Publications

Publications

  1. Pak JH, Liu CY, Huangpu J and Graham JS (1997) Construction and characterization of the soybean leaf metalloproteinase cDNA. FEBS Letters 404: 283-288 (PMID: 9119080)
  2. Liu CY, Tian Y, Shen Q, Jiang H, Ju R, Yan T, Liu C, Mang K (1998) Cloning of ACC synthase cDNA and the inhibition of fruit ripening by its antisense RNA in transgenic tomato plants. Chin J Biotech 14: 139-146 (PMID: 10196631)
  3. Liu CY, Schroder M, Kaufman RJ. (2000) Ligand-independent dimerization activates the stress response kinases IRE1 and PERK in the lumen of the endoplasmic reticulum. Journal of Biological Chemistry 275:24881-5 (PMID: 10835430)
  4. Shen X, Ellis RE, Lee K, Liu CY, Yang K, Solomon A, Yoshida H, Morimoto R, Kurnit DM, Mori K, Kaufman RJ. (2001) Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development. Cell 107: 893-903 (PMID: 11779465)
  5. Scheuner D, Song B, McEwen E, Liu CY, Laybutt R, Gillespie P, Saunders T, Bonner-Weir S, Kaufman RJ. (2001) Translational control is required for the unfolded protein response and in vivo glucose homeostasis. Molecular Cell 7:1165-76 (PMID: 11430820)
  6. Kaufman RJ, Scheuner D, Schroder M, Shen X, Lee K, Liu CY, Arnold SM. (2002) The unfolded protein response in nutrient sensing and differentiation. Nature Review Molecular Cell Biology 3:411-21 (PMID: 12042763)
  7. Liu CY, Wong HN, Schauerte JA, Kaufman RJ. (2002) The protein kinase/ endoribonuclease IRE1 alpha that signals the unfolded protein response has a luminal N-terminal ligand-independent dimerization domain. Journal of Biological Chemistry 277: 18346-56 (PMID: 11897784)
  8. Liu CY, Kaufman RJ. (2003) The unfolded protein response. Journal of Cell Science 116: 1861-2 (PMID: 12692187)
  9. Liu CY, Xu Z, Kaufman RJ. (2003) Structure and intermolecular interactions of the luminal dimerization domain of human IRE1 alpha. Journal of Biological Chemistry 278: 17680-7 (PMID: 12637535)
  10. Schroder M, Clark R, Liu CY, Kaufman RJ. (2004) The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO Journal 23: 2281-92 (PMID: 15141165; PMCID: PMC419911)
  11. Welsh DK, Yoo SH, Liu AC, Takahashi JS, Kay SA (2004) Bioluminescence imaging of individual fibroblasts reveals persistent, independently phased circadian rhythms of clock gene expression. Current Biology 14: 2289-95 (PMID: 15620658; PMCID: PMC3777438)
  12. Zhou J*, Liu CY* (co-first author), Back SH, Clark RL, Peisach D, Xu Z*, Kaufman RJ* (co-senior author)(2006) The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response. Natl. Acad. Sci. USA. 103: 14343-8 (PMID: 16973740; PMCID: PMC1566190)
  13. Liu AC*, Welsh DK* (co-first author), Ko CH, Tran HG, Zhang EE, Priest AA, Buhr ED, Singer O, Meeker K, Verma IM, Doyle FJ, Takahashi JS, Kay SA (2007) Intercellular coupling confers robustness against mutations in the SCN circadian clock network. Cell 129: 605-616 (PMID: 17482552; PMCID: PMC3749832)
  14. Liu AC, Lewis WG, Kay SA (2007) Mammalian circadian signaling networks and therapeutic targets. Nature Chemical Biology 3 (10): 631-640 (PMID: 17876320)
  15. Liu AC, Tran HG, Zhang EE, Priest AA, Welsh DK, Kay SA (2008) Redundant function of REV-ERB alpha and beta and non-essential role for BMAL1 cycling in transcriptional regulation of intracellular circadian rhythms. PLoS Genetics 4(2): e1000023 (PMID: 18454201; PMCID: PMC2265523)
  16. Hirota T, Lewis WG, Liu AC, Lee JW, Schultz PG, Kay SA. (2008) A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3 beta. Proc Natl Acad Sci USA 105 (52): 20746–20751 (PMID: 19104043; PMCID: PMC2606900)
