Publications
Rothman JS, Borges-Merjane C, Holderith N, Jonas P, Silver RA
Validation of a stereological method for estimating particle size and density from 2D projections with high accuracy.
PLoS ONE 18(3): e0277148. [https://doi.org/10.1371/journal.pone.0277148]
Frederic Lanore, N. Alex Cayco-Gajic, Harsha Gurnani, Diccon Coyle & R. Angus Silver
Cerebellar granule cell axons support high-dimensional representations
Nature Neuroscience [doi:/10.1038/s41593-021-00873-x]
Antoine M. Valera, Fiona C. Neufeldt, Paul A. Kirkby, John E. Mitchell, and R. Angus Silver
Precompensation of 3D field distortions in remote focus two-photon microscopy
Biomed. Opt. Express 12, 3717-3728 [doi:10.1364/BOE.425588]
Harsha Gurnani and R. Angus Silver
Multidimensional population activity in an electrically coupled inhibitory circuit in the cerebellar cortex
Neuron, Volume 109, Issue 10, 1739 – 1753.e8 [doi:10.1016/j.neuron.2021.03.027]
Griffiths VA, Valera AM, Lau JY, Roš H, Younts TJ, Marin B, Baragli C, Coyle D, Evans GJ, Konstantinou G, Koimtzis T, Nadella KMNS, Punde SA, Kirkby PA, Bianco IH, and Silver RA
Real-time 3D movement correction for two-photon imaging in behaving animals
Nature Methods, 17;741. [doi:10.1038/s41592-020-0851-7]
Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, Courcol J-D, Arkhipov A
The SONATA data format for efficient description of large-scale network models.
PLoS Computational Biology, 16 (2), e1007696. [doi:10.1371/journal.pcbi.1007696 ]
Frederic Lanore, Jason S. Rothman, Diccon Coyle, R. Angus Silver
Norepinephrine controls the gain of the inhibitory circuit in the cerebellar input layer
bioRxiv 567172; [doi: 10.1101/567172]
Cayco-Gajic NA,Silver RA
Re-evaluating Circuit Mechanisms Underlying Pattern Separation.
Neuron 2019 Feb 20;101(4):584-602. PMID: 30790539. [doi: 10.1016/j.neuron.2019.01.044]
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GMG, Lytton WW
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
Elife, 8. [doi:10.7554/eLife.44494]
Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Sadra Sadeh, Eugenio Piasini, Justas Birgiolas, Robert C. Cannon, N. Alex Cayco-Gajic, Sharon Crook, Andrew P. Davison, Salvador Dura-Bernal, András Ecker, Michael L. Hines, Giovanni Idili, Frederic Lanore, Stephen D. Larson, William W. Lytton, Amitava Majumdar, Robert A. McDougal, Subhashini Sivagnanam, Sergio Solinas, Rokas Stanislovas, Sacha J. van Albada, Werner van Geit, R. Angus Silver
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits
Neuron, Volume 103, Issue 3, 2019, Pages 395-411.e5, ISSN 0896-6273. [doi:10.1016/j.neuron.2019.05.019]
Gleeson, P., Lung, D., Grosu, R., Hasani, R., & Larson, S. D.
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans
Philos Trans R Soc Lond B Biol Sci, 373 (1758). [doi:10.1098/rstb.2017.0379]
Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G.
Geppetto: a reusable modular open platform for exploring neuroscience data and models.
Philos Trans R Soc Lond B Biol Sci. 2018 Sep 10;373(1758). pii: 20170380. PMID:30201843 [doi: 10.1098/rstb.2017.0380]
Jason S. Rothman, R. Angus Silver
NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data
Frontiers in Neuroinformatics, 12:14 (2018) [DOI Link]
Padraig Gleeson, Andrew P. Davison, R. Angus Silver, Giorgio A. Ascoli
A Commitment to Open Source in Neuroscience
Neuron (NeuroViews) Volume 96, Issue 5 (2017) [DOI Link]
Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline JB.
Toward standard practices for sharing computer code and programs in neuroscience.
Nat Neurosci. 2017 May 25;20(6):770-773. PMID: 28542156 [doi: 10.1038/nn.4550.]
