Publications

Selected Publications

• Cai, Y.D., G.K. Chow, S. Hidalgo, X. Liu, K.C. Jackson, C.D. Vasquez, Z.Y. Gao, V.H. Lam, C.A. Tabuloc, H. Zheng, C. Zhao, J.C. Chiu (2024). Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. bioRxiv doi: https://doi.org/10.1101/2024.05.10.593646 [html].

• Liu, X., Y.D Cai, A.J.P. Mendiola, X. Xu, Y. Luo, H. Zheng, C. Zhao, C.H. Chen, Y. Xiang, J.C. Chiu (2024). Mealtime alters daily rhythm in nuclear O-GlcNAcome to regulate hepatic gene expression. bioRxiv doi: https://doi.org/10.1101/2024.06.13.598946 [html].

• Tabuloc, C.A., C.R. Carlson, F. Ganjisaffar, C.C. Truong, C.H. Chen, K.M. Lewald, S. Hidalgo, N.L. Nicola, C.E. Jones, A.A. Sail, F.G. Zalom, J.C. Chiu (2024). Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance. Scientific Reports 14(1): 19867.  doi: 10.1038/s41598-024-70037-x [html]. bioRxiv doi: https://doi.org/10.1101/2024.06.17.599459 [html].

• Liu, X., Y.D. Cai, J.C. Chiu (2024). Regulation of protein O-GlcNAcylation by circadian, metabolic, and cellular signals. J Biol Chem 300(2): 105616. DOI:https://doi.org/10.1016/j.jbc.2023.105616 [html].

• Y. Umezaki, S. Hidalgo, E. Nguyen, T. Nguyen, J. Suh, S.S. Uchino, J.C. Chiu, F.N. Hamada (2024). Taste triggers a homeostatic temperature control in Drosophila. eLife doi: https://doi.org/10.7554/eLife.94703.1 [html].

• Wei, Q., Z.L. Feng, Y.D. Cai, J.C. He, F.X. Lai, P.J. Wan, W.X. Wang, Q. Yao, J.C. Chiu, Q. Fu (2024). Characterization of light-dependent rhythm of courtship vibrational signals in Nilaparavata lugens: essential involvement of cryptochrome genes. Pest Manag Sci 80(2): 508-517. doi: https://doi.org/10.1002/ps.7782  [html].

• Hidalgo, S., M. Anguiano, C.A. Tabuloc, J.C. Chiu (2023). Seasonal cues act through the circadian clock and pigment-dispersing factor to control EYES ABSENT and downstream physiological changes. Curr Biol 33(4): 675-687.e5 [html]. Previously published in bioRvix doi: https://doi.org/10.1101/2022.10.27.514061 [html].

• Tabuloc, C.A., Y.D. Cai, R.S. Kwok, E.C. Chan, S. Hidalgo, J.C. Chiu (2023). CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters. PLOS Genetics 19(2): e1010649. https://doi.org/10.1371/journal.pgen.1010649 [html].

• Hidalgo, S., J.C. Chiu (2023). Integration of photoperiodic and temperature cues by the circadian clock to regulate insect seasonal adaptations. J Comp Physiol A 210(4): 585-599. doi:  https://doi.org/10.1007/s00359-023-01667-1  [html].

• Lewald, K.M., C.A. Tabuloc, K.E. Godfrey, J. Arno, C.R. Perini, J.C. Guedes, J.C. Chiu (2023). Genome assembly and population sequencing reveal three populations and signatures of insecticide resistance of Tuta absoluta in Latin America. Genome Biol Evol 14(4):evad060 [html]. Previously in bioRxiv doi:https//doi.org/10.1101/2022.12.15.520645 [html].

