Selected Publications (*equal contribution. ^#correspondence author)

             (2/2023-present) [Associate Professor, University of Utah]

• Shi J*, Zhang X*, Cai C, Liu S, Yu J, James E, Liu L, Emery B, McMurray Bires M, Torres-Arce E, Rawal H, Ramsay J, Kunisaki J, Zhou C, Milstone DS, Patti ME, Yang X, Jenkins T, Quinlan AR. Cairns BR, Schimmel P, Hotaling JM, Aston KI^#, Zhou T^#, Chen Q^#. Conserved shifts in sperm small non-coding RNA profiles during mouse and human aging. The EMBO Journal (2026) https://doi.org/10.1038/s44318-025-00687-8 [Journal] [PDF] [News story] [Twitter/X digest]
• Cai C*, Yu J*, Zhang X, Zhou T^#, Chen Q^#. A model for propagation of RNA structural memory through biomolecular condensates. Nature Cell Biology (2025) https://doi.org/10.1038/s41556-025-01736-4 [Journal] [PDF] [Twitter/X digest]
• Rawal HC, Chen Q^#, Zhou T^#. FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. Bioinformatics (2025) https://doi.org/10.1093/bioinformatics/btaf526 [Journal] [PDF]
• Pessina P, Nevo M, Shi J, Kodali S, Casas E, Cui Y, Richards AL, Park EJ, Chen X, Levin-Ferreyra F, Stevenson E, Krogan NJ, Swaney DL, Ying Q, Chen Q, Brumbaugh J^#, Di Stefano B^#. Selective RNA sequestration in biomolecular condensates directs cell fate transitions. Nature Biotechnology (2025) DOI: 10.1038/s41587-025-02853-z [Journal] [PDF]
• Shi J^#, Zhang Y^#, Li Y, Zhang L, Yan M, Zhang X, Chen Q, Zhang Y^#. Optimized identification and characterization of small RNAs with PANDORA-seq. Nature Protocols (2025) Nov;20(11):3314-3338. [Journal] [PDF]
• Yu J*, Zhang X*, Cai C, Zhou T^#, Chen Q^#. Small RNA and Toll-Like receptor interactions: origins and disease mechanisms. Trends in Biochemical Sciences (2025) https://doi.org/10.1016/j.tibs.2025.01.004 [Journal] [PDF] (Cover Story)
• Yuan X, Su Y, Johnson B, Kirchner M, Zhang X, Xu S, Jiang S, Wu J, Shi S, Russo JJ, Chen Q, Zhang S^#. Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications. Journal of the American Chemical Society (2024) DOI: 10.1021/jacs.4c07280 [Journal] [PDF]
• Cai C, Chen Q^#. Father’s diet influences son’s metabolic health through sperm RNA. Nature (2024) 630(8017):571-573. https://doi.org/10.1038/d41586-024-01502-w [Journal] [PDF] [News]
• Kuhle B, Chen Q, Schimmel P^#. tRNA Renovatio: Rebirth through fragmentation. Molecular Cell (2023) Nov 16;83(22):3953-3971. https://doi.org/10.1016/j.molcel.2023.09.016 [Journal] [PDF]
• Chen Q^#, Zhou T^#. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. Journal of Biological Chemistry (2023) 299(10) 105225. https://doi.org/10.1016/j.jbc.2023.105225 [Journal] [PDF][tRNA thematic series]
• Zhang X, Chen Q^#. EDC exposure in 3D genome memory in transgenerational obesity. Nature Reviews Endocrinology (2023) doi.org/10.1038/s41574-023-00810-x [Journal] [PDF] 
      
  (2/2019-2/2023)  [Assistant Professor - Associate Professor, University of California, Riverside]

• Chen Q^#. Sperm RNA-mediated epigenetic inheritance in mammals: challenges and opportunities. Reproduction, Fertility and Development (2022) doi:10.1071/RD22218 [Journal] [PDF]

• Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z^#. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development (2022) Nov 1;149(21):dev200819. doi: 10.1242/dev.200819 [Journal] [PDF]
• Shi J, Zhou T^#, Chen Q^#. Exploring the expanding universe of small RNAs. Nature Cell Biology (2022) Apr;24(4):415–423. doi: 10.1038/s41556-022-00880-5 [Journal] [PDF] (cover story)
• Chen Q^#, Zhang X, Shi J, Yan M, Zhou T^#. Origins and evolving functionalities of tRNA-derived small RNAs. Trends in Biochemical Sciences (2021) Oct;46(10):790-804. [Journal] [PDF]
• Liu C, Liu H, Zhang H, Wang L, Li M, Cai F, Wang X, Wang L, Zhang R, Yang S, Liu W, Liang Y, Wang L, Song X, Su S, Gao H, Jiang J, Li J, Luo M, Gao F, Chen Q, Li W^#, Chen ZJ^#. Paternal USP26 mutations raise Klinefelter syndrome risk in the offspring of mice and humans. The EMBO Journal  (2021) May 12;e106864. doi: 10.15252/embj.2020106864 [Journal] [PDF]
• Shi J*, Zhang Y*, Tan D*, Zhang X*, Yan M*, Zhang Y*, Franklin R*, Shahbazi M, Mackinlay K, Liu S, Kuhle B, James ER, Zhang L, Qu Y, Zhai Q, Zhao W, Zhao L, Zhou C, Gu W, Murn J, Guo J, Carrell DT, Wang Y, Chen X, Cairns BR, Yang XL, Schimmel P, Zernicka-Goetz M, Cheloufi S^#, Zhang Y^#, Zhou T^#, Chen Q^#. PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nature Cell Biology  (2021) Apr;23(4):424-436. DOI: 10.1038/s41556-021-00652-7 [Journal] [PDF] [Twitter digest] [News story]
• Qu Y*, Chen Q*, Guo S*, Ma C, Lu Y, Shi J, Liu S, Zhou T, Noda T, Qian J, Zhang L, Zhu X, Lei X, Cao Y, Li W, Li W, Plachta N, Matzuk MM, Ikawa M, Duan E^#, Zhang Y^#, Wang H^#. Cooperation-based sperm clusters mediate sperm oviduct entry and fertilization. Protein & Cell (2021) doi:10.1007/s13238-021-00825-y [Journal] [PDF] [Movies]
• Gu W^#,*, Shi J*, Liu H*, Zhang X*, Zhou JJ, Li M, Zhou D, Li R, Lv J, Wen G, Zhu S, Qi T, Li W, Wang X, Wang Z, Zhu H, Zhou C, Knox KS, Wang T, Chen Q^#, Qian Z^#, Zhou T^#. Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer. Molecular Cancer. 2020 Nov 12;19(1):159. [Journal] [PDF]
  
• Zhang X*, Trebak F*, Souza LA; Shi J, Zhou T, Kehoe PG, Chen Q^#, Feng Earley Y^#. Small RNA modifications in Alzheimer's disease. Neurobiology of Disease (2020) Nov;145:105058. [Journal] [PDF] 
  
• Zhang Y^#, Chen Q^#. Human sperm RNA code senses dietary sugar. Nature Reviews Endocrinology (2020) Apr;16(4):200-201. [Journal] [PDF]
  
• Zhang X, Chen Q^#. A twist between ROS and sperm-mediated intergenerational epigenetic inheritance. Molecular Cell (2020) May 7;78(3):371-373.3 [Journal] [PDF]
  
• Zhang Y*, Shi J*, Rassoulzadegan M, Tuorto F, Chen Q^#. Sperm RNA code programmes the metabolic health of offspring. Nature Reviews Endocrinology  (2019) Aug;15(8):489-498. [Journal] [PDF]
• Zhang Y, Chen Q^#. The expanding repertoire of hereditary information carriers. Development  (2019) Mar 15;146(6):dev170902. doi: 10.1242/dev.170902 [Journal] [PDF]

           (10/2015-1/2019) [Assistant Professor, University of Nevada, Reno]