Sadra Sadeh, R. Angus Silver, Thomas D. Mrsic-Flogel & Dylan Richard Muir
Assessing the Role of Inhibition in Stabilizing Neocortical Networks Requires Large-Scale Perturbation of the Inhibitory Population
Journal of Neuroscience, 37 (49) 12050-12067 [DOI Link]
N. Alex Cayco-Gajic, Claudia Clopath & R. Angus Silver
Sparse synaptic connectivity is required for decorrelation and pattern separation in feedforward networks
Nature Communications 8, Article number: 1116 (2017) [DOI Link]
Jason S. Rothman, Laszlo Kocsis, Etienne Herzog, Zoltan Nusser, and R. Angus Silver
Physical determinants of vesicle mobility and supply at a central synapse
Elife. 2016 Aug 19;5. pii: e15133 [PubMed] [DOI Link]
K M Naga Srinivas Nadella, Hana Roš, Chiara Baragli, Victoria A Griffiths, George Konstantinou, Theo Koimtzis, Geoffrey J Evans, Paul A Kirkby & R Angus Silver
Random-access scanning microscopy for 3D imaging in awake behaving animals
Nat Methods. 2016 Dec;13(12):1001-1004 [PubMed] [DOI Link]
R. Angus Silver, Andrew F. MacAskill and Mark Farrant
Neurotransmitter receptors on dendrites.
In Dendrites (3rd Edition)
Szoboszlay M.*, Lőrincz A.*, Lanore F.*, Vervaeke K., Silver R.A. and Nusser Z.
Functional properties of dendritic gap junctions in cerebellar Golgi cells.
*equal 1st author, Neuron [PubMed][doi:10.1016/j.neuron.2016.03.029]
Lanore F. and Silver R.A.
Extracting quantal properties of transmission at central synapses.
Advanced Patch-Clamp Analysis for Neuroscientists, pp 193–211. New York, NY: Springer New York
George Konstantinou, Paul A. Kirkby, Geoffrey J. Evans, K. M. Naga Srinivas Nadella, Victoria A. Griffiths, John E. Mitchell, and R. Angus Silver
Dynamic wavefront shaping with an acousto-optic lens for laser scanning microscopy.
Opt. Express 24, 6283-6299. DOI:10.1364/OE.24.006283
Evans GJ, Kirkby PA, Naga Srinivas Nadella KM, Marin B and Silver RA.
Development and application of a ray-based model of light propagation through a spherical acousto-optic lens.
Opt Express. 2015 Sep 7;23(18):23493-510. DOI: 10.1364/OE.23.023493.
Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman JS, Shigemoto R, Silver RA, DiGregorio DA, Takahashi T.
Nanoscale Distribution of Presynaptic Ca(2+) Channels and Its Impact on Vesicular Release during Development.
Neuron. 85(1):145-58 [PubMed] [DOI Link]
Lanore F, Silver RA (2014).
Reading dendritic activity with gap junctions.
Nat Neurosci. 17(12):1625-7 [PubMed] [DOI Link]
Billings G, Piasini E, Lorincz A, Nusser Z and Silver RA (2014).
Network Structure within the Cerebellar Input Layer Enables Lossless Sparse Encoding.
Neuron. 83(4):960-74 [PubMed]
Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E and Silver RA (2014).
LEMS: A language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.
Frontiers in Neuroinformatics. 8:79 [DOI Link]
Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA, Gleeson P (2014).
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.
Frontiers in Neuroinformatics. 8:38 [PubMed] [DOI Link]
Farinella M, Ruedt DT, Gleeson P, Lanore F, Silver RA (2014).
Glutamate-bound NMDARs arising from in vivo-like network activity extend spatio-temporal integration in a L5 cortical pyramidal cell model.
PLoS Computational Biology. 10(4):e1003590 [PubMed] [DOI Link]
Rothman JS, Silver RA (2014).
Data-driven modeling of synaptic transmission and integration.
Prog Mol Biol Transl Sci. 123:305-50 [PubMed] [DOI Link]
Fernandez-Alfonso T, Nadella KM, Iacaruso MF, Pichler B, Ros H, Kirkby PA, Silver RA (2014).
Monitoring synaptic and neuronal activity in 3D with synthetic and genetic indicators using a compact acousto-optic lens two-photon microscope.
J Neurosci Methods. 30;222:69-81 [PubMed] [DOI Link]
Hallermann S, Silver RA (2013).
Sustaining rapid vesicular release at active zones: potential roles for vesicle tethering.
Trends in Neuroscience. 36(3):185-94 [PubMed] [DOI Link]
Schwartz EJ, Rothman JS, Dugue GP, Diana M, Rousseau C, Silver RA, Dieudonne S (2012).
NMDA Receptors with Incomplete Mg2+ Block Enable Low-Frequency Transmission through the Cerebellar Cortex.
Journal of Neuroscience. 32(20):6878-6893 [PubMed] [DOI Link]
Vervaeke K, Lorincz A, Nusser Z, Silver RA (2012).