• Lewald, K.M., W. Song, D. Eweis-LaBolle, C. Truong, K.E. Godfrey, J.C. Chiu (2023). Probe-based quantitative PCR and RPA-Cas12a molecular diagnostics for detection of the tomato pest Phthorimaea absoluta. J Econ Entomol toad079. [html]

• Hidalgo, S. J.C. Chiu (2023). CRUMB: a shiny-based app to analyze rhythmic feeding in Drosophila using the FLIC system. F1000Research 12:374. [html]. 

• Philpott, J.M., A.M. Freeberg, J.  Park, K. Lee, C.G. Ricci, S.R. Hunt, R. Narasimamurthy, D.H. Segal, R. Robles, Y.D. Cai, S. Tripathi, J. A. McCammon, D.M. Virshup, J.C. Chiu, C. Lee, C.L. Partch (2023). PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period. Molecular Cell 83(10):1677-1692. [html]  Previously in bioRxiv. doi: https://doi.org/10.1101/2022.06.24.497549. 

• Pelham, J.F., A.E. Mosier, S.C. Altshuler, M.L. Rhodes, C.L. Kirchhoff, W.B. Fall, C. Mann, L.S. Baik, J.C. Chiu, J.M. Hurley (2023). Conformational changes in the negative arm of the circadian clock correlate with dynamic interactomes involved in post-transcriptionally regulation. Cell Reports 42(4): 112376 [html]. Previously in bioRxiv. doi: https://doi.org/10.1101/2021.11.20.469315.

• Hidalgo, S. J.C. Chiu (2022). Glutamate and clock help bean bugs track seasonal reproductive changes. PLOS Biol 20(9): e3001796. [html]

• Liu, X., J.C. Chiu (2022). Nutrient-sensitive protein O-GlcNAcylation shapes daily biological rhythms. Open Biol 12(9):220215 [html].

• Umezaki, Y. S. Hidalgo, E. Nguyen, T. Nguyen, J. Suh, S.S. Uchino, J.C. Chiu, F.N. Hamada (2022). Internal needs drive the cephalic phase response in Drosophila melanogaster. bioRxiv doi: https://doi.org/10.1101/2022.09.30.510382 [html]

• Cai, Y.D., S.I. Hidalgo Sotelo, K.C. Jackson, J,C, Chiu (2022). Assaying Circadian Locomotor Activity Rhythm in Drosophila. In: Hirota, T., Hatori, M., Panda, S. (eds) Circadian Clocks. Neuromethods, vol 186. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2577-4_3 [html].

• Joshi, R.*, Y.D. Cai*, Y. Xia, J.C. Chiu, P. Emery (2022). PERIOD phosphoclusters control temperature compensation of the Drosophila circadian clock. Frontiers in Physiology 13:888262.  doi: 10.3389/fphys.2022.888262.  *Co-first authors [html]

• Ganjisaffar, F., B.E. Gress, M.R. Demkovich, N.L. Nicola, J.C. Chiu, F.G. Zalom (2022). Spatio-temporal variation of spinosad susceptibility in Drosophila suzukii, a three-year study in California's Monterey Bay Region. J Econ Entomol 115(4): 872-890. [html]

• Ganjisaffar, F., M.R. Demkovich, N.L. J.C. Chiu, F.G. Zalom (2022). Characterization of field-derived Drosophila suzukii resistance to pyrethroids in California Berry production. J Econ Entomol Aug 12:toac118. Online ahead of print [html]

• Liu X.H., I. Blaženović, A.J. Contreras, T.M. Pham, C.A. Tabuloc, Y.H. Li, J. Ji, O. Fiehn and J.C. Chiu (2021). Hexosamine biosynthetic pathway and O-GlcNAc processing enzymes regulate daily rhythms in protein O-linked N-acetylglucosaminylation. Nature Communications 12:4173 [html]

• Cai, Y.D., J.C. Chiu (2021). Timeless in animal circadian clocks and beyond. FEBS Journal (Online ahead of print). doi: 10.1111/febs.16253. [html] 

