Citations for Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014)

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Roberts A, Conte D, Hull M, Merrison-Hort R, al Azad AK, Buhl E, Borisyuk R, Soffe SR (2014) Can simple rules control development of a pioneer vertebrate neuronal network generating behavior? J Neurosci 34:608-21 [PubMed]

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Borisyuk R, Al Azad AK, Conte D, Roberts A, Soffe SR (2014) A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. PLoS One 9:e89461 [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
Borisyuk R, Merrison-Hort R, Soffe SR, Koutsikou S, Li WC (2017) To swim or not to swim: A population-level model of Xenopus tadpole decision making and locomotor behaviour. Biosystems 161:3-14 [Journal] [PubMed]
Ferrario A, Merrison-Hort R, Soffe SR, Borisyuk R (2018) Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network. Elife [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
(3 refs)

Borisyuk R, Al Azad AK, Conte D, Roberts A, Soffe SR (2014) A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. PLoS One 9:e89461 [PubMed]

References and models cited by this paper

References and models that cite this paper

Audet C, Dennis JE (2003) Analysis of generalized pattern searches SIAM J Optim 13:889-903
Borisyuk R, Al Azad AK, Conte D, Roberts A, Soffe SR (2011) Modeling the connectome of a simple spinal cord. Front Neuroinform 5:20 [Journal] [PubMed]
Borisyuk R, Cooke T, Roberts A (2008) Stochasticity and functionality of neural systems: mathematical modelling of axon growth in the spinal cord of tadpole. Biosystems 93:101-14 [Journal] [PubMed]
Charron F, Stein E, Jeong J, McMahon AP, Tessier-Lavigne M (2003) The morphogen sonic hedgehog is an axonal chemoattractant that collaborates with netrin-1 in midline axon guidance. Cell 113:11-23 [PubMed]
Chilton JK (2006) Molecular mechanisms of axon guidance. Dev Biol 292:13-24 [Journal] [PubMed]
Dickson BJ (2002) Molecular mechanisms of axon guidance. Science 298:1959-64 [Journal] [PubMed]
Forbes EM, Thompson AW, Yuan J, Goodhill GJ (2012) Calcium and cAMP levels interact to determine attraction versus repulsion in axon guidance. Neuron 74:490-503 [Journal] [PubMed]
Godfrey KB, Eglen SJ, Swindale NV (2009) A multi-component model of the developing retinocollicular pathway incorporating axonal and synaptic growth. PLoS Comput Biol 5:e1000600 [Journal] [PubMed]
Goodhill GJ (1997) Diffusion in axon guidance. Eur J Neurosci 9:1414-21 [PubMed]
Goodhill GJ (1998) Mathematical guidance for axons. Trends Neurosci 21:226-31 [PubMed]
Goodhill GJ (2003) A theoretical model of axon guidance by the Robo code. Neural Comput 15:549-64 [PubMed]
Goodhill GJ, Baier H (1998) Axon guidance: stretching gradients to the limit. Neural Comput 10:521-7 [PubMed]
Gordon-Weeks PR (2000) Neuronal growth cones
Goulding M, Pfaff SL (2005) Development of circuits that generate simple rhythmic behaviors in vertebrates. Curr Opin Neurobiol 15:14-20 [Journal] [PubMed]
Helms AW, Johnson JE (2003) Specification of dorsal spinal cord interneurons. Curr Opin Neurobiol 13:42-9 [PubMed]
Hentschel HG, van Ooyen A (1999) Models of axon guidance and bundling during development. Proc Biol Sci 266:2231-8 [Journal] [PubMed]
Imondi R, Kaprielian Z (2001) Commissural axon pathfinding on the contralateral side of the floor plate: a role for B-class ephrins in specifying the dorsoventral position of longitudinally projecting commissural axons. Development 128:4859-71 [PubMed]
Jessell TM (2000) Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nat Rev Genet 1:20-9 [Journal] [PubMed]
Jung H, O'Hare CM, Holt CE (2011) Translational regulation in growth cones. Curr Opin Genet Dev 21:458-64 [Journal] [PubMed]
Krottje JK, van Ooyen A (2007) A mathematical framework for modeling axon guidance. Bull Math Biol 69:3-31 [Journal] [PubMed]