  17. Mirsky HP, Liu AC, Welsh DK, Kay SA, and Doyle FJ. (2009) A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci USA 106: 11107-12 (PMID: 19549830; PMCID: PMC2699375)
  18. Zhang EE*, Liu AC* (co-first author), Hirota T*, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, Janes J, Su AI, Hogenesch JB* and Kay SA* (co-senior author) (2009) A Genome-wide siRNA screen for modifiers of the circadian clock in human cells. Cell 139: 199-210 (PMCID: PMC2777987; PMID: 19765810)
  19. Ko CH, Yamada YR, Welsh DK, Buhr ED, Liu AC, Zhang EE, Ralph MR, Kay SA, Forger D, Takahashi JS (2010) Emergence of noise-induced oscillations in the central circadian pacemaker. PLoS Biology 8(10): e1000513 (PMID: 20967239; PMCID: PMC2953532)
  20. Zhang EE*, Liu Y* (co-first author), Dentin R, Pongsawakul PY, Liu AC, Hirota T, Nusinow DA, Sun X, Landais S, Kodama Y, Brenner DA, Montminy MR* and Kay SA* (co-senior author) (2010) CRY mediates circadian regulation of cAMP signaling and hepatic gluconeogenesis. Nature Medicine 16: 1152-1156 (PMID: 20852621; PMCID: PMC2952072)
  21. Ukai-Tadenuma M, Yamada R, Xu H, Ripperger JA, Liu AC and Ueda HR (2011) Delay in feedback repression by Cry1 is required for circadian clock function. Cell 144: 268-281 (PMID: 21236481)
  22. Marpegan L, Swanstrom AE, Chung K, Simon T, Haydon PG, Khan SK, Liu AC, Herzog ED and Beaulé C (2011) Circadian regulation of ATP release in astrocytes. Journal of Neuroscience 31:8342-8350 (PMID: 21653839; PMCID: PMC3135876)
  23. Ramanathan C, Khan SK, Kathale ND, Xu H, Liu AC (2012) Monitoring cell-autonomous circadian clock rhythms of gene expression using luciferase bioluminescence reporters. Journal of Visualized Experiments (67), e4234 3791/4234 (PMID: 23052244; PMCID: PMC3490247)
  24. Khan SK, Xu H, Ukai-Tadenuma M, Burton B, Wang Y, Ueda HR and Liu AC (2012) Identification of cryptochrome differentiating domain required for feedback repression in circadian clock function. Journal of Biological Chemistry 287 (31): 25917-26 (PMID: 22692217; PMCID: PMC3406676)
  25. Evans JA, Pan H, Liu AC, Welsh DK (2012) Cry1-/- circadian rhythmicity depends on SCN intercellular coupling. Journal of Biological Rhythms 27 (6): 443-452 (PMID: 23223370; PMCID: PMC3578226)
  26. Cao R, Robinson B, Xu H, Gkogkas C, Khoutorsky A, Alain T, Yanagiya A, Nevarko T, Liu AC, Amir S, and Sonenberg N (2013) Translational control of entrainment and synchrony of the suprachiasmatic circadian clock by mTOR/4E-BP1 signaling. Neuron 79(4):712-24 (PMID: 23972597; PMCID: PMC3856944)
  27. Anafi RC, Lee Y, Sato TK, Venkataraman A, Ramanathan C, Kavakli IH, Hughes ME, Baggs JE, Growe JP, Liu AC, Kim J, Hogenesch JB (2014) Machine learning helps identify CHRONO as a circadian clock component. PLoS Biology 12(4): e1001840 (PMID: 24737000; PMCID: PMC3988006)
  28. Ramanathan C, Xu H, Khan SK, Shen Y, Gitis PJ, Welsh DK, Hogenesch JB, and Liu AC (2014) Cell type-specific functions of Period genes revealed by novel adipocyte and hepatocyte circadian clock models. PLoS Genetics 10(4): e1004244 (PMID: 24699442; PMCID: PMC3974647)
  29. Kathale ND and Liu AC (2014) Prevalence of cycling genes and drug targets calls for prospective chronotherapeutics (commentary). Proc Natl Acad Sci USA 111: 15869-70 (PMID: 25368193; PMCID: PMC4234540)
  30. Cao R, Gkogkas CG, Zavalia ND, Blum ID, Yanagiya A, Tsukumo Y, Xu H, Lee C, Storch KF, Liu AC, Amir S*and Sonenberg N* (co-senior author) (2015). Light-regulated translational control of circadian behavior by eIF4E phosphorylation. Nature Neuroscience 18(6):855-62 (PMID: 25915475; PMCID: PMC4446158)
