Founded in 2001, the Department of Neurobiology at the University of Massachusetts Medical School has evolved into a unique and integrated hub of investigators addressing fundamental problems in neurobiology, from single molecules to behavior, primarily using invertebrate model organisms. Combining cell biological, physiological and behavioral analyses with a critical interventionist angle afforded by cutting-edge genetic approaches, the Department aims to understand the complexity of brain development and function. This collection showcases journal articles and other publications and presentations written by faculty and researchers of the Department of Neurobiology.

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Publications from 2016

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Drosophila Vision Depends on Carcinine Uptake by an Organic Cation Transporter, Ratna Chaturvedi, Zhuo Luan, Peiyi Guo, and Hong-Sheng Li

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Attenuated traumatic axonal injury and improved functional outcome after traumatic brain injury in mice lacking Sarm1, Nils Henninger, James P. Bouley, Elif M. Sikoglu, Jiyan An, Constance M. Moore, Jean A. King, Robert Bowser, Marc R. Freeman, and Robert H. Brown Jr.

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Genomic Access to Monarch Migration Using TALEN and CRISPR/Cas9-Mediated Targeted Mutagenesis, Matthew J. Markert, Ying Zhang, Metewo Selase Enuameh, Steven M. Reppert, Scot A. Wolfe, and Christine Merlin

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Microglia contribute to circuit defects in Mecp2 null mice independent of microglia-specific loss of Mecp2 expression, Dorothy P. Schafer, Christopher T. Heller, Georgia Gunner, Molly Heller, Christopher Gordon, Timothy Hammond, Yochai Wolf, Steffen Jung, and Beth Stevens

Publications from 2015

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Glypican Is a Modulator of Netrin-Mediated Axon Guidance, Cassandra Blanchette, Paola N. Perrat, Andrea Thackeray, and Claire Y. Benard

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FIB/SEM technology and high-throughput 3D reconstruction of dendritic spines and synapses in GFP-labeled adult-generated neurons, Carles Bosch, Albert Martinez, Nuria Masachs, Catia M. Teixeira, Isabel Fernaud, Fausto Ulloa, Esther Perez-Martinez, Carlos Lois, Joan X. Comella, Javier DeFelipe, Angel Merchan-Perez, and Eduardo Soriano

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An enhanced gene targeting toolkit for Drosophila: Golic+, Hui-Min Chen, Ya-ling Huang, Barret D. Pfeiffer, Xiaohao Yao, and Tzumin Lee

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Connecting Circadian Genes to Neurodegenerative Pathways in Fruit Flies, Patrick Emery

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Letting Go of JuNK by Disassembly of Adhesive Complexes, Jonathan E. Farley and Marc R. Freeman

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Drosophila TRPA1 isoforms detect UV light via photochemical production of H2O2, Ananya R. Guntur, Pengyu Gu, Kendra Takle, Jingyi Chen, Yang Xiang, and Chung-Hui Yang

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Transcriptional Control of Synaptic Remodeling through Regulated Expression of an Immunoglobulin Superfamily Protein, Siwei He, Alison Philbrook, Rebecca McWhirter, Christopher V. Gabel, Daniel G. Taub, Maximilian H. Carter, Isabella M. Hanna, Michael M. Francis, and David M. Miller 3rd

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Sweet taste and nutrient value subdivide rewarding dopaminergic neurons in Drosophila, Wolf Huetteroth, Emmanuel Perisse, Suewei Lin, Martin Klappenbach, Christopher J. Burke, and Scott Waddell

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Tachykinin acts upstream of autocrine Hedgehog signaling during nociceptive sensitization in Drosophila, Seol Hee Im, Kendra Takle, Juyeon Jo, Daniel T. Babcock, Zhiguo Ma, Yang Xiang, and Michael J. Galko

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Using Drosophila models of Huntington's disease as a translatable tool, Elizabeth A. Lewis and Gaynor A. Smith

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The putative Na(+)/Cl(-)-dependent neurotransmitter/osmolyte transporter inebriated in the Drosophila hindgut is essential for the maintenance of systemic water homeostasis, Zhuo Luan, Caitlin Quigley, and Hong-Sheng Li

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Mesoscopic patterns of neural activity support songbird cortical sequences, Jeffrey E. Markowitz, William A. Liberti III, Grigori Guitchounts, Tarciso Velho, Carlos Lois, and Timothy J. Gardner

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Caenorhabditis elegans exhibit a coupling between the defecation motor program and directed locomotion, Stanislav Nagy, Yung-Chi Huang, Mark J. Alkema, and David Biron

