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Miller Lab

Miller Lab Publications

2024

Smith JJ , Taylor SR , Blum JA , Feng W , Collings R , Gitler AD , Miller DM , Kratsios P , A molecular atlas of adult C. elegans motor neurons reveals ancient diversity delineated by conserved transcription factor codes Cell reports. 2024 Feb 29; 43 (3). 113857

2023

Ripoll-Sánchez L , Watteyne J , Sun H , Fernandez R , Taylor SR , Weinreb A , Bentley BL , Hammarlund M , Miller DM , Hobert O , Beets I , Vértes PE , Schafer WR , The neuropeptidergic connectome of C. elegans Neuron. 2023 Nov 6; 111 (22). 3570-3589.e5
Freitag R , Stern J , Masters J , Kowalski G , Miller DM , Eley JG , High-Dose Ionizing Radiation Impairs Healthy Dendrite Growth in Advances in radiation oncology. 2023 Dec 05; 9 (3). 101415
Cuentas-Condori A , Chen S , Krout M , Gallik KL , Tipps J , Gailey C , Flautt L , Kim H , Mulcahy B , Zhen M , Richmond JE , Miller DM , The epithelial Na channel UNC-8 promotes an endocytic mechanism that recycles presynaptic components to new boutons in remodeling neurons Cell reports. 2023 Oct 30; 42 (11). 113327
Kropp PA , Rogers P , Kelly SE , McWhirter R , Goff WD , Levitan IM , Miller DM , Golden A , Patient-specific variants of NFU1/NFU-1 disrupt cholinergic signaling in a model of multiple mitochondrial dysfunctions syndrome 1 Disease models & mechanisms. 2023 Feb 01; 16 (2).

2022

Ochs ME , McWhirter RM , Unckless RL , Miller DM , Lundquist EA , Caenorhabditis elegans ETR-1/CELF has broad effects on the muscle cell transcriptome, including genes that regulate translation and neuroblast migration BMC genomics. 2022 Jan 06; 23 (1). 13

2021

Cuentas-Condori A , Miller DM , Imaging Dendritic Spines in Caenorhabditis elegans Journal of visualized experiments : JoVE. 2021 Sep 27; (175).
Palumbos SD , Skelton R , McWhirter R , Mitchell A , Swann I , Heifner S , Von Stetina S , Miller DM , cAMP controls a trafficking mechanism that maintains the neuron specificity and subcellular placement of electrical synapses Developmental cell. 2021 Nov 05; 56 (23). 3235-3249.e4
Johnson CK , Miller DM , Bianchi L , Effect of the protease plasmin on hyperactive DEG/ENaC channels MEC-4(d) and UNC-8(d) microPublication biology. 2021 Jun 21; 2021
Miller-Fleming TW , Cuentas-Condori A , Manning L , Palumbos S , Richmond JE , Miller DM , Transcriptional control of parallel-acting pathways that remove specific presynaptic proteins in remodeling neurons The Journal of neuroscience : the official journal of the Society for Neuroscience. 2021 May 27;
Glenwinkel L , Taylor SR , Langebeck-Jensen K , Pereira L , Reilly MB , Basavaraju M , Rafi I , Yemini E , Pocock R , Sestan N , Hammarlund M , Miller DM , Hobert O , In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the nervous system eLife. 2021 Jun 24; 10
Barrett A , McWhirter R , Taylor SR , Weinreb A , Miller DM , Hammarlund M , A head-to-head comparison of ribodepletion and polyA selection approaches for C. elegans low input RNA-sequencing libraries G3 (Bethesda, Md.). 2021 Apr 15;
Taylor SR , Santpere G , Weinreb A , Barrett A , Reilly MB , Xu C , Varol E , Oikonomou P , Glenwinkel L , McWhirter R , Poff A , Basavaraju M , Rafi I , Yemini E , Cook SJ , Abrams A , Vidal B , Cros C , Tavazoie S , Sestan N , Hammarlund M , Hobert O , Miller DM , Molecular topography of an entire nervous system Cell. 2021 Jul 02;

2020

Cuentas-Condori A , Miller Rd DM , Synaptic remodeling, lessons from C. elegans Journal of neurogenetics. 2020 Aug 18; 1-16