• Cai Y.D., Y. Xue, C. Truong, J. Del-Carmen Li, C. Ochoa, J.T. Vanselow, K.A. Murphy, Y.H. Li, X. Liu, B.L. Kunimoto, H. Zheng, C. Zhao, Y. Zhang, A. Schlosser, J.C. Chiu (2021). CK2 inhibits TIMELESS nuclear export and modulates CLOCK transcriptional activity to regulate circadian rhythms. Curr Biol 31(3): 502-514. [html]

• Lewald, K.M., A. Abrieux, D.A. Wilson, Y. Lee, W.R. Conner, ....... J.C. Chiu (2021). Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental U.S. G3 (Bethesda) Oct 2:jkab343. doi: 10.1093/g3journal/jkab343. [html]

• Durkin, S.M., M. Chakraborty, A. Abrieux, K.M. Lewald, A. Gadau, N. Svetec, J. Peng, M. Kopyto, C.B. Langer, J.C. Chiu, J.J. Emerson, L. Zhao (2021). Behavioral and genomic sensory adaptations underlying the pest activity of Drosophila suzukii. Mol Biol Evol 38(6); 2532-2546. [html]

• Perini, C.R., C.A. Tabuloc, J.C. Chiu, F.G. Zalom, R.F. Stacke, O. Bernardii, D.R. Nelson, J.C. Guedes (2021). Transcriptome analysis of pyrethroid-resistant Chrysodeixis includes reveals overexpression of metabolic detoxification genes. J Econ Entomol 114(1):274-283. [html]

• Abrieux, A., Y. Xue, Y. Cai, K.M. Lewald, H.N. Nguyen, Y. Zhang, J.C. Chiu. (2020). EYES ABSENT and TIMELESS integrate photoperiodic and temperature cues to regulate seasonal physiology in Drosophila. Proc. Natl. Acad. Sci. U.S.A. 117(26): 15293-15304. [html|pdf|press release]

• Sarikaya D.P., J. Cridland, A. Tarakji, H. Sheehy, S. Davis, A. Kochummen, R. Hatmaker, N. Khan, J.C. Chiu, D.J. Begun (2020). Phenotypic coupling of sleep and starvation resistance evolves in D. melanogaster. BMC Evol Biol 20:126. [html]

• Abrieux, A., J.C. Chiu (2020). Manipulation of circadian rhythm and seasonal biology using light as a strategy for insect control. In "Optical Manipulation of Pests and Beneficials Arthropod", ed. David Ben-Yakir. CABI Press.

• Lewald, K.M., J.C. Chiu (2020). Harnessing transcriptomics to study insect biology. In "Transcriptomics in Entomological Research", ed. Matan Shelomi. CABI Press.

• Xue, Y., J.C. Chiu, Y. Zhang (2019). SUR-8 interacts with PP1-87B to stabilize PERIOD and regulate circadian rhythms in Drosophila. PLOS Genetics 15(11): e1008475. [html]

• Liu, Z., C.A. Tabuloc, Y. Xue, Y. Cai, P. McIntire, Y. Niu, V.H. Lam, J.C. Chiu, Y. Zhang (2019). Splice variants of DOMINO control Drosophila circadian behavior and pacemaker neuron maintenance. PLOS Genetics 15(10): e1008474. [html]

• Li, Y.H., X.H. Liu, J. T. Vanselow, H.Y. Zhang, A. Schlosser, J.C. Chiu (2019). O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression. PLOS Genetics 15(1): e1007953. [html]

• Tabuloc, C.A., K.M. Lewald, W.R. Conner, Y. Lee, E.K. Lee, A.B. Cain, K.E. Godfrey, J. Arnó, N. Agusti, C.R. Perini, J.C. Guedes, F.G. Zalom, J.C. Chiu (2019). Sequencing of Tuta absoluta genome to develop SNP genotyping assays for species identification. J Pest Sci 92(4): 1397-1407. [html]

• Lam, V.H., J.C. Chiu (2019). Evolution and design of invertebrate circadian clocks. In "Oxford Handbook of Invertebrate Neurobiology", ed. J. H. Byrne. Oxford University Press. doi: 10.1093/oxfordhb/9780190456757.013.25.

