Publications

Selected publications, peer-reviewed articles, and preprints from Ying Liu and collaborators.

Selected Publications

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  1. Liu Y*#, Miao T*, Wang A, Ezequiel D, Kim A-R, Zhang Z, Sun X, Binari R, Asara JM, Hu Y, Goncalves M, Janowitz T, Perrimon N#. Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer. bioRxiv. 2025. DOI *Equal contribution; #Corresponding author
  2. Liu Ying#, Dantas E, Ferrer M, Miao T, Qadiri M, Liu Yifang, Comjean A, Davidson EE, Perrier T, Ahmed T, Hu Y, Goncalves MD, Janowitz T, Perrimon N#. Hepatic gluconeogenesis and PDK3 upregulation drive cancer cachexia in flies and mice. Nature Metabolism. 2025;7:823–841. DOI #Corresponding author
  3. Qadiri M*, Liu Y*, Kim A-R, Han M, Zhou E, Veal A, Lu T-C, Li H, Hu Y, Perrimon N. FlyPhoneDB2: A computational framework for analyzing cell-cell communication in Drosophila scRNA-seq data integrating AlphaFold-multimer predictions. Computational and Structural Biotechnology Journal. 2025;27:2814–2822. DOI *Equal contribution
  4. Cheng C*, Liu Y*#, Chen Y, Li J, Xu W, Perrimon N#, Song W#. The Power of Drosophila in Modeling Cancer Cachexia. In: The Drosophila Model in Cancer: Volume II, Deng W-M, Gonzaléz C (Eds.), Springer Nature Switzerland. 2025:83–100. DOI *Equal contribution; #Corresponding author
  5. Kaur T*, Repiso A*, Liu Y*, Doria P, Urgell J, Rodriguez-Escudero L, Karkali K, Hu Y, Perrimon N, Martin-Blanco E. Failure of DNA repair leads to the tumorigenic transformation of a regenerating blastema in Drosophila imaginal discs. bioRxiv. 2025. DOI *Equal contribution
  6. Xu J*#, Liu Y*#, Yang F, Cao Y, Chen W, Li JSS, Zhang S, Comjean A, Hu Y, Perrimon N#. Mechanistic characterization of a Drosophila model of paraneoplastic nephrotic syndrome. Nature Communications. 2024;15:1241. DOI *Equal contribution; #Corresponding author
  7. Liu Y#, Saavedra P, Perrimon N#. Cancer cachexia: lessons from Drosophila. Disease Models & Mechanisms. 2022;15:dmm049298. DOI #Corresponding author
  8. Liu Y, Mattila J, Hietakangas V. Systematic screen for Drosophila transcriptional regulators phosphorylated in response to insulin/mTOR pathway. G3: Genes, Genomes, Genetics. 2020;10:2843–2849. DOI
  9. Liu Y*, Cerejeira Matos R*, Heino TI, Hietakangas V. PWP1 promotes nutrient-responsive expression of 5S ribosomal RNA. Biology Open. 2018;7:bio037911. DOI *Equal contribution
  10. Liu Y, Mattila J, Ventelä S, Yadav L, Zhang W, Lamichane N, Sundström J, Kauko O, Grénman R, Varjosalo M, Westermarck J, Hietakangas V. PWP1 mediates nutrient-dependent growth control through nucleolar regulation of ribosomal gene expression. Developmental Cell. 2017;43:240–252.e5. DOI

