Kathy Liu Lab

List of Publications

At Penn

shared first authorship       *corresponding author

  1. Owens M, Lavorando E, Liu KF*: Gene regulation by sex chromosome-encoded homologous proteins. Genes & Dev., accepted (2024)
  2. Owens M, Yanas A, Liu KF*: Sex chromosome-encoded protein homologs: current progress and open questions. Nat. Struct. Mol. Biol., accepted (2024)
  3. Chen Y, Owens M†, Liu KF*: Coordination of RNA modifications in the brain and beyond. Mol. Psych., 28, 2737–2749 (2023)
  4. Shen H, Owens M, Yanas A, Lavorando E, Tang HY, and Liu KF* (2023): Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate hollow condensates of DDX3X disease variants. BioRxiv, (2023) (DOI: 10.1101/2023.03.19.533240)
  5. Gonskikh Y, Stoute J, Shen H, Budinich K, Pingul B, Schultz K, Elashal H, Marmorstein R, Shi J, Liu KF* (2023): Non-catalytic regulation of 18S rRNA methyltransferase DIMT1 in acute myeloid leukemia. Genes & Dev. (2023) (DOI:10.1101/gad.350298.122)
  6. Maldonado-Lopez A, Huang S, Pacella G, Ko EK, Shen H, Stoute J, Sinkfield M, Anderson A, Prouty S, Li H, Seykora JT, Liu KF, and Capell B* (2023): METTL3 maintains epithelial homeostasis through m6A-dependent regulation of chromatin modifiers. BioRxiv, (2023) (DOI: 10.1101/2022.12.14.520484)
  7. Basavappa M; Ferretti M; Dittmar M; Stoute J; Sullivan M; Whig K; Shen H; Liu KF; Schultz D; Beiting D; Lynch K; Henao-Mejia J; Cherry S* (2022): The novel lncRNA ALPHA specifically targets chikungunya virus to control infection. Mol. Cell, (DOI: 10.1016/j.molcel.2022.08.030)
  8. Perlegos A, Shields E, Shen H, Liu KF, and Bonini N* (2022): Mettl3-dependent m6A modification attenuates the brain stress response in Drosophila, Nat. Commun., 13, 5387 (DOI: 10.1038/s41467-022-33085-3)
  9. Shen H, Yanas A, Owens MC, Zhang C, Fritsch C, Fare CM, Copley KE, Shorter J, Goldman YE, and Liu KF* (2022): Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separationMol. Cell, 82, 1-16. (DOI: 10.1016/j.molcel.2022.04.022)
  10. Santoleri D, Lim HW, Emmett MJ, Stoute J, Gavin MJ, Sostre-Colón J, Uehara K, Welles J, Liu KF, Lazar MA, Titchenell PM. (2022) Global-run on sequencing identifies Gm11967 as an Akt-dependent long noncoding RNA involved in insulin sensitivity. iScience16;25(6):104410. (DOI: 10.1016/j.isci.2022.104410)
  11. Owens MC, Zhang C, and Liu KF* (2021): Recent technical advances in the study of nucleic acid modifications. Mol. Cell, 81(20), 4114-4136 (DOI: 10.1016/j.molcel.2021.07.036)
  12. Shen H, Gonskikh Y, Stoute J, and Liu KF* (2021): Human DIMT1 generates N26,6A dimethylation-containing small RNAsJ. Biol. Chem., 297, 2021, 101146 (DOI: 10.1016/j.jbc.2021.101146)
  13. Stoute J and Liu KF* (2021): CLIP-Seq to identify targets and interactions of RNA binding proteins and RNA modifying enzymesMethods Enzymol., 297, 2021, 101146 (DOI: 10.1016/bs.mie.2021.08.001)
  14. Shen H, Ontiveros RJ, Owens MC, Liu MY, Ghanty U, Kohli RM, and Liu KF* (2020): TET-mediated 5-methylcytosine oxidation in tRNA promotes translation. J. Biol. Chem.296, 2021, 100087 (DOI: 10.1074/jbc.RA120.014226)
  15. Ontiveros RJ, Shen H, Stoute J, Yanas A, Cui Y, Zhang Y, and Liu KF* (2020)  Coordination of mRNA and tRNA methylations by TRMT10A. PNAS 117(14), 7782-7791 (PNAS direct submission) (DOI: 10.1073/pnas.1913448117
  16. Shen H, Stoute J, and Liu KF* (2020) Structural and catalytic roles of the human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation. J. Biol. Chem., 295, 12058-12070 (DOI: 10.1074/jbc.RA120.014236)
  17. Wang Y, Liu KF, Yang Y, Davis I, and Liu A* (2020)  Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens. PNAS 117(33), 19720-19730 (PNAS direct submission) (DOI: 10.1073/pnas.2005327117)  
  18. Yanas A and Liu KF* (2019) RNA modifications and the link to human disease. Methods Enzymol., 2019;626:133-146 (DOI: 10.1016/bs.mie.2019.08.003)
  19. Ontiveros RJ, Stoute J, and Liu KF* (2019) The chemical diversity of RNA modifications. Biochem. J., 476(8), 1227-1245 (DOI: 10.1042/BCJ20180445)
  20. Yang Y, Liu F*, and Liu A* (2018) Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. J. Biol. Chem., 293 (27), 10415-10424 (DOI: 10.1074/jbc.RA118.002698) (featured JBC cover story)