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Presynaptic BK channel localization is dependent on the hierarchical organization of alpha-catulin and dystrobrevin and fine-tuned by CaV2 calcium channels, Kelly H. Oh, Linu S. Abraham, Chandler Gegg, Christian Silvestri, Yung-Chi Huang, Mark J. Alkema, Jacob Furst, Daniela Raicu, and Hongkyun Kim

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Nucleus to Synapse Nesprin1 Railroad Tracks Direct Synapse Maturation through RNA Localization, Mary Packard, Vahbiz Jokhi, Baojin Ding, Catalina Ruiz-Canada, James A. Ashley, and Vivian Budnik

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A Change in the Ion Selectivity of Ligand-Gated Ion Channels Provides a Mechanism to Switch Behavior, Jennifer K. Pirri, Diego Rayes, and Mark J. Alkema

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Genes Required for Wallerian Degeneration Also Govern Dendrite Degeneration: A Dissertation, Timothy M. Rooney

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Age-Dependent TDP-43-Mediated Motor Neuron Degeneration Requires GSK3, hat-trick, and xmas-2, Jemeen Sreedharan, Lukas J. Neukomm, Robert H. Brown Jr., and Marc R. Freeman

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Calcium and SOL Protease Mediate Temperature Resetting of Circadian Clocks, Ozgur Tataroglu, Xiaohao Yao, Ania Busza, Jinli Ling, John S. O'Neill, and Patrick Emery

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Pan-neuronal imaging in roaming Caenorhabditis elegans, Vivek Venkatachalam, Ni Ji, Xian Wang, Christopher M. Clark, James Kameron Mitchell, Mason Klein, Christopher J. Tabone, Jeremy Florman, Hongfei Ji, Joel Greenwood, Andrew D. Chisholm, Jagan Srinivasan, Mark J. Alkema, Mei Zhen, and Aravinthan D.T. Samuel

Publications from 2014

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A conserved dopamine-cholecystokinin signaling pathway shapes context-dependent Caenorhabditis elegans behavior, Raja Bhattacharya, Denis Touroutine, Belinda Barbagallo, Jason Climer, Christopher M. Lambert, Christopher M. Clark, Mark J. Alkema, and Michael M. Francis

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Neuroscience. Astrocytes eyeball axonal mitochondria, Thomas C. Burdett and Marc R. Freeman

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Drosophila learn opposing components of a compound food stimulus, Gaurav Das, Martin Klappenbach, Eleftheria Vrontou, Emmanuel Perisse, Christopher M. Clark, Christopher J. Burke, and Scott Waddell

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PI3K signaling and Stat92E converge to modulate glial responsiveness to axonal injury, Johnna E. Doherty, Amy E. Sheehan, Rachel Bradshaw, A. Nicole Fox, Tsai-yi Lu, and Marc R. Freeman

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Glial wingless/Wnt regulates glutamate receptor clustering and synaptic physiology at the Drosophila neuromuscular junction, Kimberly S. Kerr, Yuly F. Fuentes Medel, Cassandra Brewer, Romina Barria, James A. Ashley, Katharine C. Abruzzi, Amy E. Sheehan, Ozge E. Tasdemir, Marc R. Freeman, and Vivian Budnik

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Morning and evening oscillators cooperate to reset circadian behavior in response to light input, Pallavi Lamba, Diana Wentworth, Patrick Emery, and Yong Zhang

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DRK/DOS/SOS Converge with Crk/Mbc/dCed-12 to Activate Rac1 during Glial Engulfment of Axonal Debris, Tsai-yi Lu, Johnna E. Doherty, and Marc R. Freeman

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Activity-dependent regulation of astrocyte GAT levels during synaptogenesis, Allie Muthukumar, Tobias Stork, and Marc R. Freeman

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Rapid in vivo forward genetic approach for identifying axon death genes in Drosophila, Lukas J. Neukomm, Thomas C. Burdett, Michael A. Gonzalez, Stephan Zuchner, and Marc R. Freeman

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Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila, Fillip Port, Hui-Min Chen, Tzumin Lee, and Simon L. Bullock

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Drosophila models of neuronal injury, Timothy M. Rooney and Marc R. Freeman

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Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans, Frederick B. Shipley, Christopher M. Clark, Mark J. Alkema, and Andrew M. Leifer

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Neuron-glia interactions through the Heartless FGF receptor signaling pathway mediate morphogenesis of Drosophila astrocytes, Tobias Stork, Amy E. Sheehan, Ozge E. Tasdemir-Yilmaz, and Marc R. Freeman

