Biography

Dr. Orie T. Shafer is a Professor of Biology and a Linda & Jack Gill Chair at Indiana University Bloomington, affiliated with the Gill Institute for Neuroscience. He leads a research program focused on the neural and genetic mechanisms of circadian timekeeping and sleep regulation using the fruit fly Drosophila melanogaster as a model organism.

Dr. Shafer earned his B.S. from Purdue University and his Ph.D. in Biology from the University of Washington. His early work helped define the anatomical and molecular organization of the Drosophila clock neuron network and contributed to the recognition of new subclasses of clock neurons. Since establishing his own lab at the University of Michigan in 2009, he has developed innovative methods to interrogate functional connectivity within living clock neuron networks. His lab uses genetic, behavioral, and imaging approaches to uncover how genes and neural networks circadian circuits control sleep and daily rhythms.

Dr. Shafer’s research has yielded influential publications in leading journals such as Science, Nature, The Proceedings of the National Academy of Sciences, Current Biology, and The Journal of Neuroscience. His recent work aims to reshape how Drosophila melanogaster is used to discover molecular and neural mechanisms of homeostatic sleep regulation and the circadian timing of sleep.

His work has broad relevance for understanding how internal clocks integrate environmental cues and maintain proper sleep-wake cycles, with implications for human circadian biology, public health and safety, and neurological disorders.

