Publications

   U of Chicago
  1. ​Brown JS, Zhang D, Chen W, Lee HC. "Sensitized piRNA reporter identifies multiple RNA processing factors involved in piRNA-mediated gene silencing" bioRxiv, https://www.biorxiv.org/content/10.1101/2023.01.22.525052v1
  2. Du Z, Kun S, Brown JS, He T, Wu WS, Zhang Y, Lee HC#, and Zhang D#. “P bodies coat germ granules to promote transgenerational gene silencing in C. elegans” bioRxiv, https://www.biorxiv.org/content/10.1101/2022.11.01.514641v1       #co-corresponding author
  3. Wu WS*, Brown JS*, Shiue SC, Lee DE, Zhang D, Lee HC. 2023 "Transcriptome-wide analyses of piRNA binding sites suggest distinct mechanisms regulate piRNA silencing in C. elegans" RNA. doi:10.1261/rna.079441.122. PMID:36737102
  4. Lei K, McKinney SA, Ross EJ, Lee HC, and Alvarado AS. 2023 “Pluripotency retention and exogenous mRNA introduction in planarian stem cells in culture”. iScience 26(2)106001. doi:10.1016/j.isci.2023.106001
  5. Chen W*, Brown JS*, He T, Wu WS, Tu S, Weng Z, Zhang D, Lee HC. 2022 “GLH/VASA helicases promote germ granule formation to ensure the fidelity of piRNA-mediated transcriptome surveillance” Nat. Commun. doi:10.1038/s41467-022-32880-2
  6. Wu WS*, Brown JS*, Chen PH, Shiue SC, Lee DN, Lee HC, 2022 “CLASH Analyst, A webserver to identify in vivo RNA-RNA Interactions from CLASH data; Non-Coding RNA. 8(1), 6; https://doi.org/10.3390/ncrna8010006
  7. Chen W*, Hu Y*, Lang CF, Brown JS, Schwabach S, Song X, Zhang Y, Munro E, Bennett K, Zhang D, Lee HC. 2020 "The Dynamics of P Granule Liquid Droplets Are Regulated by the Caenorhabditiselegans Germline RNA Helicase GLH-1 via Its ATP Hydrolysis Cycle" Genetics. PMID: 32245789.
  8. Wu WS*, Brown JS*, Chen TT, Chu YH, Huang WC, Tu S, Lee HC. 2019 “piRTarBase, a database of piRNA targeting sites and their role in gene regulation” Nucleic Acids Res. doi:10.1093/nar/gky956 
  9. ​Wu WS, Huang WC, Brown J, Zhang D, Song X, Chen H, Tu S, Weng Z, Lee HC, 2018 “pirScan, a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans”, Nucleic Acids Res. doi:10.1093/nar/gky277.
  10. Seth M, Shirayama M, Tang W, Shen EZ, Tu S, Lee HC, Weng Z, Mello CC. 2018 "The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans." Cell Rep. 27;22(9):2254-2264
  11. Zhang D*, Tu S*, Stubna M, Wu WS, Huang WC, Weng Z, Lee HC. 2018 “The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes”, Science. 359, 587-592 
  12. ​Tang W, Tu S, Lee HC, Weng Z, Mello CC. 2016 “The RNAse PARN-1 trimes piRNA 3’ ends to promote transcriptome surveillance in C. elegans”, Cell. 164(5):974-984.​
     * Co-first authors

    Earlier
  1. ​Lee HC*, Gu W*, Shirayama M, Youngman E, Conte DJ, Mello CC. 2012 “C. elegans piRNAs  medicate the genome-wide surveillance of germline transcripts”, Cell. Jul 6; 150 (1): 78-87.
  2. Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D, Mello CC. 2012 “ piRNAs initiate an epigenetic memory of non-self RNA in the C. elegans germline”, Cell. Jul 6 ;150 (1): 65-77
  3. Gu W, Lee HC, Chaves D, Youngman E, Pazour GJ, Conte DJ, Mello CC. 2012 “C. elegans piRNA are processed from capped-small RNAs transcribed from promoter throughout the genome”. Cell. 151(7):1488-500.
  4. Lee HC*, Aalto AP*, Yang Q, Chang CC, Huang G, Fisher D, Cha J, Poranen MM, Bamford DH and Liu Y. 2010 “The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring Replication Protein A and a DNA helicase”,  PLOS Biol. Oct 5;8(10). pii: e1000496.
  5. Lee HC*, Li L*, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, and Liu Y. 2010 “Diverse pathway generates microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi”, Mol Cell. 38 (6): 803-814 (Cover)
  6. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, and Liu Y. 2009. “qiRNA is a new type of small interfering RNA induced by DNA damage”, Nature. 459 (14):274-278  (Cover)
  7. Choudhary S*, Lee HC*, Maiti M*, He Q, Cheng P, Liu Q, and Liu Y. 2007. A double-stranded RNA response program important for RNA interference efficiency. Mol Cell Biol. 27(11):3995-4005  (Cover)                                           * These authors contributed equally to this study. 
  8. Maiti M, Lee HC, and Liu Y. 2007.  “QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands”, Genes & Dev. 21(5):590-600
  9. He Q, Cha J, He Q, Lee HC, Yang Y, and Liu Y. 2006. CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop. Genes & Dev. 20(18):2552-65
 * Co-first authors