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Neuronal regeneration in C. elegans requires subcellular calcium release by ryanodine receptor channels and can be enhanced by optogenetic stimulation, Lin Sun, James Shay, Melissa McLoed, Kevin Roodhouse, Samuel H. Chung, Christopher M. Clark, Jennifer K. Pirri, Mark J. Alkema, and Christopher V. Gabel

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Astrocytes engage unique molecular programs to engulf pruned neuronal debris from distinct subsets of neurons, Ozge E. Tasdemir-Yilmaz and Marc R. Freeman

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Trim9 regulates activity-dependent fine-scale topography in Drosophila, Limin Yang, Ruonan Li, Takuya Kaneko, Kendra Takle, Rei K. Morikawa, Laura Essex, Xin Wang, Jie Zhou, Kazuo Emoto, Yang Xiang, and Bing Ye

Publications from 2013

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Post-translational modification by cysteine protects Cu/Zn-superoxide dismutase from oxidative damage, Jared R. Auclair, Joshua L. Johnson, Qian Liu, Joseph P. Salisbury, Melissa S. Rotunno, Gregory A. Petsko, Dagmar Ringe, Robert H. Brown Jr., Daryl A. Bosco, and Jeffrey N. Agar

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Targeted expression of human folylpolyglutamate synthase for selective enhancement of methotrexate chemotherapy in osteosarcoma cells, K. Bienemann, M. S. Staege, S. J. Howe, Miguel Sena-Esteves, H. Hanenberg, and C. M. Kramm

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A rare presentation of hypertrophic olivary degeneration secondary to primary central nervous system lymphoma, David Cachia, Saef Izzy, Thomas W. Smith, and Carolina Ionete

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Cell biology in neuroscience: Architects in neural circuit design: glia control neuron numbers and connectivity, Megan M. Corty and Marc R. Freeman

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Probing the enigma: unraveling glial cell biology in invertebrates, Jaeda Coutinho-Budd and Marc R. Freeman

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Monoaminergic orchestration of motor programs in a complex C. elegans behavior, Jamie L. Donnelly, Christopher M. Clark, Andrew M. Leifer, Jennifer K. Pirri, Marian Haburcak, Michael M. Francis, Aravinthan D. T. Samuel, and Mark J. Alkema

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A large-scale behavioral screen to identify neurons controlling motor programs in the Drosophila brain, Thomas F. Flood, Michael Gorczyca, Benjamin H. White, Kei Ito, and Motojiro Yoshihara

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A single pair of interneurons commands the Drosophila feeding motor program, Thomas F. Flood, Shinya Iguchi, Michael Gorczyca, Benjamin White, Kei Ito, and Motojiro Yoshihara

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A single pair of interneurons commands the Drosophila feeding motor program, Thomas F. Flood, Shinya Iguchi, Michael Gorczyca, Benjamin White, Kei Ito, and Motojiro Yoshihara

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Evolving concepts of gliogenesis: a look way back and ahead to the next 25 years, Marc R. Freeman and David H. Rowitch

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Coldness triggers northward flight in remigrant monarch butterflies, Patrick A. Guerra and Steven M. Reppert

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Anatomical basis of sun compass navigation II: The neuronal composition of the central complex of the monarch butterfly, Stanley Heinze, Jeremy Florman, Surainder Asokaraj, Basil el Jundi, and Steven M. Reppert

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Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope, Vahbiz Jokhi, James A. Ashley, John J. Nunnari, Akiko Noma, Naoto ito, Noriko Wakabayashi-Ito, Melissa J. Moore, and Vivian Budnik

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Regulation of postsynaptic retrograde signaling by presynaptic exosome release, Ceren Korkut, Yihang Li, Kate Koles, Cassandra Brewer, James A. Ashley, Motojiro Yoshihara, and Vivian Budnik

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Extremes of lineage plasticity in the Drosophila brain, Suewei Lin, Elizabeth C. Marin, Ching-Po Yang, Chih-Fei Kao, Bettye A. Apenteng, Yaling Huang, Michael B. O'Connor, James W. Truman, and Tzumin Lee

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The c-Jun kinase signaling cascade promotes glial engulfment activity through activation of draper and phagocytic function, Jennifer M. MacDonald, Johnna E. Doherty, Rachel Hackett, and Marc R. Freeman

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Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases, Christine Merlin, Lauren E. Beaver, Orley R. Taylor, Scot A. Wolfe, and Steven M. Reppert