Publications

  • Abhilash, L. and Shafer, O.T., (2022) A two-process model of Drosophila sleep reveals an inter-dependence between circadian clock speed and the rate of sleep pressure decay. bioRxiv 2022.08.12.503775; DOI: 10.1101/2022.08.12.503775
  • Chowdhury, B., Abhilash L., Ortega, A. Liu, S., and Shafer, O.T., (2022) Homeostatic Control of Deep sleep in Drosophila: Implications for Discovering Correlates of Sleep Pressure. bioRxiv 2022.09.30.510368; DOI: 10.1101/2022.09.30.510368
  • Abhilash, L., and Shafer, O.T., (2023) Parametric effects of light acting via multiple photoreceptor types contribute significantly to circadian entrainment in Drosophila melanogaster. Proc. R. Soc. B. 290: 20230149 [PMID: 37700655]
  • Emery, P., Klarsfeld, A., Stanewsky, R., and Shafer O.T. (2023) Sensitive Timing: A Reappraisal of Chronobiology's Foundational Texts. J. Biol. Rhythm. 38: 245-258 [PMID: 37226809]
  • Shafer, O.T., Gutierrez G.J., Li, K., Mildenhall, A., Spira, D., Marty, J., Lazar, A.A., and Fernandez M.P., (2022) Connectomic Analysis of the Drosophila Lateral Neuron Clock Cells Reveals the Synaptic Basis of Functional Pacemaker Classes. eLife 11:e79139  [PMID: 35766361]
  • Persons, J.L., Abhilash, L., Lopatkin, A.J., Roelofs, A., Bell, E.V., Fernandez, M.P., and Shafer O.T. (2022) PHASE: An Open-Source Program for the Analysis of Drosophila Phase, Activity and Sleep Under Entrainment. J. Biol. Rhythm. 37: 455-467 [PMID: 35727044]
  • B Kostadinov, HL Pettibone, EV Bell, X Zhou, A Pranevicius, OT Shafer and Fernandez, MP (2021). Open-source computational framework for studying Drosophila behavioral phase. STAR protocols 2 (1), 100285
  • OT Shafer, AC Keene (2021). The Regulation of Drosophila Sleep. Current Biology 31 (1), R38-R49
  • Florencia Fernandez-Chiappe, Christiane Hermann-Luibl, Alina Peteranderl, Nils Reinhard, Pingkalai R Senthilan, Marie Hieke, Mareike Selcho, Taishi Yoshii, Orie T Shafer, Nara I Muraro, Charlotte Helfrich-Förster (2020) . Dopamine Signaling in Wake-Promoting Clock Neurons Is Not Required for the Normal Regulation of Sleep in Drosophila. Journal of Neuroscience 40 (50), 9617-9633
  • B Chowdhury, OT Shafer (2020). Why the young sleep longer. Elife 9, e56833
  • Anthony Fiorino, Dakotah Thompson, Swathi Yadlapalli, Chang Jiang, Orie T Shafer, Pramod Reddy, Edgar Meyhofer. Parallelized, real-time, metabolic-rate measurements from individual Drosophila. Scientific reports 8 (1), 1-10
  • IU Hsu, JW Linsley, JE Varineau, OT Shafer, JY Kuwada (2018). Dstac is required for normal circadian activity rhythms in Drosophila. Chronobiology international 35 (7), 1016-1026
  • Fernández MP, Pettibone HL, Bogart JT, Roell CJ, Davey CE, Pranevicius A, Huynh KV, Lennox SM, Kostadinov BS and Shafer OT. (2020) Sites of Circadian Clock Neuron Plasticity Mediate Sensory Integration and Entrainment in Drosophila. Current Biology 30, 2225–2237.
  • Yadlapalli, S., Jiang, C., Bahle, A., Reddy, P., Meyhofer, E., Shafer, O.T. (2018). Circadian clock neurons constantly monitor environmental temperature to set sleep timing. Nature. doi: 10.1038/nature25740. PubMed
  • Yadlapalli, S., Shafer, O.T. (2017). Thermoregulation: How a brain keeps its cool. eLife. 2017;6:e28109. doi: 10.7554/eLife.28109. PubMed
  • Abruzzi, K.C., Zadina, A., Luo, W., Wiyanto, E., Rahman, R., Guo, F., Shafer, O., Rosbash, M. (2017). RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides. PLoS Genetics, 13(2), [e1006613]. doi: 10.1371/journal.pgen.1006613. PubMed
  • Yao, Z., Bennett, A. J., Clem, J. L., & Shafer, O. T. (2016). The Drosophila Clock Neuron Network Features Diverse Coupling Modes and Requires Network-wide Coherence for Robust Circadian Rhythms. Cell Reports, 17(11), 2873-2881. doi: 10.1016/j.celrep.2016.11.053. PubMed
  • Schlichting, M., Menegazzi, P., Lelito, K.R., Yao, Z., Buhl, E., Benetta, E.D., Bahle, A., Denike, J., Hodge, J.J., Helfrich-Förster, C., Shafer, O.T. (2016). A neural network underlying circadian entrainment and photoperiodic adjustment of sleep and activity in Drosophila. Journal of Neuroscience, 36(35), 9084-9096. doi: 10.1523/JNEUROSCI.0992-16.2016. PubMed
  • Oh, Y., Yoon, S. E., Zhang, Q., Chae, H. S., Daubnerová, I., Shafer, O. T., Choe, J., Kim, Y. J. (2014). A Homeostatic Sleep-Stabilizing Pathway in Drosophila Composed of the Sex Peptide Receptor and Its Ligand, the Myoinhibitory Peptide. PLoS Biology, 12(10). doi: 10.1371/journal.pbio.1001974. PubMed
  • Collins, B., Kaplan, H. S., Cavey, M., Lelito, K. R., Bahle, A. H., Zhu, Z., Macara, A.M., Roman, G., Shafer, O.T., Blau, J. (2014). Differentially Timed Extracellular Signals Synchronize Pacemaker Neuron Clocks. PLoS Biology, 12(9). doi: 10.1371/journal.pbio.1001959. PubMed
  • Shafer, O. T., & Yao, Z. (2014). Pigment-dispersing factor signaling and circadian rhythms in insect locomotor activity. Current Opinion in Insect Science, 1, 73-80. doi: 10.1016/j.cois.2014.05.002. PubMed
  • Yao, Z. and Shafer, O.T. (2014). The Drosophila Circadian Clock Is a Variably Coupled Network of Multiple Peptidergic Units. Science. 343(6178): 1516-1520. doi: 10.1126. PubMed

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