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 2012

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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

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Wandering neuronal migration in the postnatal vertebrate forebrain, Benjamin B. Scott, Timothy Gardner, Ni Ji, Michale S. Fee, and Carlos Lois

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Molecular diversity of Dscam and self-recognition, Lei Shi and Tzumin Lee

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Nuclear envelope budding enables large ribonucleoprotein particle export during synaptic Wnt signaling, Sean D. Speese, James A. Ashley, Vahbiz Jokhi, John J. Nunnari, Romina Barria, Yihang Li, Bulent Ataman, Alex C. Koon, Young-Tae Chang, Qian Li, Melissa J. Moore, and Vivian Budnik

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Analysis of glial cell development and function in Drosophila, Tobias Stork, Rebecca Bernardos, and Marc R. Freeman

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Combining comparative proteomics and molecular genetics uncovers regulators of synaptic and axonal stability and degeneration in vivo, Thomas M. Wishart, Timothy M. Rooney, Douglas J. Lamont, Ann K. Wright, A. Jennifer Morgon, Mandy Jackson, Marc R. Freeman, and Thomas H. Gillingwater

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Acute genetic manipulation of neuronal activity for the functional dissection of neural circuits-a dream come true for the pioneers of behavioral genetics, Moto Yoshihara and Kei Ito

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Integrative gene regulatory network analysis reveals light-induced regional gene expression phase shift programs in the mouse suprachiasmatic nucleus, Haisun Zhu, Rajanikanth Vadigepalli, Rachel Rafferty, Gregory E. Gonye, David R. Weaver, and James S. Schwaber

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Distinct molecular pathways mediate glial activation and engulfment of axonal debris after axotomy, Jennifer S. Ziegenfuss, Johnna E. Doherty, and Marc R. Freeman

Publications from 2011

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Glia instruct developmental neuronal remodeling through TGF-beta signaling, Takeshi Awasaki, Ya-ling Huang, Michael B. O'Connor, and Tzumin Lee

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New tools for the analysis of glial cell biology in Drosophila, Takeshi Awasaki and Tzumin Lee

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Orphan nuclear receptors control neuronal remodeling during fly metamorphosis, Takeshi Awasaki and Tzumin Lee

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Wnt signaling during synaptic development and plasticity, Vivian Budnik and Patricia C. Salinas

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Remembering nutrient quality of sugar in Drosophila, Christopher J. Burke and Scott Waddell

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Photic resetting and entrainment in CLOCK-deficient mice, Robert Dallmann, Jason P. DeBruyne, and David R. Weaver

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From synapse to nucleus and back again--communication over distance within neurons, Mike Fainzilber, Vivian Budnik, Rosalind A. Segal, and Michael R. Kreutz

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Invertebrate glia. Introduction, David Featherstone and Marc R. Freeman

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Human cryptochrome exhibits light-dependent magnetosensitivity, Lauren E. Foley, Robert J. Gegear, and Steven M. Reppert

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Sun compass integration of skylight cues in migratory monarch butterflies, Stanley Heinze and Steven M. Reppert

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Bringing fly brains in line, Wolf Huetteroth and Scott Waddell

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Hungry flies tune to vinegar, Wolf Huetteroth and Scott Waddell

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Autoregulatory and paracrine control of synaptic and behavioral plasticity by octopaminergic signaling, Alex C. Koon, James A. Ashley, Romina Barria, Shamik DasGupta, Ruth Brain, Scott Waddell, Mark J. Alkema, and Vivian Budnik

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Drosophila appetitive olfactory conditioning, Michael Jonathan Krashes and Scott Waddell

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Drosophila aversive olfactory conditioning, Michael Jonathan Krashes and Scott Waddell

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The period of the circadian oscillator is primarily determined by the balance between casein kinase 1 and protein phosphatase 1, Hyeong-min Lee, Rongmin Chen, Hyukmin Kim, Jean-Pierre Etchegaray, David R. Weaver, and Choogon Lee

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Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila, Pei-Tseng Lee, Hsuan-Wen Lin, Yu-Hsuan Chang, Tsai-Feng Fu, Josh Dubnau, Jay Hirsh, Tzumin Lee, and Ann-Shyn Chiang

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An Expressed Sequence Tag collection from the male antennae of the Noctuid moth Spodoptera littoralis: a resource for olfactory and pheromone detection research, Fabrice Legeai, Sebastien Malpel, Nicolas Montagne, Christelle Monsempes, Francois Cousserans, Christine Merlin, Marie-Christine Francois, Martine Maibeche-Coisne, Frederick Gavory, Julie Poulain, and Emmanuelle Jacquin-Joly