• Shi J*, Zhang Y*, Zhou T^#, Chen Q^#. tsRNAs: the Swiss army knife for translational regulation. Trends in Biochemical Sciences (2019) 44, 185-189. [Journal] [PDF]
  
• Wang J, Wang L, Feng G, Wang Y, Li Y, Li X, Liu C, Jiao G, Huang C, Shi J, Zhou T, Chen Q, Liu Z, Li W^#, Zhou Q^#. Asymmetric Expression of LincGET Biases Cell Fate in Two-Cell Mouse Embryos. Cell  (2018) Dec 13;175(7):1887-1901.e18 [Journal] [PDF]
  

• Liu Y, Chen Q^#. 150 years of Darwin’s theory of intercellular flow of hereditary information. Nature Reviews Molecular Cell Biology  (2018) 19, 749–750 [Journal] [PDF]

• Zhou T^#, Xie X, Li M, Shi J, Zhou JJ, Knox KS, Wang T, Chen Q, Gu W^#. Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. RNA. 2018; 24(11):1443-1456. [Journal] [PDF]
  
• Chen Q*, Shi J*, Tao Y, Zernicka-Goetz M^#. Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nature Communications (2018) 9:1819. DOI: 10.1038/s41467-018-04155-2 [Journal] [PDF]
• Shi J^#, Ko EA, Sanders KM, Chen Q^#, Zhou T^#. SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA- and tRNA- derived small RNAs. Genomics Proteomics & Bioinformatics  (2018) Apr;16(2):144-151 [Journal] [PDF]
• Zhang Y*, Zhang X*, Shi J*, Tuorto F*, Li X*, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y^#, Zhou Q^#, Duan E^#, Chen Q^#. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nature Cell Biology (2018) 20, 535–540. DOI: 10.1038/s41556-018-0087-2 [Journal] [PDF]
  -Highlighted in: Dad’s diet – smRNA methylation signatures in sperm pass on disease risk. Nat Rev Endocrinol. 2018 [PDF]   

• Zhang Y, Shi J, Chen Q^#. tsRNAs: new players in mammalian retrotransposon control. Cell Research (2017)27(11):1307-1308 [Journal][PDF] 
• Zhang X*, Cozen AE*, Liu Y,  Chen Q^# , Lowe TM^#. Small RNA Modifications: Integral to Function and Disease. Trends in Molecular Medicine. (2016) Dec;22(12):1025-1034. [Journal] [PDF]
  
• Chen Q^#, Yan W^#, Duan E^#. Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. Nature Reviews Genetics. (2016) Dec;17(12):733-743. [Journal] [PDF]
• Chen Q*^,#, Yan M*, Cao Z*, Li X*, Zhang Y*, Shi J*, Feng GH, Peng H, Zhang X, Zhang Y, Qian J, Duan E^#, Zhai Q^#, Zhou Q^#. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science. (2016) Jan 22;351(6271):397-400. [Journal] [PDF]
  -Editorial by: Sperm RNA fragments modify offspring metabolism. Science. 2016 Jan 1;351(6268):13. [PDF]
  -Highlighted in: Non-coding RNA: Inheritance of diet-induced metabolic changes via tsRNAs. Nat Rev Genet. 2016; 17(3):128. [PDF]
  -Highlighted in: Transferring Fragments of Paternal Metabolism to the Offspring. Cell Metab. 2016; 23(3), 401-402. [PDF]
  -Highlighted in: tRNA fragments: novel players in intergenerational inheritance. Cell Res. 2016;26(4):395-6. [PDF]
  -Highlighted in: Epigenetic Heredity: Transfer RNA Has Gone to Pieces. FASEB J. 2016;30(5):1691-3 [PDF]
  -Highlighted in: Small RNAs in Sperm, Affected by Diet, Transmit Information to Offspring. Biol Reprod. 2016;94(4):73. [PDF]
  -Highlighted in: Fat dad, fat kids: sperm small RNAs in control! Science Bulletin, 2016; 61(6) 428-429.  [PDF]
  
  

  (7/2011-9/2015) [Junior factulty & Co-PI at Institute of Zoology, Chinese Academy of Sciences]

