Publications

Selected Publications

  • Lam, V.H., J.C. Chiu (2017). 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.
  • Mishra, R., J.C. Chiu, G. Hua, N.R. Yawari, M.J. Adang, A.A. Sial (2017). High throughput sequencing reveals Drosophila suzukii responses to insecticides. Insect Science. June 21. doi: 10.1111/1744-7917.12498. [Epub ahead of print]
  • 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. OttJ. 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]