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Optogenetic manipulation of neural activity in freely moving Caenorhabditis elegans, Andrew M. Leifer, Christopher Fang-Yen, Marc Gershow, Mark J. Alkema, and Aravinthan D. T. Samuel

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The C. elegans Touch Response Facilitates Escape From Predacious Fungi, Sean M. Maguire, Christopher M. Clark, Jennifer K. Pirri, John J. Nunnari, and Mark J. Alkema

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Associative memory: without a trace, Emmanuel Perisse and Scott Waddell

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A Pair of Inhibitory Neurons Are Required to Sustain Labile Memory in the Drosophila Mushroom Body, Jena L. Pitman, Wolf Huetteroth, Christopher J. Burke, Michael Jonathan Krashes, Sen-Lin Lai, Tzumin Lee, and Scott Waddell

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Distinct patterns of Period gene expression in the suprachiasmatic nucleus underlie circadian clock photoentrainment by advances or delays, William J. Schwartz, Mahboubeh Tavakoli-Nezhad, Christopher M. Lambert, David R. Weaver, and Horacio O. de la Iglesia

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Anisotropic path searching for automatic neuron reconstruction, Jun Xie, Ting Zhao, Tzumin Lee, Eugene Myers, and Hanchuan Peng

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Disrupting the circadian clock: Gene-specific effects on aging, cancer, and other phenotypes, Elizabeth A. Yu and David R. Weaver

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The monarch butterfly genome yields insights into long-distance migration, Shuai Zhan, Christine Merlin, Jeffrey L. Boore, and Steven M. Reppert

Publications from 2010

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A dominant mutation in a neuronal acetylcholine receptor subunit leads to motor neuron degeneration in Caenorhabditis elegans, Belinda Barbagallo, Hilary A. Prescott, Patrick Boyle, Jason Climer, and Michael M. Francis

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Temporally- and spatially-regulated transcriptional activity of the nicotinic acetylcholine receptor beta4 subunit gene promoter., Lei Bruschweiler-Li, Yuly F. Fuentes Medel, Michael D. Scofield, Ellen B. T. Trang, Sarah A. Binke, and Paul D. Gardner

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Wallerian degeneration, wld(s), and nmnat, Michael P. Coleman and Marc R. Freeman

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Altered body mass regulation in male mPeriod mutant mice on high-fat diet, Robert Dallmann and David R. Weaver

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A new role for microRNA-9 in human neural progenitor cells, Celine Delaloy and Fen-Biao Gao

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The role of Drosophila Lamin C in muscle function and gene expression, George Dialynas, Sean D. Speese, Vivian Budnik, Pamela K. Geyer, and Lori L. Wallrath

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Casein kinase 1 delta (CK1delta) regulates period length of the mouse suprachiasmatic circadian clock in vitro, Jean-Pierre Etchegaray, Elizabeth A. Yu, Premananda Indic, Robert Dallmann, and David R. Weaver

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Specification and morphogenesis of astrocytes, Marc R. Freeman

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Menage a Trio during BMP-Mediated Retrograde Signaling at the NMJ, Yuly F. Fuentes Medel and Vivian Budnik

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Context-dependent functions of specific microRNAs in neuronal development, Fen-Biao Gao

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Animal cryptochromes mediate magnetoreception by an unconventional photochemical mechanism, Robert J. Gegear, Lauren E. Foley, Amy L. Casselman, and Steven M. Reppert

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MicroRNA-29b regulates the expression level of human progranulin, a secreted glycoprotein implicated in frontotemporal dementia, Jian Jiao, Lauren D. Herl, Robert V. Farese, and Fen-Biao Gao

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Birth time/order-dependent neuron type specification, Chih-Fei Kao and Tzumin Lee

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Clock and cycle limit starvation-induced sleep loss in Drosophila, Alex Carl Keene, Erik R. Duboue, Daniel M. McDonald, Monica Dus, Greg S.B. Suh, Scott Waddell, and Justin Blau

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Lineage-specific effects of Notch/Numb signaling in post-embryonic development of the Drosophila brain, Suewei Lin, Sen-Lin Lai, Hung-Hsiang Yu, Takahiro Chihara, Liqun Luo, and Tzumin Lee

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Activation of autophagy during cell death requires the engulfment receptor Draper, Christina K. McPhee, Mary A. Logan, Marc R. Freeman, and Eric H. Baehrecke

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Activity paradigm to induce Drosophila larval neuromuscular junction growth, Preethi Ramachandran and Vivian Budnik