Other Publications

  1. Bosch JA, Beltran PMJ, Cavers C, LaGraff JT, Melanson R, Singh A, Chen W, Hu Y, Tattikota SG, Liu Y, Hashmi Y, Asara JM, Branon T, Ting AY, Carr SA, Perrimon N. Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking. Nature Communications. 2026;17:5425. DOI
  2. Miao T, Liu Y, Qadiri M, Asara JM, Hu Y, Sun X, Dibble C, Perrimon N. Renal Coenzyme A (CoA) production from VB5 fuels stem cell proliferation and tumor growth. Nature Communications. 2026;17:5383. DOI
  3. Deniz O, Liu Y, Kirkinen T, Kokki K, Gaertner K, Clavell-Revelles P, Mattila J, Hietakangas V. Spalt-related is an inhibitor of mTORC1-mediated growth activated by the integrated stress response. The EMBO Journal. 2026;45(16):5919–5942. DOI
  4. Ewen-Campen B, Chen W, Tattikota SG, Liu Y, Hu Y, Perrimon N. The Drosophila proventriculus lacks stem cells but compensates for age-related cell loss via endoreplication-mediated cell growth. Nature Communications. 2026;17:2086. DOI
  5. Han M, Xia B, Kim A-R, Filine E, Stoneburner E, Miao T, Liu Y, Zirin J, Perrimon N. Phage display-mediated immuno-PCR to detect low-abundance secreted proteins in Drosophila. Proceedings of the National Academy of Sciences (PNAS). 2026;123(15):e2531777123. DOI
  6. Lane E, Petsakou A, Liu Y, Chen W, Qadiri M, Hu Y, Perrimon N. Cholinergic signaling modulates intestinal pathophysiology in a Drosophila model of cystic fibrosis. PLoS Genetics. 2026;22(2):e1012048. DOI
  7. Hu Y, Rodiger J, Liu Yifang, Gao C, Liu Ying, Qadiri M, Veal A, Bulyk ML, Perrimon N. TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila. Genetics. 2026:iyaf082. DOI
  8. Li J, Huang K, Dibra I, Liu Y, Perrimon N, Simons M. Desaturase-dependent secretory functions of hepatocyte-like cells control systemic lipid metabolism during starvation in Drosophila. Nature Communications. 2025;16:10409. DOI
  9. Li JSS, Liu Y, Kim A-R, Qadiri M, Xu J, Xia B, Binari R, Asara JM, Hu Y, Perrimon N. The epigenetic factor Zrf1 regulates intestinal stem cell proliferation during midgut regeneration. PLoS Genetics. 2025;21(10):e1011910. DOI
  10. Petsakou A, Liu Yifang, Liu Ying, Comjean A, Hu Y, Perrimon N. Cholinergic neurons trigger epithelial Ca2+ currents to heal the gut. Nature. 2023;623:122–131. DOI
  11. Saavedra P, Dumesic PA, Hu Y, Filine E, Jouandin P, Binari R, Wilensky SE, Rodiger J, Wang H, Chen W, Liu Y, Spiegelman BM, Perrimon N. REPTOR and CREBRF encode key regulators of muscle energy metabolism. Nature Communications. 2023;14:4943. DOI
  12. Al-Sawaf O, Weiss J, Skrzypski M, Lam JM, Karasaki T, Zambrana F, Kidd AC, Frankell A, Watkins TBK, Martinez-Ruiz C, Sokac M, Collins S, Veeriah S, Magno N, Naceur-Lombardelli C, Prymas P, Toncheva A, Jayanth N, Salgado R, Bridge CP, Christiani D, Mak R, Bay C, Rosenthal M, Sattar N, Welsh P, Liu Y, Perrimon N et al. Body composition and lung cancer-associated cachexia in TRACERx. Nature Medicine. 2023;29:846–858. DOI
  13. Havula E, Ghazanfar S, Lamichane N, Francis D, Hasygar K, Liu Y, Alton LA, Johnstone J, Needham EJ, Pulpitel T. Genetic variation of macronutrient tolerance in Drosophila melanogaster. Nature Communications. 2022;13:1637. DOI
  14. Huang K, Liu Y, Perrimon N. Roles of insect oenocytes in physiology and their relevance to studies of human metabolic diseases: a mini review. Frontiers in Insect Science. 2022;2:859847. DOI
  15. Hasygar K, Deniz O, Liu Y, Gullmets J, Hynynen R, Ruhanen H, Kokki K, Käkelä R, Hietakangas V. Coordinated control of adiposity and growth by anti-anabolic kinase ERK7. EMBO Reports. 2021;22:e49602. DOI
  16. Qiao X, Liu Y, Prada ML, Mohan AK, Gupta A, Jaiswal A, Sharma M, Merisaari J, Haikala HM, Talvinen K, Yetukuri L, Pylvänäinen JW, Klefström J, Kronqvist P, Meinander A, Aittokallio T, Hietakangas V, Eilers M, Westermarck J. UBR5 is coamplified with MYC in breast tumors and encodes an ubiquitin ligase that limits MYC-dependent apoptosis. Cancer Research. 2020;80:1414–1427. DOI
  17. Liu Y, Zhang Y-B, Liu T-K, Gui J-F. Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family. PLOS ONE. 2013;8:e66859. DOI
  18. Zhang Y-B, Liu T-K, Jiang J, Shi J, Liu Y, Li S, Gui J-F. Identification of a novel Gig2 gene family specific to non-amniote vertebrates. PLOS ONE. 2013;8:e60588. DOI
  19. Liu T-K, Zhang Y-B, Liu Y, Sun F, Gui J-F. Cooperative roles of fish protein kinase containing Z-DNA binding domains and double-stranded RNA-dependent protein kinase in interferon-mediated antiviral response. Journal of Virology. 2011;85:12769–12780. DOI
  20. Sun F, Zhang Y-B, Liu T-K, Gan L, Yu F-F, Liu Y, Gui J-F. Characterization of fish IRF3 as an IFN-inducible protein reveals evolving regulation of IFN response in vertebrates. The Journal of Immunology. 2010;185:7573–7582. DOI
  21. Yu F-F, Zhang Y-B, Liu T-K, Liu Y, Sun F, Jiang J, Gui J-F. Fish virus-induced interferon exerts antiviral function through Stat1 pathway. Molecular Immunology. 2010;47:2330–2341. DOI