• Lam, V.H., Y.H. Li, X. Liu, K.A. Murphy, J.S. Diehl, R.S. Kwok, J.C. Chiu (2018). CK1alpha collaborates with DOUBLETIME to regulate PERIOD function in the Drosophila circadian clock. J Neurosci 38(50):10631-10643. [html]

• Turelli, M., B.S. Cooper, K.M. Richardson, P.S. Ginsberg, B. Peckenpaugh, C.X. Antelope, K.J. Kim, M.R. May, A. Abrieux, D.A. Wilson, M.J. Bronsky, B.R. Moore, J.J. Gao, M.B. Eisen, J. C. Chiu, W.R. Conner, A.A. Hoffmann (2018). Rapid global spread of wRi-like Wilbachia across multiple Drosophila. Curr Biol 28(6): 963-971. [html]

• Mishra, R., J.C. Chiu, G. Hua, N.R. Tawari, M.J. Adang, A.A. Sial (2018). High throughput sequencing reveals Drosophila suzukii responses to insecticides. Insect Sci 25(6): 928-945. [html]

• Hughes, M.E., K.C. Abruzzi, R. Allada, ...... J.C. Chiu.......J.B. Hogenesch (2017). Guidelines for Genome-Scale Analysis of Biological Rhythms. J Biol Rhythms 32(5): 380-393. [html]

• Freedman, M.G., H. Dingle, C.A. Tabuloc, J.C. Chiu, L.H. Yang, M.P. Zalucki (2017). Non-migratory monarch butterflies, Danaus plexippus (L.) retain developmental plasticity and a navigational mechanism associated with migration. Biological Journal of the Linnean Society 123(2): 265-278. [html]

• Battenberg, K., E.K. Lee, J.C. Chiu, A.M. Berry, D. Potter (2017). OrthoReD: Tool for orthology predictions from reduced datasets. BMC Bioinformatics 18(1):310. [html]

• Abrieux, A., J.C. Chiu (2016). Oral delivery of dsRNA by microbes: beyond pest control. Commun. Inter.  Biol. 9(6): doi.org/10.1080/1942. [html]

• Fu, J., K.A. Murphy, M. Zhou, Y.H. Li, V.H. Lam, C.A. Tabuloc, J.C. Chiu, and Y. Liu (2016). Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD. Genes & Dev. 30(15):1761-1775. doi:10.1101/gad.281030.116. [html]

• Kwok, R.S., V.H. Lam, J.C. Chiu (2016). Understanding the role of chromatin remodeling in the regulation of circadian transcription in Drosophila. FLY; DOI: 10.1080/19336934.2016.1143993. [html]

• Shearer, P.W., J.D. West, V.M. Walton, P.H. Brown; N. Svetec, J.C. Chiu (2016). Seasonal cues induce phenotypic plasticity of Drosophila suzukii to enhance winter survival. BMC Ecology 16:11. doi:10.1186/s12898-016-0070-3 [html]

• Maliti D.V., C.D. Marsden, B.J. Main, N.J. Govella, Y. Yamasaki, T.C. Collier, K. Kreppel, J.C. Chiu, G.C. Lanzaro, H.M. Ferguson, Y. Lee (2016). Investigating associations between biting time in the malaria vector Anopheles arabiensis Patton and single nucleotide polymorphisms in circadian clock genes: support for sub-structure among An. arabiensis in the Kilobero valley of Tanzania. Parasites & vectors 9(1):109. [html]

• Murphy, K.A., C.A. Tabuloc, K.R. Cervantes, J.C. Chiu (2016). Ingestion of genetically modified yeast symbiont reduces fitness of an insect pest via RNA interference. Sci. Rep. 6, 22587; DOI: 10.1038/srep22587. [html]