2019

Konietzka J , Fritz M , Spiri S , McWhirter R , Leha A , Palumbos S , Costa WS , Oranth A , Gottschalk A , Miller DM , Hajnal A , Bringmann H , Epidermal Growth Factor Signaling Promotes Sleep through a Combined Series and Parallel Neural Circuit Current biology : CB. 2019 Dec 12; 30 (1). 1-16.e13
Cuentas-Condori A , Mulcahy B , He S , Palumbos S , Zhen M , Miller DM , C. elegans neurons have functional dendritic spines eLife. 2019 Oct 4; 8
Sundararajan L , Smith CJ , Watson JD , Millis BA , Tyska MJ , Miller DM , Actin assembly and non-muscle myosin activity drive dendrite retraction in an UNC-6/Netrin dependent self-avoidance response PLoS Genetics. 2019 Jun 20; 15 (6). e1008228
Sundararajan L , Stern J , Miller DM , Mechanisms that regulate morphogenesis of a highly branched neuron in C. elegans Developmental Biology. 2019 Apr 17; 451 (1). 53-67
He Siwei , Cuentas-Condori Andrea , Miller David M , NATF (Native And Tissue-Specific Fluorescence): A Strategy for Bright, Tissue-Specific GFP Labeling of Native Proteins in Caenorhabditis elegans Genetics. 2019 Apr 5;

2018

Oranth A , Schultheis C , Tolstenkov O , Erbguth K , Nagpal J , Hain D , Brauner M , Wabnig S , Steuer Costa W , McWhirter RD , Zels S , Palumbos S , Miller Iii DM , Beets I , Gottschalk A , Food Sensation Modulates Locomotion by Dopamine and Neuropeptide Signaling in a Distributed Neuronal Network Neuron. 2018 Nov 01; 100 (6). 1414-1428.e10
Sundararajan L , Miller DM , Neuronal Fat and Dendrite Morphogenesis: The Goldilocks Effect Trends in Neurosciences. 2018 Mar 13; 41 (5). 250-252
Matthewman C , Johnson CK , Miller DM , Bianchi L , Functional features of the “finger” domain of the DEG/ENaC channels MEC-4 and UNC-8 American Journal of Physiology-Cell Physiology. 2018 Apr 25; 315 (2). C155-C163
Zou W , Dong X , Broederdorf TR , Shen A , Kramer DA , Shi R , Liang X , Miller DM , Xiang YK , Yasuda R , Chen B , Shen K , A Dendritic Guidance Receptor Complex Brings Together Distinct Actin Regulators to Drive Efficient F-Actin Assembly and Branching Developmental Cell. 2018 May 7; 45 (3). 362-375.e3
Hammarlund M , Hobert O , Miller DM , Sestan N , The CeNGEN Project: The Complete Gene Expression Map of an Entire Nervous System Neuron. 2018 Aug 8; 99 (3). 430-433

2017

Bermingham DP , Hardaway JA , Refai O , Marks CR , Snider SL , Sturgeon SM , Spencer WC , Colbran RJ , Miller DM , Blakely RD , The Atypical MAP Kinase SWIP-13/ERK8 Regulates Dopamine Transporters through a Rho-Dependent Mechanism The Journal of neuroscience : the official journal of the Society for Neuroscience. 2017 Aug 21; 37 (38). 9288-9304
O'Brien BMJ , Palumbos SD , Novakovic M , Shang X , Sundararajan L , Miller DM , Separate transcriptionally regulated pathways specify distinct classes of sister dendrites in a nociceptive neuron Developmental biology. 2017 Oct 13; 432 (2). 248-257