Gap Junctions Compensate for Sublinear Dendritic Integration in an Inhibitory Network.
Science. 335(6076), 1624-1628 [PubMed]
Minneci F, Kanichay RT, Silver RA (2012).
Estimation of the time course of neurotransmitter release at central synapses from the first latency of postsynaptic currents.
J Neurosci Methods. 205(1), 49-64 [PubMed]
Chaigneau E, Wright AJ, Poland SP, Girkin JM, Silver RA (2011).
Impact of wavefront distortion and scattering on 2-photon microscopy in mammalian brain tissue.
Opt Express. 19(23), 22755-74 [PubMed]
Hallermann S, Fejtova A, Schmidt H, Weyhersmuller A, Silver RA, Gundelfinger ED, Eilers J (2010).
Bassoon speeds vesicle reloading at a central excitatory synapse.
Neuron. 68(4-6), 710-723 [PubMed]
Steuber V, Schultheiss NW, Silver RA, De Schutter E, Jaeger D (2010).
Determinants of synaptic integration and heterogeneity in rebound firing explored with data-driven models of deep cerebellar nucleus cells.
J Comput Neurosci. 30(3), 633-58 [PubMed]
Vervaeke K, Lorincz A, Gleeson P, Farinella M, Nusser Z, Silver RA (2010).
Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input.
Neuron. 67(3), 435-51 [PubMed]
Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA (2010).
NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.
PLoS Comput Biol 6(6) [PubMed] [DOI Link]
Kirkby PA, Nadella KMNS, Silver RA (2010).
A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy.
Optics Express 18(13), 13720-13744 [PubMed] [DOI Link]
Silver RA (2010).
Neuronal arithmetic.
Nat Rev Neurosci 11(7), 474-489 [PubMed] [DOI Link]
Describing and exchanging models of neurons and neuronal networks with NeuroML.
BMC NEUROSCIENCE. ( Vol. 10 ). BIOMED CENTRAL LTD. [DOI Link]
Rothman JS, Cathala L, Steuber V, Silver RA (2009).
Synaptic depression enables neuronal gain control.
Nature 457(7232), 1015-1018 [PubMed] [DOI Link]
Arenz A, Silver RA, Schaefer AT, Margrie TW (2008).
The contribution of single synapses to sensory representation in vivo.
Science 321(5891), 977-980 [PubMed] [DOI link]
Gleeson P, Steuber V, Silver RA (2008).
Using neuroConstruct to develop and modify biologically detailed 3D neuronal network models in health and disease.
In Soltesz, I., Staley, K. (Eds.). Computational Neuroscience in Epilepsy. Elsevier.
Kanichay RT, Silver RA (2008).
Synaptic and cellular properties of the feedforward inhibitory circuit within the input layer of the cerebellar cortex.
Journal of Neuroscience 28(36), 8955-8967 [PubMed]
Kirkby PA, Silver RA, Nadella KMNS (2008).
Imaging Apparatus and Methods
[Online]
Silver RA, Kanichay RT (2008).
Neuroscience: Refreshing connections.
Science 320(5873), 183-184 [PubMed] [DOI link]
Crook S, Gleeson P, Howell F, Svitak J, Silver RA (2007).
MorphML: Level 1 of the NeuroML Standards for Neuronal Morphology Data and Model Specification.
Neuroinformatics 5(2), 96-104 [PubMed]
Digregorio DA, Rothman JS, Nielsen TA, Silver RA (2007).
Desensitization properties of AMPA receptors at the cerebellar mossy fiber granule cell synapse.
Journal of Neuroscience 27(31), 8344-8357 [PubMed] [DOI link]
Gleeson P, Steuber V, Silver RA (2007).
neuroConstruct: a tool for modeling networks of neurons in 3D space.
Neuron 54(2), 219-235 [PubMed] [DOI link]
Saviane C, Silver RA (2007).
Estimation of quantal parameters with multiple-probaility fluctuation analysis.
In Patch-Clamp Methods and Protocols (403 ed. pp.303-317). Humana Press.
Silver RA, Farrant M (2007).
Neurotransmitter-gated channels in dendrites.
In Stuart, G., Spruston, N., Hausser, M. (Eds.). Dendrites (2nd ed. pp.190-223). Oxford: Oxford University Press.
Steuber V, Mittmann W, Hoebeek FE, Silver RA, De Zeeuw CI, Hausser M, De Schutter E (2007).
Cerebellar LTD and pattern recognition by Purkinje cells.
