethylating agents. (2022). Mol Ther Nucleic Acids 29, 370-383.

Jee H#, Park E, Hur K, Kang M, Kim Y#. (2022). High-intensity Aerobic Exercise Suppresses Cancer Growth by Regulating Skeletal Muscle-derived Oncogenes and Tumor Suppressors. Front Mol Biosci 9, 818470.

Park S*, Ku J*, Lee S-M, Hwang H, Lee N, Kim H, Yoon K-J, Kim Y#, Choi SQ#. (2022). Potential toxicity of inorganic ions in particulate matter: Ion permeation in lung and disruption of cell metabolism. Sci. Total Environ 824, 153818.

Yoon J*, Lee M-S*, Ali AA, Oh YR, Choi YS, Kim S, Lee N, Jang SG, Ahamad N, Kwok S-K, Hyon JY, Cha S, Lee YJ#, Im SG#, Kim Y#. Targeting mitochondrial double-stranded RNAs ameleiorates autoimmune characteristics of Sjogren's syndrome. bioRxiv (Published as Yoon et al. Mol Ther Nucleic Acids 2022)

Na H, Kang B-H, Ku J, Kim Y, Jeong K-H. (2021). On-chip Paper Electrophoresis for Ultrafast Screening for Infectious Diseases. Biochip J 15, 305-311.

Shin S-B, Kim D-H, Kim D-E, Aldonza MBD, Kim Y, Yim H. (2021). Dual Targeting of EGFR with PLK1 Exerts Therapeutic Synergism in Taxane-Resistant Lung Adenocarcinoma by Suppressing ABC Transporters. Cancers 13, 4413.

Thatayatikom A, Jun I, Bhattacharyya I, Berg K, Lee YJ, Kim Y, Adewumi A, Zhang W, Thatayatikom S, Shah A, Beal C, Modica R, Elder ME, Cha S. (2021). The diagnostic performance of early Sjogren's syndrome autoantibodies in juvenile Sjogren's syndrome: The University of Florida Pediatric Cohort Study. Front immunol 12, 2373.

Aldonza MBD*, Cha J*, Yong I*, Ku J, Lee D, Sinitcyn P, Cho R, Delos Reyes RD, Kim D, Sung H-J, Kim S, Kang M, Ku Y, Park G, Ryu HS, Cho S, Kim TM, Kim P#, Cho JY#, Kim Y#. Widespread multi-targeted therapy resistance via drug-induced secretome fucosylation. bioRxiv (Published as Aldonza et al. in eLife)

Aldonza MBD, Delos Reyes RD, Kim YS, Ku J, Barsallo AM, Hong J, Lee SK, Ryu HS, Park YK, Cho JY#, Kim Y#. (2021). Chemotherapy confers a conserved secondary tolerance to EGFR inhibition via AXL-mediated signaling bypass. Sci Rep 11, 8016.

Song J, Kim S, Kim HY, Hur K, Kim Y, Park HG. (2021). A novel method to detect mutation in DNA by utilizing exponential amplification reaction triggered by the CRISPR-Cas9 system. Nanoscale 13, 7193-7201.

Ku Y*, Park JH*, Cho R*, Lee Y, Park HM, Kim M, Hur K, Byun S, Liu J, Lee YS, Shum D, Shin DY, Koh Y, Cho JY, Yoon SS, Hong J#, Kim Y#. (2021). Noncanonical immune response to the inhibition of DNA methylation via stabilization of endogenous retrovirus dsRNAs. Proc Natl Acad Sci U S A. 118, e2016289118

Ryu DH, Ryu D, Baek Y, Cho H, Kim G, Kim YS, Lee Y, Kim Y, Ye JC, Min H-S, Park YK. (2021). DeepRegularizer: Rapid Resolution Enhancement of Tomographic Imaging using Deep Learning. IEEE Trans Med Imaging 40, 1508-1518.

Ku J*, Kim R*, Kim D, Kim D, Song S, Lee K, Lee N, Kim M, Yoon S-S, Kwon NH, Kim S, Kim Y#, Koh Y#. (2020). Single-cell analysis ofAIMP2 splice variants informs on drug sensitivity and prognosis in hematologic cancer. Commun Biol 3, 630.

Ku Y*, Park JH*, Cho R*, Lee Y, Park HM, Kim M, Hur K, Byun S, Liu J, Shum D, Shin DY, Koh Y, Cho JY, Yoon SS, Hong J#, Kim Y#. Non-canonical immune response to the inhibition of DNA methylation via stabilization of endogenous retrovirus dsRNAs. bioRxiv  (Published as Ku et al. PNAS 2021)

Kim S*, Lee K*, Choi Y, Ku J, Lee Y#, Kim Y#. Mitochondrial dsRNAs activate PKR and TLR3 to promote chondrocyte degeneration in osteoarthritis. bioRxiv (Published as Kim et al. Cell Reports 2022)

Ku J*, Kim S*, Park J, Kim T-S, Kharbash R, Shin E-C, Char K, Kim Y#, Li S#. (2020). Reactive Polymer Targeting dsRNA as Universal Virus Detection Platform with Enhanced Sensitivity. Biomacromolecules. 21, 2440-2454.

Ali AA*, Kharbash R*, Kim Y. (2020). Chemo- and Biosensing Applications of Spiropyran and Its Derivatives - A Review. Analytica Chimica Acta. 110, 199-223.

Aldonza MBD, Ku J, Hong JY, Kim D, Yu S, Lee MS, Prayogo M, Tan S, Kim D, Han J, Lee S, Im S, Ryu H, Kim Y. (2020). Prior acquired resistance to paclitaxel relays diverse EGFR-targeted therapy persistence mechanisms. Science Advances. 6, eaav7416.