2016

O'Brien B , Miller DM , Neurodevelopment: Three’s a Crowd, Four Is a Receptor Complex Current Biology. 2016 Sep 12; 26 (17). R799-801
Byrne AB , McWhirter RD , Sekine Y , Strittmatter SM , Miller DM , Hammarlund M , Inhibiting poly(ADP-ribosylation) improves axon regeneration eLife. 2016 Oct 04; 5
Matthewman C , Miller-Fleming TW , Miller DM , Bianchi L , Ca2+ permeability and Na+ conductance in cellular toxicity caused by hyperactive DEG/ENaC channels American Journal of Physiology-Cell Physiology. 2016 Oct 19; 311 (6). C920-C930
Lim MA , Chitturi J , Laskova V , Meng J , Findeis D , Wiekenberg A , Mulcahy B , Luo L , Li Y , Lu Y , Hung W , Qu Y , Ho CY , Holmyard D , Ji N , McWhirter R , Samuel AD , Miller DM , Schnabel R , Calarco JA , Zhen M , Neuroendocrine modulation sustains the forward motor state eLife. 2016 Nov 18; 5
Miller-Fleming W , Petersen C , Manning Laura , Matthewman Cristina , Gornet Megan , Beers Allison , Hori Sayaki , Mitani Shohei , Bianchi Laura , Richmond Janet , Miller M , The DEG/ENaC cation channel protein UNC-8 drives activity-dependent synapse removal in remodeling GABAergic neurons eLife. 2016 Jul 12; 5 e14599

2015

Hardaway JA , Sturgeon SM , Snarrenberg CL , Li Z , Xu XZ , Bermingham DP , Odiase P , Spencer WC , Miller DM , Carvelli L , Hardie SL , Blakely RD , Glial Expression of the Caenorhabditis elegans Gene swip-10 Supports Glutamate Dependent Control of … The Journal of neuroscience : the official journal of the Society for Neuroscience. 2015 Jun 24; 35 (25). 9409-23
He S , Philbrook A , McWhirter R , Gabel CV , Taub DG , Carter MH , Hanna IM , Francis MM , Miller DM , Transcriptional Control of Synaptic Remodeling through Regulated Expression of an Immunoglobulin Sup… Current biology : CB. 2015 Oct 5; 25 (19). 2541-8

2014

Spencer WC , McWhirter R , Miller T , Strasbourger P , Thompson O , Hillier LW , Waterston RH , Miller DM , Isolation of specific neurons from C. elegans larvae for gene expression profiling. PloS One. 2014 ; 9 (11). e112102
Gerstein MB , Rozowsky J , Yan KK , Wang D , Cheng C , Brown JB , Davis CA , Hillier L , Sisu C , Li JJ , Pei B , Harmanci AO , Duff MO , Djebali S , Alexander RP , Alver BH , Auerbach R , Bell K , Bickel PJ , Boeck ME , Boley NP , Booth BW , Cherbas L , Cherbas P , Di C , Dobin A , Drenkow J , Ewing B , Fang G , Fastuca M , Feingold EA , Frankish A , Gao G , Good PJ , Guigó R , Hammonds A , Harrow J , Hoskins RA , Howald C , Hu L , Huang H , Hubbard TJ , Huynh C , Jha S , Kasper D , Kato M , Kaufman TC , Kitchen RR , Ladewig E , Lagarde J , Lai E , Leng J , Lu Z , MacCoss M , May G , McWhirter R , Merrihew G , Miller DM , Mortazavi A , Murad R , Oliver B , Olson S , Park PJ , Pazin MJ , Perrimon N , Pervouchine D , Reinke V , Reymond A , Robinson G , Samsonova A , Saunders GI , Schlesinger F , Sethi A , Slack FJ , Spencer WC , Stoiber MH , Strasbourger P , Tanzer A , Thompson OA , Wan KH , Wang G , Wang H , Watkins KL , Wen J , Wen K , Xue C , Yang L , Yip K , Zaleski C , Zhang Y , Zheng H , Brenner SE , Graveley BR , Celniker SE , Gingeras TR , Waterston R , Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug ; 512 (7515). 445-8

2013

Smith CJ , O'Brien T , Chatzigeorgiou M , Spencer WC , Feingold-Link E , Husson SJ , Hori S , Mitani S , Gottschalk A , Schafer WR , Miller DM , Sensory Neuron Fates Are Distinguished by a Transcriptional Switch that Regulates Dendrite Branch St… Neuron. 2013 Jul 24; 79 (2). 266-80
Wang Y , Matthewman C , Han L , Miller T , Miller DM , Bianchi L , Neurotoxic unc-8 mutants encode constitutively active DEG/ENaC channels that are blocked by divalent… The Journal of general physiology. 2013 Aug ; 142 (2). 157-69