Before Penn


  1. Wei J, Liu F, Lu Z, Fei Q, Ai Y, He PC, Shi H, Cui X, Su R, Klungland A, Jia G, Chen J, He C. (2018) Differential m6A, m6Am, and m1A demethylation mediated by FTO in the cell nucleus and cytoplasm. Mol. Cell 71(6), 973-985 (DOI: 10.1016/j.molcel.2018.08.011) (shared first authorship)
  2. Liu F and He C (2017) A new modification for mammalian messenger RNA. J. Biol. Chem. 292(35) 14704 –14705 (DOI: 10.1074/jbc.H117.798298)
  3. Ferreira F, Shin I, Sosova I, Dornevil K, Jain Shailly, Dewey D, Liu F, and Liu A (2017Hypertryptophanemia due to tryptophan 2,3-dioxygenase deficiency. Mol. Genet. Metab. 120(4), 317-324 (DOI: 10.1016/j.ymgme.2017.02.009)
  4. Liu F, Clark W, Luo G, Wang XY, Fu Y, Wei J, Wang X, Hao Z, Dai Q, Zheng G, Ma H, Han D, Evans M, Klungland A, Pan T, and He C (2016) ALKBH1-mediated tRNA demethylation regulates translation. Cell, 167(3): 816-828 (DOI: 10.1016/j.cell.2016.09.038) (featured in the news at Genetic Engineering & Biotechnology News, Phys.org, and Science Daily)
  5. Liu F, Geng J, Gummper RH, Barman A, Davis I, Hamelberg D, Ozarowski A, and Liu A (2015) An iron reservoir to the catalytic metal: The rubredoxin iron in an extradiol dioxygenase. J. Biol. Chem. 290(25): 15621-15634. (DOI: 10.1074/jbc.M115.650259) (shared first authorship)
  6. Huo L, Liu F, Iwaki H, Hasegawa Y, and Liu A (2015) Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD): A structural and mechanistic unveiling. Proteins 83(1): 178-197 (DOI: 10.1002/prot.24722) (shared first authorship)
  7. Huo L, Davis I, Liu F, Andi B, Esaki S, Iwaki H, Hasegawa Y, Orville AM, and Liu A (2015) Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action. Nat. Commun. 6:5935 (DOI: 10.1038/ncomms6935) (Featured in the news at National Science Foundation Science360 and Medical News Today)
  8. Chen W, Zhang L, Zheng G, Fu Y, Ji Q, Liu F, Chen H and He C (2014) Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett. 588(6): 892-898 (DOI: 10.1016/j.febslet.2014.02.021)
  9. Geng J, Davis I, Liu F, and Liu A (2014) Bis-Fe(IV): nature's sniper for long-range oxidation. J. Biol. Inorg. Chem. 19: 1057-1641 (DOI: 10.1007/s00775-014-1123-8
  10. Liu F, Rehmani I, Fu R, Esaki S, Chen L, de Serrano V, and Liu A (2013) Pirin is an iron-dependent redox regulator of NF-κB. PNAS, 110: 9722-9727 (DOI: 10.1073/pnas.1221743110) (PNAS direct submission; Faculty of 1000 recommended article)
  11. Yukl ET, Liu F, Krzystek J, Shin S, Jensen LMR, Davidson VL, Wilmot CM, and Liu A (2013) Diradical intermediate within the context of tryptophan tryptophylquinone biosynthesis. PNAS, 110: 4569-4573 (DOI: 10.1073/pnas.1215011110) (PNAS direct submission; Faculty of 1000 recommended article)
  12. Rehmani I, Liu F, and Liu A (2013) Ch. 8 Cell Signaling and Transcription, In Molecular Basis of Oxidative Stress: Chemistry, Mechanisms, and Disease Pathogenesis, edited by Frederick A. Villamena, John Wiley & Sons, Inc. pp. 179-201 (ISBN: 978-0-470-57218-4) (DOI: 10.1002/9781118355886)
  13. Lewis NA, Liu F, Seymour L, Magnusen A, Erves TR, Arca JF, Becκford FA, Venκatraman R, Gonzáez-Sarrías A, Fronczeκ FR, van Derveer DG, Seeram NP, Liu A, Jarrett WJ, Holder AH (2012) Synthesis, characterization and preliminary in vitro studies of vanadium(IV) complexes with a Schiff base and thiosemicarbazones as mixed-ligands. Eur. J. Inorg. Chem. 4, 664-677 (DOI: 10.1002/ejic.201100898)
  14. Fu R, Liu F, Davidson VL, and Liu A (2009) Heme iron nitrosyl complex of MauG reveals efficient redox equilibrium between hemes with only one heme exclusively binding exogenous ligands. Biochemistry 48: 11603-11605 (DOI: 10.1021/bi9017544)

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