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Dissection of Drosophila larval body-wall muscles, Preethi Ramachandran and Vivian Budnik

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Electron microscopy of Drosophila larval neuromuscular junctions, Preethi Ramachandran and Vivian Budnik

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Fm1-43 labeling of Drosophila larval neuromuscular junctions, Preethi Ramachandran and Vivian Budnik

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Immunocytochemical staining of Drosophila larval body-wall muscles, Preethi Ramachandran and Vivian Budnik

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Internalization and trafficking assay for Drosophila larvae, Preethi Ramachandran and Vivian Budnik

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Preparation of early Drosophila embryonic fillets (before cuticle deposition), Preethi Ramachandran and Vivian Budnik

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Preparation of early Drosophila embryonic fillets (before cuticle deposition), Preethi Ramachandran and Vivian Budnik

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Preparation of late Drosophila embryonic fillets, Preethi Ramachandran and Vivian Budnik

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Navigational mechanisms of migrating monarch butterflies, Steven M. Reppert, Robert J. Gegear, and Christine Merlin

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Dependence on a retinophilin/myosin complex for stability of PKC and INAD and termination of phototransduction, Kartik Venkatachalam, David Wasserman, Xiaoyue Wang, Ruoxia Li, Eric Mills, Rebecca Elsaesser, Hong-Sheng Li, and Craig Montell

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Dopamine reveals neural circuit mechanisms of fly memory, Scott Waddell

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A complete developmental sequence of a Drosophila neuronal lineage as revealed by twin-spot MARCM, Hung-Hsiang Yu, Chih-Fei Kao, Yisheng He, Peng Ding, Jui-Chun Kao, and Tzumin Lee

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Light and temperature control the contribution of specific DN1 neurons to Drosophila circadian behavior, Yong Zhang, Yixiao Liu, Diana Wentworth, Paul E. Hardin, and Patrick Emery

Publications from 2009

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Oxygen sensation: into thick air, Mark J. Alkema

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Wld S requires Nmnat1 enzymatic activity and N16-VCP interactions to suppress Wallerian degeneration, Michelle A. Avery, Amy E. Sheehan, Kimberly S. Kerr, Jing Wang, and Marc R. Freeman

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The small, secreted immunoglobulin protein ZIG-3 maintains axon position in Caenorhabditis elegans, Claire Y. Benard, Nartono Tjoe, Thomas Boulin, Janine Recio, and Oliver Hobert

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Ensheathing glia function as phagocytes in the adult Drosophila brain, Johnna E. Doherty, Mary A. Logan, Ozge E. Tasdemir, and Marc R. Freeman

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A constant light-genetic screen identifies KISMET as a regulator of circadian photoresponses, Raphaëlle Dubruille, Alejandro D. Murad, Michael Rosbash, and Patrick Emery

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Casein kinase 1 delta regulates the pace of the mammalian circadian clock, Jean-Pierre Etchegaray, Kazuhiko K. Machida, Elizabeth Noton, Cara M. Constance, Robert Dallmann, Marianne N. Di Napoli, Jason P. DeBruyne, Christopher M. Lambert, Elizabeth A. Yu, Steven M. Reppert, and David R. Weaver

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Glia and muscle sculpt neuromuscular arbors by engulfing destabilized synaptic boutons and shed presynaptic debris, Yuly F. Fuentes Medel, Mary A. Logan, James A. Ashley, Bulent Ataman, Vivian Budnik, and Marc R. Freeman

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A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors, Christian A. Grove, Federico De Masi, M. Inmaculada Barrasa, Daniel E. Newburger, Mark J. Alkema, Martha L. Bulyk, and Albertha J. M. Walhout

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The circadian clock protein Period 1 regulates expression of the renal epithelial sodium channel in mice, Michelle L. Gumz, Lisa R. Stow, I. Jeanette Lynch, Megan M. Greenlee, Alicia Rudin, Brian D. Cain, David R. Weaver, and Charles D. Wingo

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The Drosophila Activin-like ligand Dawdle signals preferentially through one isoform of the Type-I receptor Baboon, Philip A. Jensen, Xiaoyan Zheng, Tzumin Lee, and Michael B. O'Connor

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Vascular rhythms and adaptation: do your arteries know what time it is, John F. Keaney Jr. and David R. Weaver