2012

Husson SJ , Costa WS , Wabnig S , Stirman JN , Watson JD , Spencer WC , Akerboom J , Looger LL , Treinin M , Miller DM , Lu H , Gottschalk A , Optogenetic analysis of a nociceptor neuron and network reveals ion channels acting downstream of pr… Current biology : CB. 2012 May 8; 22 (9). 743-52
Smith CJ , Watson JD , VanHoven MK , Colón-Ramos DA , Miller DM , Netrin (UNC-6) mediates dendritic self-avoidance. Nature Neuroscience. 2012 May ; 15 (5). 731-7
Schneider J , Skelton RL , Von Stetina SE , Middelkoop TC , van Oudenaarden A , Korswagen HC , Miller DM , UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit. Development. 2012 Jun ; 139 (12). 2234-45
Shakes DC , Miller DM , Nonet ML , Immunofluorescence microscopy. Methods in cell biology. 2012 ; 107 35-66

2011

Lu ZJ , Yip KY , Wang G , Shou C , Hillier LW , Khurana E , Agarwal A , Auerbach R , Rozowsky J , Cheng C , Kato M , Miller DM , Slack F , Snyder M , Waterston RH , Reinke V , Gerstein MB , Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, seconda… Genome research. 2011 Feb ; 21 (2). 276-85
Petersen SC , Watson JD , Richmond JE , Sarov M , Walthall WW , Miller DM , A transcriptional program promotes remodeling of GABAergic synapses in Caenorhabditis elegans. Journal of Neuroscience. 2011 Oct 26; 31 (43). 15362-75
Spencer WC , Zeller G , Watson JD , Henz SR , Watkins KL , McWhirter RD , Petersen S , Sreedharan VT , Widmer C , Jo J , Reinke V , Petrella L , Strome S , Von Stetina SE , Katz M , Shaham S , Rätsch G , Miller DM , A spatial and temporal map of C. elegans gene expression. Genome Research. 2011 Feb ; 21 (2). 325-41
Hallem EA , Spencer WC , McWhirter RD , Zeller G , Henz SR , Rätsch G , Miller DM , Horvitz HR , Sternberg PW , Ringstad N , Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America. 2011 Jan 4; 108 (1). 254-9
Albeg A , Smith CJ , Chatzigeorgiou M , Feitelson DG , Hall DH , Schafer WR , Miller DM , Treinin M , C. elegans multi-dendritic sensory neurons: morphology and function. Molecular and cellular neurosciences. 2011 Jan ; 46 (1). 308-17