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Are monarch butterflies true navigators? The jury is still out, Karen S. Oberhauser, Orley R. Taylor, Steven M. Reppert, Hugh Dingle, Kelly R. Nail, Robert M. Pyle, and Carl Stenoien

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Shocking revelations and saccharin sweetness in the study of Drosophila olfactory memory, Emmanuel Perisse, Christopher J. Burke, Wolf Huetteroth, and Scott Waddell

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Different kenyon cell populations drive learned approach and avoidance in Drosophila, Emmanuel Perisse, Yan Yin, Andrew C. Lin, Suewei Lin, Wolf Huetteroth, and Scott Waddell

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Transposition-driven genomic heterogeneity in the Drosophila brain, Paola N. Perrat, Shamik DasGupta, Jie Wang, William E. Theurkauf, Zhiping Weng, Michael Rosbash, and Scott Waddell

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ACR-12 ionotropic acetylcholine receptor complexes regulate inhibitory motor neuron activity in Caenorhabditis elegans, Hilary A. Petrash, Alison Philbrook, Marian Haburcak, Belinda Barbagallo, and Michael M. Francis

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A tale of two receptors: Dual roles for ionotropic acetylcholine receptors in regulating motor neuron excitation and inhibition, Alison Philbrook, Belinda Barbagallo, and Michael M. Francis

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Increased cell-intrinsic excitability induces synaptic changes in new neurons in the adult dentate gyrus that require npas4, Shuyin Sim, Salome Antolin, Chia-Wei Lin, Yingxi Lin, and Carlos Lois

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GW182 controls Drosophila circadian behavior and PDF-receptor signaling, Yong Zhang and Patrick Emery

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A role for Drosophila ATX2 in activation of PER translation and circadian behavior, Yong Zhang, Jinli Ling, Chunyan Yuan, Raphaelle Dubruille, and Patrick Emery

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MonarchBase: the monarch butterfly genome database, Shuai Zhan and Steven M. Reppert

Publications from 2012

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Wld(S) Prevents Axon Degeneration through Increased Mitochondrial Flux and Enhanced Mitochondrial Ca(2+) Buffering., Michelle A. Avery, Timothy M. Rooney, Jignesh D. Pandya, Thomas M. Wishart, Thomas H. Gillingwater, James W. Geddes, Patrick G. Sullivan, and Marc R. Freeman

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The Secreted Immunoglobulin Domain Proteins ZIG-5 and ZIG-8 Cooperate with L1CAM/SAX-7 to Maintain Nervous System Integrity, Claire Y. Benard, Cassandra Blanchette, Janine Recio, and Oliver Hobert

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Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers, Thomas Brody, Amarendra S. Yavatkar, Alexander Kuzin, Mukta Kundu, Leonard J. Tyson, Jermaine Ross, Tzu-Yang Lin, Chi-Hon Lee, Takeshi Awasaki, Tzumin Lee, and Ward F. Odenwald

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Layered reward signalling through octopamine and dopamine in Drosophila, Christopher J. Burke, Wolf Huetteroth, David Owald, Emmanuel Perisse, Michael J. Krashes, Gaurav Das, Daryl Gohl, Marion Silies, Sarah Certel, and Scott Waddell

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Circadian rhythms: An electric jolt to the clock, Patrick Emery

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Integration of a retrograde signal during synapse formation by glia-secreted TGF-beta ligand, Yuly F. Fuentes-Medel, James A. Ashley, Romina Barria, Rachel Maloney, Marc R. Freeman, and Vivian Budnik

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Discordant timing between antennae disrupts sun compass orientation in migratory monarch butterflies, Patrick A. Guerra, Christine Merlin, Robert J. Gegear, and Steven M. Reppert

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Anatomical basis of sun compass navigation I: the general layout of the monarch butterfly brain, Stanley Heinze and Steven M. Reppert

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Protein Gq modulates termination of phototransduction and prevents retinal degeneration, Wen Hu, Didi Wan, Xiaoming Yu, Jinguo Cao, Peiyi Guo, Hong-Sheng Li, and Junhai Han

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Wnt signaling regulates acetylcholine receptor translocation and synaptic plasticity in the adult nervous system, Michael Jensen, Frederic J. Hoerndli, Penelope J. Brockie, Rui Wang, Erica Johnson, Dane Maxfield, Michael M. Francis, David M. Madsen, and Andres V. Maricq

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Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation, Hina Kalra, Vivian Budnik, and Suresh Mathivanan