• Murphy, K.A., J.D. West, R.S. Kwok, J.C. Chiu (2016). Accelerating research on Spotted Wing Drosophila management using genomic technologies. J. Pest Sci. DOI 10.1007/s10340-016-0741-z. [html]

• Yildirim, E., J.C. Chiu, I. Edery (2016). Identification of light-sensitive phosphorylation sites on PERIOD that regulate the pace of circadian rhythms in Drosophila. Mol. Cell. Biol. 36(6): 855-870. [html]

• Hamby, K.A., D.E. Bellamy, J.C. Chiu, J.C. Lee, V.M. Walton, N.G. Wiman, R.M. York, A. Biondi (2016). Biotic and abiotic factors impacting development, behavior, phenology, and reproductive biology of Drosophila suzukii. J. Pest Sci. DOI: 10.1007/s10340-016-0756-5.

• Wiman, N.G., D.T. Dalton, G. Anfora, A. Biondi, J.C. Chiu, K.M. Daane, [....] V.M. Walton (2016). Drosophila suzukii population response to environment and management strategies. J. Pest Sci. DOI: 10.1007/s10340-016-0757-4.

• Borowiec, M.L., E.K. Lee, J.C. Chiu, D.C. Plachetzki (2015). Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 16:987. [html|pdf]

• Kwok, R.S., Y.H. Li, A.J. Lei, I. Edery, J.C. Chiu (2015). The catalytic and non-catalytic functions of the Brahma chromatin-remodeling protein collaborate to fine-tune circadian transcription in Drosophila. PLoS Genetics 11(7):e1005307. [html|pdf].

• Murphy, K.A., T.R. Unruh, L.M. Zhou, F.G. Zalom, P.W. Shearer, E.H. Beers, V.M. Walton, B. MIller, J.C. Chiu (2015). Using comparative genomics to develop a molecular diagnostic for the identification of an emerging pest Drosophila suzukii. Bull. Entomol. Res. 105:364-372. [html|pdf].

• Svetec, N., L. Zhao, P. Saelao, J.C. Chiu, D.J. Begun (2015). Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster. BMC Evol. Biol. 15(1):316. doi: 10.1186/s12862-015-0316-2 [html|pdf]

• Neafsey, D.E., R.M. Waterhouse, M.R. Abai, [.........], J.C. Chiu, [........], K.A. Murphy, [......], N.J. Besansky (2015). Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes. Science 347(6217):1258522. [html]

• Jasper, W.C., T.A. Linksvayer, J. Atallah, D. Friedman, J.C. Chiu, and B.R. Johnson (2015). Large scale coding sequence change underlies the evolution of post-developmental novelty in honey bees. Mol. Biol. Evol. 32(2):334-346. [html]

• Wiman, N.G., V.M. Walton, D.T. Dalton, G. Anfora, H.J. Burrack, J.C. Chiu, K.M. Daane, A. Grassi, B. Miller, S. Tochen, X. Wang, C. Ioriatti (2014). Integrating temperature-dependent life table data into a matrix projection model for Drosophila suzukii population estimation. PLoS ONE 9(9):e106909. [html|pdf]

• Chiu, J. C., X. Jiang, L. Zhao, C. A. Hamm, J. M. Cridland, P. Saelao, K. A. Hamby, E. K. Lee, R. S. Kwok, G. Zhang, F. G. Zalom, V. M. Walton, and D. J. Begun (2013). Genome of Drosophila suzukii, the Spotted Wing Drosophila. G3: Genes, Genomes, Genetics 3(12):2257-71. doi: 10.1534/g3.113.008185. [html|pdf|press release]

• Johnson, B. R., M. L. Borowiec, J. C. Chiu, E. K. Lee, J. Atallah, and P. S. Ward (2013). Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr. Biol. 23(20):1-5. [html|pdf|press release]