2010

Gerstein MB , Lu ZJ , Van Nostrand EL , Cheng C , Arshinoff BI , Liu T , Yip KY , Robilotto R , Rechtsteiner A , Ikegami K , Alves P , Chateigner A , Perry M , Morris M , Auerbach RK , Feng X , Leng J , Vielle A , Niu W , Rhrissorrakrai K , Agarwal A , Alexander RP , Barber G , Brdlik CM , Brennan J , Brouillet JJ , Carr A , Cheung MS , Clawson H , Contrino S , Dannenberg LO , Dernburg AF , Desai A , Dick L , Dosé AC , Du J , Egelhofer T , Ercan S , Euskirchen G , Ewing B , Feingold EA , Gassmann R , Good PJ , Green P , Gullier F , Gutwein M , Guyer MS , Habegger L , Han T , Henikoff JG , Henz SR , Hinrichs A , Holster H , Hyman T , Iniguez AL , Janette J , Jensen M , Kato M , Kent WJ , Kephart E , Khivansara V , Khurana E , Kim JK , Kolasinska-Zwierz P , Lai EC , Latorre I , Leahey A , Lewis S , Lloyd P , Lochovsky L , Lowdon RF , Lubling Y , Lyne R , MacCoss M , Mackowiak SD , Mangone M , McKay S , Mecenas D , Merrihew G , Miller DM , Muroyama A , Murray JI , Ooi SL , Pham H , Phippen T , Preston EA , Rajewsky N , Rätsch G , Rosenbaum H , Rozowsky J , Rutherford K , Ruzanov P , Sarov M , Sasidharan R , Sboner A , Scheid P , Segal E , Shin H , Shou C , Slack FJ , Slightam C , Smith R , Spencer WC , Stinson EO , Taing S , Takasaki T , Vafeados D , Voronina K , Wang G , Washington NL , Whittle CM , Wu B , Yan KK , Zeller G , Zha Z , Zhong M , Zhou X , , Ahringer J , Strome S , Gunsalus KC , Micklem G , Liu XS , Reinke V , Kim SK , Hillier LW , Henikoff S , Piano F , Snyder M , Stein L , Lieb JD , Waterston RH , Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 2010 Dec 24; 330 (6012). 1775-87
Hammock EA , Eagleson KL , Barlow S , Earls LR , Miller DM , Levitt P , Homologs of genes expressed in Caenorhabditis elegans GABAergic neurons are also found in the develo… Neural development. 2010 ; 5 32
Thorne CA , Hanson AJ , Schneider J , Tahinci E , Orton D , Cselenyi CS , Jernigan KK , Meyers KC , Hang BI , Waterson AG , Kim K , Melancon B , Ghidu VP , Sulikowski GA , LaFleur B , Salic A , Lee LA , Miller DM , Lee E , Small-molecule inhibition of Wnt signaling through activation of casein kinase 1α. Nature chemical biology. 2010 Nov ; 6 (11). 829-36
Earls LR , Hacker ML , Watson JD , Miller DM , Coenzyme Q protects Caenorhabditis elegans GABA neurons from calcium-dependent degeneration. Proceedings of the National Academy of Sciences of the United States of America. 2010 Aug 10; 107 (32). 14460-5
Smith CJ , Watson JD , Spencer WC , O'Brien T , Cha B , Albeg A , Treinin M , Miller DM , Time-lapse imaging and cell-specific expression profiling reveal dynamic branching and molecular det… Developmental Biology. 2010 Sep 1; 345 (1). 18-33
Chatzigeorgiou M , Yoo S , Watson JD , Lee WH , Spencer WC , Kindt KS , Hwang SW , Miller DM , Treinin M , Driscoll M , Schafer WR , Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors. Nature neuroscience. 2010 Jul ; 13 (7). 861-8

2009

Meissner B , Warner A , Wong K , Dube N , Lorch A , McKay SJ , Khattra J , Rogalski T , Somasiri A , Chaudhry I , Fox RM , Miller DM , Baillie DL , Holt RA , Jones SJ , Marra MA , Moerman DG , An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elega… PLoS genetics. 2009 Jun ; 5 (6). e1000537
Helmcke KJ , Syversen T , Miller DM , Aschner M , Characterization of the effects of methylmercury on Caenorhabditis elegans. Toxicology and applied pharmacology. 2009 Oct 15; 240 (2). 265-72

2008

Watson JD , Wang S , Von Stetina SE , Spencer WC , Levy S , Dexheimer PJ , Kurn N , Heath JD , Miller DM , Complementary RNA amplification methods enhance microarray identification of transcripts expressed i… BMC genomics. 2008 ; 9 84

2007

Miller DM , Synapses here and not everywhere Science (New York, N.Y.). 2007 Aug 17; 317 (5840). 907-8
Von Stetina SE , Watson JD , Fox RM , Olszewski KL , Spencer WC , Roy PJ , Miller DM , Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in … Genome biology. 2007 ; 8 (7). R135
Von Stetina SE , Fox RM , Watkins KL , Starich TA , Shaw JE , Miller DM , UNC-4 represses CEH-12/HB9 to specify synaptic inputs to VA motor neurons in C. elegans. Genes & development. 2007 Feb 1; 21 (3). 332-46
Fox RM , Watson JD , Von Stetina SE , McDermott J , Brodigan TM , Fukushige T , Krause M , Miller DM , The embryonic muscle transcriptome of Caenorhabditis elegans. Genome biology. 2007 ; 8 (9). R188