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Circadian rhythm of temperature preference and its neural control in Drosophila, Haruna Kaneko, Lauren M. Head, Jinli Ling, Xin Tang, Yilin Liu, Paul E. Hardin, Patrick Emery, and Fumika N. Hamada

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Hierarchical deployment of factors regulating temporal fate in a diverse neuronal lineage of the Drosophila central brain, Chih-Fei Kao, Hung-Hsiang Yu, Yisheng He, Jui-Chun Kao, and Tzumin Lee

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Increasing heterogeneity in the organization of synaptic inputs of mature olfactory bulb neurons generated in newborn rats, Wolfgang Kelsch, Shuyin Sim, and Carlos Lois

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Genetic labeling of neuronal subsets through enhancer trapping in mice, Wolfgang Kelsch, Alberto Stolfi, and Carlos Lois

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Exosomes go with the Wnt, Kate Koles and Vivian Budnik

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Wnt Signaling in Neuromuscular Junction Development, Kate Koles and Vivian Budnik

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Mechanism of evenness interrupted (Evi)-exosome release at synaptic boutons, Kate Koles, John J. Nunnari, Ceren Korkut, Romina Barria, Cassandra Brewer, Yihang Li, John D. Leszyk, Bing Zhang, and Vivian Budnik

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Inhibitory control of synaptic and behavioral plasticity by octopaminergic signaling, Alex C. Koon and Vivian Budnik

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Antibodies for assessing circadian clock proteins in the rodent suprachiasmatic nucleus, Joseph Lesauter, Christopher M. Lambert, Margaret R. Robotham, Zina Model, Rae Silver, and David R. Weaver

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KAYAK-alpha modulates circadian transcriptional feedback loops in Drosophila pacemaker neurons, Jinli Ling, Raphaelle Dubruille, and Patrick Emery

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Lineage analysis of Drosophila lateral antennal lobe neurons reveals notch-dependent binary temporal fate decisions, Suewei Lin, Chih-Fei Kao, Hung-Hsiang Yu, Ya-ling Huang, and Tzumin Lee

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Generating neuronal diversity in the Drosophila central nervous system, Suewei Lin and Tzumin Lee

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Negative regulation of glial engulfment activity by Draper terminates glial responses to axon injury, Mary A. Logan, Rachel Hackett, Johnna E. Doherty, Amy E. Sheehan, Sean D. Speese, and Marc R. Freeman

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Genetics in non-genetic model systems, Carlos Lois and James O. Groves

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Inwardly rectifying potassium channels in Drosophila, Zhuo Luan and Hong-Sheng Li

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Coincident generation of pyramidal neurons and protoplasmic astrocytes in neocortical columns, Sanjay Magavi, Drew Friedmann, Garrett Banks, Alberto Stolfi, and Carlos Lois

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Unraveling navigational strategies in migratory insects, Christine Merlin, Stanley Heinze, and Steven M. Reppert

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Similarity of Visual Selectivity among Clonally Related Neurons in Visual Cortex, Gen Ohtsuki, Megumi Nishiyama, Takashi Yoshida, Tomonari Murakami, Mark Histed, Carlos Lois, and Kenichi Ohki

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dSarm/Sarm1 is required for activation of an injury-induced axon death pathway, Jeannette M. Osterloh, Jing Yang, Timothy M. Rooney, A. Nicole Fox, Robert Adalbert, Eric H. Powell, Amy E. Sheehan, Michelle A. Avery, Rachel Hackett, Mary A. Logan, Jennifer M. MacDonald, Jennifer S. Ziegenfuss, Stefan Milde, Ying-Ju Hou, Carl Nathan, Aihao Ding, Robert H. Brown Jr., Laura Comforti, Michael Coleman, Marc Tessier-Lavigne, Stephan Zuchner, and Marc R. Freeman

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The neuroethology of C. elegans escape, Jennifer K. Pirri and Mark J. Alkema

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Disruption of gene expression rhythms in mice lacking secretory vesicle proteins IA-2 and IA-2β, Sohan Punia, Kyle K. Rumery, Elizabeth A. Yu, Christopher M. Lambert, Abner L. Notkins, and David R. Weaver

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Intercellular calcium signaling in a gap junction-coupled cell network establishes asymmetric neuronal fates in C. elegans, Jennifer A. Schumacher, Yi-Wen Hsieh, Shiuhwei Chen, Jennifer K. Pirri, Mark J. Alkema, Wen-hong Li, Chieh Chang, and Chiou-Fen Chuang