• Hamby, K. A., R. S. Kwok, F. G. Zalom, and J. C. Chiu (2013). Integrating circadian activity and gene expression profiles to predict chronotoxicity of Drosophila suzukii response to insecticides. PLoS ONE 8(7): e68472. doi:10.1371/journal.pone.0068472. [html|pdf|press release]

• Chiu, J. C., K. Kaub, S. Zou, P. Liedo, L. Altamirano-Robles, D. Ingram, and J. Carey (2013). Deleterious effect of suboptimal diet on rest-activity cycle in Anastrepha ludens manifests itself with age. Sci. Rep. 3(1773); DOI:10.1038/srep01773. [html|pdf]

• Chiu, J. C., H. W. Ko, and I. Edery (2011). NEMO/NLK phosphorylates PERIOD to initiate a time-delay phosphorylation circuit that sets circadian clock speed. Cell 145(3):357-370. [html|pdf|press release]

• Lee, E. K., A. Cibrian-Jaramillo, S-O Kolokotronis, M. S. Katari, A.  Stamatakis, M. Ott,  J. C. Chiu, D. P. Little, D. Wm. Stevenson, W. R. McCombie, R. A. Martienssen, G. Coruzzi, and R. DeSalle (2011). A Functional Phylogenomic View of the Seed Plants. PLoS Genetics 7(12): e1002411. [html|pdf]

• Chiu, J. C., K. H. Low, D. H. Pike, E. Yildirim, and I. Edery (2010). Assaying locomotor activity to study circadian rhythms and sleep parameters in Drosophila. J Vis. Exp. 43. [html]

• Ko, H. W., E. Y. Kim, J. C. Chiu, J. T. Vanselow, A. Kramer, and I. Edery (2010). A hierarchical phosphorylation cascade that regulates the timing of PERIOD nuclear entry reveals novel roles for proline-mediated kinases and GSK-3ß/SGG in circadian clocks. J. Neurosci. 30:12664-12675. [html|pdf]

• Egan, M., E. K. Lee, J. C. Chiu, G. Coruzzi, and R. DeSalle (2009). Gene orthology assessment with OrthologID. Methods Mol. Biol. 537:23-38. [html|pdf]

• Chiu, J. C., J. T. Vanselow, A. Kramer, and I. Edery (2008). The phospho-occupancy of an atypical SLIMB binding site on PERIOD that is phosphorylated by DOUBLETIME controls the pace of the clock. Genes. Dev. 22(13):1758-1772. [html|pdf]

• Chiu, J. C., E. K. Lee, M. G. Egan, I. N. Sarkar, G. M. Coruzzi, and R. DeSalle (2006). OrthologID: Automation of genome scale ortholog identification within a parsimony framework. Bioinformatics 22(6):699-707. [html|pdf]

• Chiu, J. C., E. Brenner, R. DeSalle, M. N. Nitabach, T. C. Holmes, and G. Coruzzi (2002). Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana. Molecular Biology and Evolution 19(7):1066-1082. [html|pdf]

• Lacombe, B., D. Becker, R. Hedrich , R. DeSalle, M. Hollmann, J. Kwak, J. I. Schroeder, N. Le Novere, G. N. Hong, E. P. Spalding, M. Tester, F. J. Turano, J. Chiu, and G. Coruzzi (2001). The identity of plant glutamate receptors. Science 292:1486-1487. [html]

• Chiu, J., R. DeSalle, H. M. Lam, L. Meisel, and G. Coruzzi (1999). Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged. Molecular Biology and Evolution 16(6): 826-838. [pdf]

• Lam, H. M., J. Chiu, M. H. Hsieh, L. Meisel, I. C. Oliveira, M. Shin, and G. Coruzzi (1998). Glutamate receptor genes in plants. Nature 396:125-126. [html|pdf]