Neuron 54(1), 121-136 [PubMed] [DOI link]
Saviane C, Silver RA (2006).
Errors in the estimation of the variance: Implications for multiple-probability fluctuation analysis.
Journal of Neuroscience Methods 153(2), 250-260 [PubMed] [DOI link]
Saviane C, Silver RA (2006).
Fast vesicle reloading and a large pool sustain high bandwidth transmission at a central synapse.
Nature 439(7079), 983-987 [PubMed] [DOI link]
Sargent PB, Saviane C, Nielsen TA, Digregorio DA, Silver RA (2005).
Rapid vesicular release, quantal variability, and spillover contribute to the precision and reliability of transmission at a glomerular synapse.
Journal of Neuroscience 25(36), 8173-8187 [PubMed]
Thompson SM, Kao JP, Kramer RH, Poskanzer KE, Silver RA, Digregorio DA, Wang SS (2005).
Flashy science: controlling neural function with light.
Journal of Neuroscience 25(45), 10358-10365 [PubMed]
Nielsen TA, Digregorio DA, Silver RA (2004).
Modulation of glutamate mobility reveals the mechanism underlying slow-rising AMPAR EPSCs and the diffusion coefficient in the synaptic cleft.
Neuron 42(5), 757-771 [PubMed] [DOI link]
Semyanov A, Walker MC, Kullmann DM, Silver RA (2004).
Tonically active GABA(A) receptors: modulating gain and maintaining the tone.
Trends in Neurosciences 27(5), 262-269 [PubMed]
Mitchell SJ, Silver RA (2003).
Shunting inhibition and mGluR-mediated disinhibition modulate the gain of granule cell input-output relationships during synaptic excitation in rat cerebellum.
Journal of Physiology. ( Vol. 547P pp.C88-).
Mitchell SJ, Silver RA (2003).
Shunting inhibition modulates neuronal gain during synaptic excitation.
Neuron 38(3), 433-445 [PubMed] [DOI link]
Momiyama A, Silver RA, Hausser M, Notomi T, Wu Y, Shigemoto R, Cull-candy SG (2003).
The density of AMPA receptors activated by a transmitter quantum at the climbing fibre-Purkinje cell synapse in immature rats.
The Journal of Physiology 549, 75-92 [PubMed]
Nielsen TA, Digregorio DA, Silver RA (2003).
Release probability-dependent changes of the AMPA receptor EPSC waveform at the rat cerebellar mossy fibre to granule cell synapse.
Journal of Physiology. ( Vol. 547P pp.C33-).
Silver RA (2003).
Estimation of nonuniform quantal parameters with multiple-probability fluctuation analysis: theory, application and limitations.
Journal of Neuroscience Methods 130(2), 127-141 [PubMed]
Silver RA, Lubke J, Sakmann B, Feldmeyer D (2003).
High-probability uniquantal transmission at excitatory synapses in barrel cortex.
Science 302, 1981-1984 [PubMed] [DOI link]
Digregorio DA, Nusser Z, Silver RA (2002).
Spillover of glutamate onto synaptic AMPA receptors enhances fast transmission at a cerebellar synapse.
Neuron 35(3), 521-533 [PubMed] [DOI link]
Feldmeyer D, Lubke J, Silver RA, Sakmann B (2002).
Synaptic connections between layer 4 spiny neurone-layer 2/3 pyramidal cell pairs in juvenile rat barrel cortex: physiology and anatomy of interlaminar signalling within a cortical column.
The Journal of Physiology 538(3), 803-822 [Pubmed]
Sargent PB, Silver RA (2002).
Stationary and non-stationary quantal analysis of glutamate release at mossy fibre-granule cell synapses in the rat cerebellum.
[Abstract]
Clements JD, Silver RA (2000).
Unveiling synaptic plasticity: a new graphical and analytical approach.
Trends in Neurosciences 23(3), 105-113 [PubMed]
Feldmeyer D, Lubke J, Silver RA, Sakmann B (2000).
Physiology of synaptic connections between spiny layer 4 neurones and layer 2/3 pyramidal cells in rat barrel cortex.
Society for Neuroscience Abstracts. ( Vol. 26 pp.2105P-).
Feldmeyer D, Silver RA, Lubke J, Sakmann B (2000).
Physiology of synaptic connections between spiny layer 4 neurones and layer 2/3 pyramidal cells in rat barrel cortex.
EUR J NEUROSCI 12, 365-365.
Lubke J, Feldmeyer D, Silver RA, Sakmann B (2000).
Morphology of synaptic connections between spiny layer 4 neurones and layer 2/3 pyramidal cells in rat barrel cortex.
