Publications

2021


  • 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. 
  • Na H, Kang B-H, Ku J, Kim Y, Jeong K-H. 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. 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. 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
  • Aldonza MBD, Delos Reyes RD, Kim YS, Ku J, Barsallo AM, Hong J, Lee SK, Ryu HS, Park YK, Cho JY#, Kim Y#. 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. 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#. 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. DeepRegularizer: Rapid Resolution Enhancement of Tomographic Imaging using Deep Learning. IEEE Trans Med Imaging 40, 1508-1518.

2020


  • 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#. Single-cell analysis of AIMP2 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. 
  • Ku J*, Kim S*, Park J, Kim T-S, Kharbash R, Shin E-C, Char K, Kim Y#, Li S#.  Reactive Polymer Targeting dsRNA as Universal Virus Detection Platform with Enhanced Sensitivity. Biomacromolecules. 21, 2440-2454.
  • Ali AA*, Kharbash R*, Kim Y.  Chemo- and Biosensing Applications of Spiropyran and Its Derivatives – A Review. Analytica Chimica Acta.  1110, 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. Prior acquired resistance to paclitaxel relays diverse EGFR-targeted therapy persistence mechanisms. Science Advances. 6, eaav7416.

2019


  • 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#, and 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. (2019). 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

2018


  • Kim S, Ku J, Park J, Kharbash R, and 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, and Kim VN#. (2018). PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs. Mol Cell71, 1051-1063.
  • Son H, Ku J, Kim Y, Li S#, and Char K#. (2018). Amine-Reactive Poly(Pentafluorophenyl Acrylate) Brush Platforms for Cleaner Protein Purification. Biomacromolecules 19, 951-961.

2017


  • Jang Y*, Kim M*, and 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.

2016


  • Park J.-E*, Yi H*, Kim Y*, Chang H, and Kim VN. (2016). Regulation of poly(A) tail and translation during the somatic cell cycle. Mol Cell.  62462-471.

2007-2015


  • Kim Y*, Yeo J*, Lee JH*, Cho J, Suh D, Kim J, and Kim VN. (2014). Deletion of human tarbp2 reveals cellular microRNA targets and cell cycle function of TRBP. Cell Rep. 9, 1061-1074.
  •  Kim Y, Lee JH, Park JE, Cho J, Yi H, and Kim VN. (2014). PKR is activated by cellular dsRNAs during mitosis and acts as a mitotic regulator. Genes Dev28, 1310-1322.
  • Kim Y, Iagovitina A, Ishihara K, Fitzgerald KM, Deplancke B, Papatsenko D, and Shvartsman SY. (2013). Context-dependent transcriptional interpretation of mitogen activated protein kinase signaling in the Drosophila embryo. Chaos23, 025105.
  • Cho J*, Chang H*, Kwon SC, Kim B, Kim Y, Choe J, Ha M, Kim YK, and Kim VN. (2012). LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells. Cell151, 765-777.
  • Grimm O*, Sanchez Zini V*, Kim Y, Casanova J, Shvartsman SY, and Wieschaus E. (2012). Torso RTK controls Capicua degradation by changing its subcellular localization. Development139, 3962-3968.
  • Helman A, Lim B, Andreu MJ, Kim Y, Shestkin T, Lu H, Jiménez H, Shvartsman SY, and Paroush Z. (2012). RTK signaling modulates the Dorsal gradient. Development139, 3032-3039.
  • Kim Y and Kim VN. (2012). MicroRNA Factory: RISC Assembly from Precursor MicroRNAs. Mol Cell46, 384-386.
  • Kanodia JS, Liang HL, Kim Y, Lim B, Zhan M, Lu H, Rushlow CA, and 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, and Shvartsman SY. (2011). A computational statistics approach for estimating the spatial range of morphogen gradients. Development138, 4867-4874.
  • Kim Y, Andreu MJ, Lim B, Chung K, Terayama M, Jiménez G, Berg CA, Lu H, and Shvartsman SY. (2011). Gene Regulation by MAPK Substrate Competition. Dev Cell20, 880-887.
  • Kim Y, Paroush Z, Nairz K, Hafen E, Jiménez G, and Shvartsman SY. (2011). Substrate-dependent control of MAPK phosphorylation in vivoMol Syst Biol. 7, 467.
  • Chung K*, Kim Y*, Kanodia JS, Gong E, Shvartsman SY, and 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, and 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, and 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, and 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, and 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, and Shvartsman SY. (2007). Modeling the bicoid gradient: Diffusion and reversible nuclear trapping of a stable protein. Dev Biol. 312, 623-630.