  31. Xu H*, Gustafson CL* (co-first author), Sammons PJ, Khan SK, Parsley NC, Ramanathan C, Lee HW, Liu AC* and Partch CL* (co-senior author) (2015) Cryptochrome 1 regulates the circadian clock through dynamic interactions with the BMAL1 C-terminus. Nature Structure Molecular Biology 22(6):476-84 (PMID: 25961797; PMCID: PMC4456216)
  32. Xu L, Ruan G, Dai H, Liu AC, Penn J, McMahon DG (2016) Mammalian retinal Müller cells have circadian clock function. Molecular Vision 22:275-283 (PMID: 27081298; PMCID: PMC4812508)
  33. Zheng Z, Kim H, Qiu, Y, Chen X, Mendez R, Dandekar A, Zhang X, Zhang C, Liu, AC, Yin L, Lin, J, Walker P, Kapatos G, Zhang K (2016) CREBH Couples Circadian Clock with Hepatic Lipid Metabolism. Diabetes 65(11): 3369-3383 (PMID: 27507854; PMCID: PMC5079639)
  34. Gustafson CL, Parsley NC, Asimgil H, Lee H, Ahlbach C, Michael AK, Xu H, Williams OL, Davis TL, Liu AC, Partch CL (2017) A slow conformational switch in the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell 66: 447–457 (PMID: 28506462)
  35. Hughes ME… Liu AC… Hogenesch JB (2017) Guidelines for genome-scale analysis of biological rhythms. Journal of Biol Rhythms 32(5):380-393 (PMID: 29098954) 
  36. Ramanathan C, Liu AC (2018) Developing mammalian cellular clock models using firefly luciferase reporter. Methods in Molecular Biology 1755:49-64 (PMID: 29671262)
  37. Wible RS*, Ramanathan C*, Sutter CH, Olesen KM, Kensler TW, Liu AC*, Sutter TR* (*equal contribution) (2018) NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus. eLife 7: e31656 (PMID: 29481323)
  38. Delahaye LB, Bloomer RJ, Butawan MB, Wyman J, Hill JL, Lee HW, Liu AC, McAllan L, Han JC and van der Merwe M (2018) Time-restricted feeding of a high-fat diet in C57BL/6 male mice reduces adiposity but does not protect against increased systemic inflammation. Appl Physiol Nutr Metab 43(10):1033-1042 (PMID: 29717885) 
  39. Ramanathan C, Kathale ND, Liu D, Lee C, Freeman DA, Hogenesch JB, Cao R*, Liu AC* (co-senior author) (2018) mTOR signaling regulates central and peripheral circadian clock function. PLoS Genetics 14(5): e1007369 (PMID: 29750810)
  40. Zheng T, Zhang B, Chen C, Ma J, Meng D, Huang J, Hu R, Liu X, Otsu K, Liu AC, Li H, Yin Z, Huang G (2019) p38 alpha signaling in dendritic cells regulates colon inflammation and tumorigenesis. Proc Natl Acad Sci USA 115(52): E12313-E12322 (PMID: 30541887)
  41. Pathaka S, Liu D, Li T, de Zavaliac N, Zhu L, Li J, Karthikeyan R, Alain T, Liu AC, Storch KF, Kaufman RJ, Jin VX, Amir S, Sonenberg N, Cao R. (2019) The eIF2α kinase GCN2 modulates period and rhythmicity of the circadian clock by translational control of Atf4. Neuron 104:724-735.e6 DOI: 10.1016/j.neuron.2019.08.007 (PMID: 31522764; PMCID: PMC6872934)
  42. Lee Y, Shen Y, Francey LJ, Ramanathan C, Sehgal A, Liu AC, Hogenesch JB. (2019) The NRON complex controls circadian clock function through regulated PER and CRY nuclear translocation. Sci Rep 9(1):11883. (PMID: 31417156; PMCID: PMC6695496) https://pubmed.ncbi.nlm.nih.gov/31417156/; DOI: 10.1038/s41598-019-48341-8
  43. Morris AR, Stanton DL, Roman D, Liu AC. (2020) Systems level understanding of circadian integration with cell physiology. J Mol Biol 432 (12):3547-3564 (PMID: 32061938; PMCID: PMC8934204) https://pubmed.ncbi.nlm.nih.gov/32061938/; DOI: 10.1016/j.jmb.2020.02.002
  44. Bian T, Corral P, Wang Y, Botello J, Kingston R, Daniels T, Salloum RG, Johnston E, Huo Z, Lu J, Liu AC, Xing C. (2020) Kava as a clinical nutrient: promises and challenges. Nutrients 12(10):3044. DOI: 10.3390/nu12103044 (PMID: 33027883; PMCID: PMC7600512)