Kim S, Ku Y, Ku J, Kim Y. (2019). Evidence of aberrant immune response by endogenous double-stranded RNAs: Attack from within. BioEssays. 41, e1900023.

Kunkeaw N, Lee YS, Im WR, Jang JJ, Song M, Yang B, Park J, Kim S, Ku Y, Kim Y, Kang S, Jo H, Jeong J, Lee H, Lee J, Kim H, Johnson BH, Kim I, Lee YS. (2019).  Mechanism mediated by a noncoding RNA, nc886, in the cytotoxicity of a DNA-reactive compound. Proc Natl Acad Sci U S A. 116, 8289-8294.

Ali AA, Kang M, Kharbash R#, Kim Y#. (2019). Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomedical Engineering. 1, 6.

Kim S, Kang M, Kim Y. (2019). Studying RNA interactors of protein kinase RNA-activated during the mammalian cell cycle. J Vis Exp. 145, e59215

Kim S, Kim Y. Biophysical and biochemical approaches in the analysis of Argonaute-microRNA complexes. In C. Joo and D Rueda (Ed.). Biophysics of RNA-Protein Interactions: A Mechanistic View (pp. 167-188). New York, NY: Springer Nature

Kim S, Ku J, Park J, Kharbash R, Li S. (2018). Preparation of Poly(pentafluorophenyl acrylate) Functionalized SiO2 Beads for Protein Purification. J Vis Exp. 141, e58843.

Kim Y*#, Park J*, Kim S*, Kim M, Kang MG, Kwak C, Kang M, Kim B, Rhee HW, Kim VN#. (2018). PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs. Mol Cell. 71, 1051-1063.

Son H, Ku J, Kim Y, Li S#, Char K#. (2018). Amine-Reactive Poly(Pentafluorophenyl Acrylate) Brush Platforms for Cleaner Protein Purification. Biomacromolecules 19, 951-961.

Jang Y*, Kim M*, Kim Y. (2017). Two faces of competition: target-mediated reverse signaling in microRNA and mitogen-activated protein kinase regulatory networks. IET Syst Biol. 11, 105-113.

 Park J.-E*, Yi H*, Kim Y*, Chang H, Kim VN. (2016). Regulation of poly(A) tail and translation during the somatic cell cycle. Mol Cell. 62,462-471.

Kim Y*, Yeo J*, Lee JH*, Cho J, Suh D, Kim J, Kim VN. (2014). Deletion of humantarbp2reveals cellular microRNA targets and cell cycle function of TRBP. Cell Rep. 9, 1061-1074.

Kim Y, Lee JH, Park JE, Cho J, Yi H, Kim VN. (2014). PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. Genes Dev. 28, 1310-1322.

Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, Shvartsman SY. (2013). Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos. 23, 025105.

Cho J*, Chang H*, Kwon SC, Kim B, Kim Y, Choe J, Ha M, Kim YK, Kim VN. (2012). LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells. Cell. 151, 765-777.

Grimm O*, Sanchez Zini V*, Kim Y, Casanova J, Shvartsman SY, Wieschaus E. (2012). Torso RTK controls Capicua degradation by changing its subcellular localization. Development. 139, 3962-3968.

Helman A, Lim B, Andreu MJ, Kim Y, Shestkin T, Lu H, Jiménez H, Shvartsman SY, Paroush Z. (2012). RTK signaling modulates the Dorsal gradient. Development. 139, 3032-3039.

Kim Y and Kim VN. (2012). MicroRNA Factory: RISC Assembly from Precursor MicroRNAs. Mol Cell. 46, 384-386.

Kanodia JS, Liang HL, Kim Y, Lim B, Zhan M, Lu H, Rushlow CA, Shvartsman SY. (2012). Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo. Biophys J. 102, 427-433.

Kanodia JS, Kim Y, Tomer R, Khan Z, Chung K, Storey JD, Lu H, Keller PJ, Shvartsman SY. (2011). A computational statistics approach for estimating the spatial range of morphogen gradients. Development. 138, 4867-4874.

Kim Y, Andreu MJ, Lim B, Chung K, Terayama M, Jiménez G, Berg CA, Lu H, Shvartsman SY. (2011). Gene Regulation by MAPK Substrate Competition. Dev Cell. 20, 880-887.

Kim Y, Paroush Z, Nairz K, Hafen E, Jiménez G, Shvartsman SY. (2011). Substrate-dependent control of MAPK phosphorylationin vivo. Mol Syst Biol. 7, 467.

Chung K*, Kim Y*, Kanodia JS, Gong E, Shvartsman SY, Lu H. (2011). A microfluidic array for large-scale ordering and orientation of embryos. Nat Methods. 8, 171-176.

Tipping M, Kim Y, Kyriakakis P, Tong M, Shvartsman SY, Veraksa A. (2010). b-arrestin Kurtz inhibits MAPK and Toll signalling in Drosophila development. EMBO J. 29, 3222-3235.

Kavousanakis ME, Kanodia JS, Kim Y, Kevrekidis IG, Shvartsman SY. (2010). A compartmental model for the bicoid gradient. Dev Biol. 345, 12-17.

Kim Y, Coppey M, Grossman R, Ajuria L, Jiménez G, Paroush Z, Shvartsman SY. (2010). MAPK Substrate Competition Integrates Patterning Signals in the Drosophila Embryo. Curr Biol. 20, 446-451.

Kanodia JS, Rikhy R, Kim Y, Lund VK, DeLotto R, Lippincott-Schwartz J, Shvartsman SY. (2009). Dynamics of the Dorsal morphogen gradient. Proc Natl Acad Sci USA. 106, 21707-21712.

Coppey M, Berezhkovskii AM, Kim Y, Boettiger AN, Shvartsman SY. (2007). Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein. Dev Biol. 312, 623-630.