EUR J NEUROSCI 12, 14-14
Mitchell SJ, Silver RA (2000).
GABA spillover from single inhibitory axons suppresses low-frequency excitatory transmission at the cerebellar glomerulus.
Journal of Neuroscience 20(23), 8651-8658 [PubMed]
Mitchell SJ, Silver RA (2000).
GABA spillover selectively inhibits low frequency excitatory transmission at cerebellar mossy fibres.
Society for Neuroscience Abstracts. ( Vol. 26 pp.882P-).
Mitchell SJ, Silver RA (2000).
Glutamate spillover suppresses inhibition by activating presynaptic mGluRs.
Nature 404(6777), 498-502 [PubMed]
Feldmeyer D, Silver RA, Lubke J, Sakmann B (1999).
Synaptic connections between spiny layer 4 neurones and layer 2/3 pyramidal cells of rat barrel cortex.
Journal of Physiology. ( Vol. 518 pp.141-).
Mitchell SJ, Silver RA (1999).
Heteroreceptor mediated presynaptic inhibition at the glomerulus of the rat cerebellum.
Society for Neuroscience Abstracts. ( Vol. 25 ).
Mitchell SJ, Silver RA (1999).
Reciprocal presynaptic inhibition at the cerebellar glomerulus of the rat.
Journal of Physiology. ( Vol. 518 pp.143-).
Silver RA, Farrant M (1999).
Neurotransmitter-gated channels in dendrites.
In Stuart, G., Spruston, N., Hausser, M. (Eds.). Dendrites ( pp.114-138). Oxford University Press.
Silver RA (1998).
Neurotransmission at synapses with single and multiple release sites.
In Faber, D. S., Korn, H., Redman, S. J., Thomson, S. M., Altman, J. (Eds.). Central Synapses: quantal mechanisms and plasticity ( pp.130-139). Strasbourg:
Silver RA, Momiyama A, Cull-candy SG (1998).
Locus of frequency-dependent depression identified with multiple-probability fluctuation analysis at rat climbing fibre-Purkinje cell synapses.
The Journal of Physiology 510, 881-902 [PubMed]
Silver RA, Momiyama A, Cull-candy SG (1997).
Transmitter release and quantal size at cerebellar climbing fibre-Purkinje cell synapses of the rat.
Journal of Physiology. ( Vol. 501P pp.14P-).
Deactivation and desensitization of non-NMDA receptors in patches and the time course of EPSCs in rat cerebellar granule cells.
The Journal of Physiology 493(1), 167-173 [PubMed]
Silver RA, Cull-candy SG, Takahashi T (1996).
Non-NMDA glutamate receptor occupancy and open probability at a rat cerebellar synapse with single and multiple release sites.
The Journal of Physiology 494(1), 231-250 [PubMed]
Silver RA, Colquhoun D, Cullcandy SG, Edmonds B (1994).
MECHANISMS UNDERLYING DECAY OF THE FAST COMPONENT OF EPSCS IN RAT CEREBELLAR GRANULE CELLS.
J PHYSIOL-LONDON 476P, P67-P68.
Sarantis M, Ballerini L, Miller B, Silver RA, Edwards M, Attwell D (1993).
Glutamate uptake from the synaptic cleft does not shape the decay of the non-NMDA component of the synaptic current.
Neuron 11(3), 541-549.
Silver RA, Traynelis SF, Cull-candy SG (1992).
Rapid-time-course miniature and evoked excitatory currents at cerebellar synapses in situ.
Nature 355(6356), 163-166.
Silver RA, Whitaker M, Bolsover SR (1992).
Intracellular ion imaging using fluorescent dyes: artefacts and limits to resolution.
Pflugers Arch 420(5-6), 595-602.
Bolsover S, Silver RA (1991).
Artifacts in calcium measurement: recognition and remedies.
Trends Cell Biol 1(2-3), 71-74.
Silver RA, Bolsover SR (1991).
Expression of T-type calcium current precedes neurite extension in neuroblastoma cells.
J Physiol (Paris) 85(2), 79-83.
Silver RA, Lamb AG, Bolsover SR (1990).
Calcium hotspots caused by L-channel clustering promote morphological changes in neuronal growth cones.
Nature 343(6260), 751-754 [DOI Link]
Silver RA, Lamb AG, Bolsover SR (1989).
Elevated cytosolic calcium in the growth cone inhibits neurite elongation in neuroblastoma cells: correlation of behavioral states with cytosolic calcium concentration.
J Neurosci 9(11), 4007-4020.
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