  45. Anton SD, Cruz-Almeida Y, Singh A, Alpert J, Bensadon B, Cabrera M, Clark DJ, Ebner NC, Esser KE, Fillingim RB, Goicolea SM, Han SM, Kallas H, Johnson A, Leeuwenburgh C, Liu AC, Manini TM, Marsiske M, Moore F, Qiu P, Mankowski RT, Mardini M, McLaren C, Ranka S, Rashidi P, Saini S, Sibille KT, Someya S, Wohlgemuth S, Tucker C, Xiao R, Pahor M. (2020) Innovations in Geroscience to Enhance Mobility in Older Adults. Experimental Gerontology 142:111123 (PMID: 33191210; PMCID: PMC7581361) https://pubmed.ncbi.nlm.nih.gov/33191210/; DOI: 10.1016/j.exger.2020.111123
  46. Ding H, Meng L, Liu AC, Gumz ML, Bryant AJ, Mcclung CA, Tseng GC, Esser KA, Huo Z. (2021) Likelihood-based Tests for Detecting Circadian Rhythmicity and Differential Circadian Patterns in Transcriptomic Applications. Briefings in Bioinformatics 22(6):bbab224. (PMID: 34117739; PMCID: PMC8575021) https://pubmed.ncbi.nlm.nih.gov/34117739/; DOI: 10.1093/bib/bbab224
  47. Hernandez AR, Hoffman JM, Hernandez CM, Cortes CJ, Jumbo-Lucioni P, Baxter MG, Esser KA, Liu AC, McMahon LL, Bizon JL, Burke SN, Buford TW, Carter CS. (2021) Reuniting the Body “Neck Up and Down” to Understand Cognitive Aging: The Nexus of Geroscience and Neuroscience. J Gerontol glab215 doi: 10.1093/gerona/glab215 (PMID: 34309630)
  48. Healy KL, Morris AR, Liu AC. (2021) Circadian Synchrony: Sleep, Nutrition, and Physical Activity. Front Netw Physiol 1:732243. doi: 10.3389/fnetp.2021.732243. (PMID: 35156088; PMCID: PMC8830366)
  49. Shen Y, Endale M, Wang W, Morris, AR, Francey LJ, Harold RL, Hammers DW, Huo Z, Partch CL, Hogenesch JB, Wu ZH, Liu AC. (2021) NF-kB modifies the mammalian circadian clock through interaction with the core clock protein BMAL1. PLoS Genet 17(11):e1009933. DOI: 10.1371/journal.pgen.1009933 (PMID: 34807912; PMCID: PMC8648109)
  50. Bryant AJ, Ebrahimi E, Nguyen A, Wolff CA, Gumz ML, Liu AC, Esser KA. (2021) A Wrinkle in Time: Circadian biology in pulmonary vascular health and disease. Am J Physiol Lung Cell Mol Physiol. doi: 10.1152/ajplung.00037.2021 (PMID: 34850650)
  51. Crislip GR, Johnston JG, Douma LG, Costello HM, Juffre A, Boyd K, Li W, Maugans CC, Gutierrez-Monreal M, Esser KA, Bryant AJ, Liu AC, Gumz ML. (2022). Circadian rhythm effects on the molecular regulation of physiological systems. Comprehensive Physiology 12(1):2769-2798. DOI: 10.1002/cphy.c210011 (PMID: 34964116)
  52. Lee YY, Endale M, Wu G, Ruben MD, Francey LJ, Morris AR, Choo NY, Anafi RC, Smith DF, Liu AC, Hogenesch JB (2023). Integration of genome-scale data identifies candidate sleep regulators. Sleep 8;46(2):zsac279 (PMID: 36462188; PMCID: PMC9905783) DOI: 10.1093/sleep/zsac279
  53. Wolff CA, Gutierrez-Monreal MA, Meng L, Zhang X, Douma LG, Costello HM, Douglas CM, Ebrahimi E, Alava BR, Morris AR, Endale MM, Crislip GR, Cheng K, Schroder EA, Delisle BP, Bryant AJ, Gumz ML, Huo Z#, Liu AC#, Esser KA# (2023). Defining the age-dependent and tissue-specific circadian transcriptome in male mice. Cell Rep 42(1):111982. DOI: 10.1016/j.celrep.2022.111982 (PMID: 36640301; PMCID: PMC9929559)
  54. Cal-Kayitmazbatir S, Francey LJ, Lee Y, Liu AC, Hogenesch JB (2023), PSMD11 modulates circadian clock function through PER and CRY nuclear translocation. PLoS One 18(3):e0283463. doi: 10.1371/journal.pone.0283463 (PMID: 36961772: PMCID: PMC10038281)
  55. Liu AC#, Shen Y#, Roman D, He H, Serbinski CR, Aschbacher-Smith L, King KA, López I, Krueger DA, Dye TJ, Smith DF, Hogenesch JB, Prada CE# (2022). Detailed Clinical and Functional Studies of New MTOR Variants in Smith-Kingsmore Syndrome Reveal Deficits of Circadian and Sleep Homeostasis. (medRxiv 269076)