• Shi J*, Chen Q*^,#, Li X*, Zheng X*, Zhang Y, Qiao J, Tang F, Tao Y^#, Zhou Q^#, Duan E^#. Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq. Development. (2015) 15;142(20):3468-77. [Journal] [PDF]
  -Highlighted in: Revisiting blastomere equality. Development 2015 142: e2002
  
• Zhang Y*, Chen Q*, Zhang H*, Wang Q*, Rong L, Jin Y, Wang H, Ma T^#, Qiao J^#, Duan E^#. Aquaporin-mediated excessive intrauterine fluid is a major contributor in hyper-estrogen induced aberrant embryo implantation. Cell Research. (2015) Jan,25(1):139-42. [Journal] [PDF]
• Zhang S*, Kong S*, Wang B, Cheng X, Chen Y, Wu W, Wang Q, Shi J, Zhang Y, Wang S, Lu J, Lydon JP, DeMayo F, Pear WS, Han H, Lin H, Li L, Wang H, Wang YL, Li B, Chen Q^#, Duan E^#, Wang H^#. Uterine Rbpj is required for embryonic-uterine orientation and decidual remodeling via Notch pathway-independent and -dependent mechanisms. Cell Research (2014), 24:925-942. [Journal] [PDF]
  -Cover Story & Highlighted in: Rbpj links uterine transformation and embryo orientation. Cell Res. (2014); 24:1031-2 [PDF]
  
• Zhang Y*, Zhang Y*, Shi J*, Zhang H, Cao Z, Gao X, Ren W, Ning Y, Ning L, Cao Y, Chen Y, Ji W, Chen Z#, Chen Q^#, Duan E^#. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection. Journal of Molecular Cell Biology (2014), 6:172-174. [Journal] [PDF]
  -Cover Story & Editor’s Recommendation: Characterization of serum-enriched tsRNAs.
• Chen Q*, Zhang Y*, Elad D, Jaffa AJ, Cao Y, Ye X^#, Duan E^#. Navigating the site for embryo implantation: Biomechanical and molecular regulation of intrauterine embryo distribution. Molecular Aspects of Medicine (2013) 34:1024-42. [Journal] [PDF]
• Peng H*, Shi J*, Zhang Y, Zhang H, Liao S, Li W, Lei L, Han C, Ning L, Cao Y, Zhou Q, Chen Q^#, Duan E^#. A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm. Cell Research (2012), 22: 1609-1612. [Journal] [PDF]
  -Highlighted in: A load of small RNAs in the sperm - how many bits of hereditary information? Cell Res. (2013);23:18-19. [PDF]

  
  (Before 7/2011) [Phd study]

• Chen Q, Duan EK^#. Aquaporins in sperm osmoadaptation: an emerging role for volume regulation. Acta Pharmacologica Sinica (2011), 32: 721-4. [Journal] [PDF]
  
• Chen Q*, Peng H*, Lei L*, Zhang Y, Kuang H, Cao Y, Shi QX, Ma T, Duan E^#. Aquaporin3 is a sperm water channel essential for postcopulatory sperm osmoadaptation and migration. Cell Research (2011), 21: 922-933. [Journal] [PDF]
  
• Chen Q*, Zhang Y*, Peng H, Lei L, Kuang H, Zhang L, Ning L, Cao Y, Duan E^#. Transient β2-Adrenoceptor activation confers pregnancy loss by disrupting embryo spacing at implantation. Journal of Biological Chemistry (2011), 286: 4349-4356. [Journal] [PDF]
• Chen Q*, Zhang Y*, Lu J, Wang Q, Wang S, Cao Y, Wang H^#, Duan E^#. Embryo-uterine cross-talk during implantation: the role of Wnt signaling. Molecular Human Reproduction (2009), 15: 215-221. [Journal] [PDF]
  
• Chen Q, Peng H, Zhang Y, Lei L, Cao Y, Duan E^#. Embryo implantation: a time for recalling and forwarding. Chinese Science Bulletin (2009),54: 4083-93. [Journal] [PDF]

TIBS (2025)