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Deletion of the secretory vesicle proteins IA-2 and IA-2beta disrupts circadian rhythms of cardiovascular and physical activity, Soo Mi Kim, Andrea Power, Steven L. Coon, Cara M. Constance, Takuya Nishimura, Hiroki Hirai, Tao Cai, Christoph Eisner, David R. Weaver, Hugh D. Piggins, David C. Klein, Jurgen Schnermann, and Abner L. Notkins

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Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless, Ceren Korkut, Bulent Ataman, Preethi Ramachandran, James A. Ashley, Romina Barria, Norberto G. Gherbesi, and Vivian Budnik

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WNTs tune up the neuromuscular junction, Ceren Korkut and Vivian Budnik

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Systems Level Processing of Memory in the Fly Brain: A Dissertation, Michael Jonathan Krashes

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A neural circuit mechanism integrating motivational state with memory expression in Drosophila, Michael Jonathan Krashes, Shamik DasGupta, Andrew Vreede, Benjamin White, J. Douglas Armstrong, and Scott Waddell

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New genetic tools for cell lineage analysis in Drosophila, Tzumin Lee

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Nuclear receptor unfulfilled regulates axonal guidance and cell identity of Drosophila mushroom body neurons, Suewei Lin, Yaling Huang, and Tzumin Lee

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Antennal circadian clocks coordinate sun compass orientation in migratory monarch butterflies, Christine Merlin, Robert J. Gegear, and Steven M. Reppert

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Neuronal death or dismemberment mediated by Sox14, Jeannette M. Osterloh and Marc R. Freeman

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A Tyramine-Gated Chloride Channel Coordinates Distinct Motor Programs of a Caenorhabditis elegans Escape Response, Jennifer K. Pirri, Adam D. McPherson, Jamie L. Donnelly, Michael M. Francis, and Mark J. Alkema

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There are many ways to train a fly, Jena L. Pitman, Shamik DasGupta, Michael J. Krashes, Benjamin Leung, Paola N. Perrat, and Scott Waddell

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Sleep: what goes up must come down, Jena L. Pitman and Scott Waddell

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A critical step for postsynaptic F-actin organization: regulation of Baz/Par-3 localization by aPKC and PTEN, Preethi Ramachandran, Romina Barria, James A. Ashley, and Vivian Budnik

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Cotranslational and posttranslational N-glycosylation of polypeptides by distinct mammalian OST isoforms, Catalina Ruiz-Canada, Daniel J. Kelleher, and Reid Gilmore

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A comparative study of Drosophila and human A-type lamins, Sandra R. Schulze, Beatrice Curio-Penny, Sean D. Speese, George Dialynas, Diane E. Cryderman, Caitrin W. McDonough, Demet Nalbant, Melissa Petersen, Vivian Budnik, Pamela K. Geyer, and Lori L. Wallrath

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Twin-spot MARCM to reveal the developmental origin and identity of neurons, Hung-Hsiang Yu, Chun-Hong Chen, Lei Shi, Yaling Huang, and Tzumin Lee

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Endodomain diversity in the Drosophila Dscam and its roles in neuronal morphogenesis, Hung-Hsiang Yu, Jacob S. Yang, Jian Wang, Yaling Huang, and Tzumin Lee

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Defining behavioral and molecular differences between summer and migratory monarch butterflies, Haisun Zhu, Robert J. Gegear, Amy L. Casselman, Sriramana Kanginakudru, and Steven M. Reppert

Publications from 2008

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Rapid activity-dependent modifications in synaptic structure and function require bidirectional Wnt signaling, Bulent Ataman, James A. Ashley, Michael Gorczyca, Preethi Ramachandran, Wernher Fouquet, Stephan J. Sigrist, and Vivian Budnik

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Organization and postembryonic development of glial cells in the adult central brain of Drosophila, Takeshi Awasaki, Sen-Lin Lai, Kei Ito, and Tzumin Lee

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RNA interference screening in Drosophila primary cells for genes involved in muscle assembly and maintenance, Jianwu Bai, Richard Binari, Jian-Quan Ni, Marina Vijayakanthan, Hong-Sheng Li, and Norbert Perrimon

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hVAPB, the causative gene of a heterogeneous group of motor neuron diseases in humans, is functionally interchangeable with its Drosophila homologue DVAP-33A at the neuromuscular junction, Andrea Chai, James Withers, Young Ho Koh, Katherine Parry, Hong Bao, Bing Zhang, Vivian Budnik, and Giuseppa Pennetta

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Learned odor discrimination in Drosophila without combinatorial odor maps in the antennal lobe, Shamik DasGupta and Scott Waddell

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A plastic clock: how circadian rhythms respond to environmental cues in Drosophila, Raphaelle Dubruille and Patrick Emery