2006

Von Stetina SE , Treinin M , Miller DM , The motor circuit International review of neurobiology. 2006 ; 69 125-67
Varadan V , Miller DM , Anastassiou D , Computational inference of the molecular logic for synaptic connectivity in C. elegans Bioinformatics (Oxford, England). 2006 ; 22 (14). e497-506

2005

Touroutine D , Fox RM , Von Stetina SE , Burdina A , Miller DM , Richmond JE , acr-16 encodes an essential subunit of the levamisole-resistant nicotinic receptor at the Caenorhabditis elegans neuromuscular junction The Journal of biological chemistry. 2005 May 24; 280 (29). 27013-21
Fox RM , Von Stetina SE , Barlow SJ , Shaffer C , Olszewski KL , Moore JH , Dupuy D , Vidal M , Miller DM , A gene expression fingerprint of C. elegans embryonic motor neurons. BMC genomics. 2005 ; 6 42

2004

Sedensky MM , Siefker JM , Koh JY , Miller DM , Morgan PG , A stomatin and a degenerin interact in lipid rafts of the nervous system of Caenorhabditis elegans American journal of physiology. Cell physiology. 2004 Apr 21; 287 (2). C468-74

2002

Christensen M , Estevez A , Yin X , Fox R , Morrison R , McDonnell M , Gleason C , Miller DM , Strange K , A primary culture system for functional analysis of C. elegans neurons and muscle cells Neuron. 2002 Feb 14; 33 (4). 503-14
Esmaeili B , Ross JM , Neades C , Miller DM , Ahringer J , The C. elegans even-skipped homologue, vab-7, specifies DB motoneurone identity and axon trajectory Development (Cambridge, England). 2002 ; 129 (4). 853-62
Nass R , Hall DH , Miller DM , Blakely RD , Neurotoxin-induced degeneration of dopamine neurons in Caenorhabditis elegans Proceedings of the National Academy of Sciences of the United States of America. 2002 Feb 26; 99 (5). 3264-9

2001

Lickteig KM , Duerr JS , Frisby DL , Hall DH , Rand JB , Miller DM , Regulation of neurotransmitter vesicles by the homeodomain protein UNC-4 and its transcriptional cor… The Journal of neuroscience : the official journal of the Society for Neuroscience. 2001 Mar 15; 21 (6). 2001-14

1999

Miller DM , Desai NS , Hardin DC , Piston DW , Patterson GH , Fleenor J , Xu S , Fire A , Two-color GFP expression system for C. elegans BioTechniques. 1999 May 1; 26 (5). 914-8, 920-1
Winnier AR , Meir JY , Ross JM , Tavernarakis N , Driscoll M , Ishihara T , Katsura I , Miller DM , UNC-4/UNC-37-dependent repression of motor neuron-specific genes controls synaptic choice in Caenorhabditis elegans Genes & Development. 1999 ; 13 (21). 2774-86

1997

Pflugrad A , Meir JY , Barnes TM , Miller DM , The Groucho-like transcription factor UNC-37 functions with the neural specificity gene unc-4 to govern motor neuron identity in C. elegans Development (Cambridge, England). 1997 ; 124 (9). 1699-709

1995

Miller DM , Niemeyer CJ , Expression of the unc-4 homeoprotein in Caenorhabditis elegans motor neurons specifies presynaptic input Development (Cambridge, England). 1995 ; 121 (9). 2877-86

1993

Miller DM , Niemeyer CJ , Chitkara P , Dominant unc-37 mutations suppress the movement defect of a homeodomain mutation in unc-4, a neural specificity gene in Caenorhabditis elegans Genetics. 1993 Nov ; 135 (3). 741-53

1992

Miller DM , Shen MM , Shamu CE , Bürglin TR , Ruvkun G , Dubois ML , Ghee M , Wilson L , C. elegans unc-4 gene encodes a homeodomain protein that determines the pattern of synaptic input to specific motor neurons Nature. 1992 Feb 27; 355 (6363). 841-5

Nass R , Miller DM , Blakely RD , C. elegans: a novel pharmacogenetic model to study Parkinson’s disease Parkinsonism & related disorders. ; 7 (3). 185-191