Lewis KE (2006) How do genes regulate simple behaviours? Understanding how different neurons in the vertebrate spinal cord are genetically specified. Philos Trans R Soc Lond B Biol Sci 361:45-66 [Journal] [PubMed]
Li WC, Cooke T, Sautois B, Soffe SR, Borisyuk R, Roberts A (2007) Axon and dendrite geography predict the specificity of synaptic connections in a functioning spinal cord network. Neural Dev 2:17 [Journal] [PubMed]
Li WC, Higashijima S, Parry DM, Roberts A, Soffe SR (2004) Primitive roles for inhibitory interneurons in developing frog spinal cord. J Neurosci 24:5840-8 [Journal] [PubMed]
Li WC, Perrins R, Soffe SR, Yoshida M, Walford A, Roberts A (2001) Defining classes of spinal interneuron and their axonal projections in hatchling Xenopus laevis tadpoles. J Comp Neurol 441:248-65 [PubMed]
Li WC, Soffe SR, Roberts A (2002) Spinal inhibitory neurons that modulate cutaneous sensory pathways during locomotion in a simple vertebrate. J Neurosci 22:10924-34
Li WC, Soffe SR, Roberts A (2003) The spinal interneurons and properties of glutamatergic synapses in a primitive vertebrate cutaneous flexion reflex. J Neurosci 23:9068-77
Li WC, Soffe SR, Wolf E, Roberts A (2006) Persistent responses to brief stimuli: feedback excitation among brainstem neurons. J Neurosci 26:4026-35 [Journal] [PubMed]
Lyuksyutova AI, Lu CC, Milanesio N, King LA, Guo N, Wang Y, Nathans J, Tessier-Lavigne M, Zou Y (2003) Anterior-posterior guidance of commissural axons by Wnt-frizzled signaling. Science 302:1984-8 [Journal] [PubMed]
Marder E, Taylor AL (2011) Multiple models to capture the variability in biological neurons and networks. Nat Neurosci 14:133-8 [Journal] [PubMed]
McCaig CD, Rajnicek AM, Song B, Zhao M (2005) Controlling cell behavior electrically: current views and future potential. Physiol Rev 85:943-78 [Journal] [PubMed]
Moon MS, Gomez TM (2005) Adjacent pioneer commissural interneuron growth cones switch from contact avoidance to axon fasciculation after midline crossing. Dev Biol 288:474-86 [Journal] [PubMed]
Mortimer D, Dayan P, Burrage K, Goodhill GJ (2011) Bayes-optimal chemotaxis. Neural Comput 23:336-73 [Journal] [PubMed]
Mortimer D, Pujic Z, Vaughan T, Thompson AW, Feldner J, Vetter I, Goodhill GJ (2010) Axon guidance by growth-rate modulation. Proc Natl Acad Sci U S A 107:5202-7 [Journal] [PubMed]
Mortimer D,Dayan P,Burrage K,Goodhill GJ (2010) Optimizing chemotaxis by measuring unbound-bound transitions Physica D-Nonlinear Phenomena 239:477-484
Mueller BK (1999) Growth cone guidance: first steps towards a deeper understanding. Annu Rev Neurosci 22:351-88 [Journal] [PubMed]
Munno DW, Syed NI (2003) Synaptogenesis in the CNS: an odyssey from wiring together to firing together. J Physiol 552:1-11 [Journal] [PubMed]
Nishiyama M, Hoshino A, Tsai L, Henley JR, Goshima Y, Tessier-Lavigne M, Poo MM, Hong K (2003) Cyclic AMP/GMP-dependent modulation of Ca2+ channels sets the polarity of nerve growth-cone turning. Nature 423:990-5 [Journal] [PubMed]
Polleux F, Ince-Dunn G, Ghosh A (2007) Transcriptional regulation of vertebrate axon guidance and synapse formation. Nat Rev Neurosci 8:331-40 [Journal] [PubMed]
Rehder V, Kater SB (1996) Filopodia on neuronal growth cones: Multifunctional structures with sensory and motor capabilities Seminars Neurosciences 8:81-88
Roberts A, Clarke JD (1982) The neuroanatomy of an amphibian embryo spinal cord. Philos Trans R Soc Lond B Biol Sci 296:195-212 [Journal] [PubMed]
Roberts A, Conte D, Hull M, Merrison-Hort R, al Azad AK, Buhl E, Borisyuk R, Soffe SR (2014) Can simple rules control development of a pioneer vertebrate neuronal network generating behavior? J Neurosci 34:608-21 [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
Roberts A, Li WC, Soffe SR (2010) How neurons generate behavior in a hatchling amphibian tadpole: an outline. Front Behav Neurosci 4:16 [Journal] [PubMed]
Rosoff WJ, Urbach JS, Esrick MA, McAllister RG, Richards LJ, Goodhill GJ (2004) A new chemotaxis assay shows the extreme sensitivity of axons to molecular gradients. Nat Neurosci 7:678-82 [Journal] [PubMed]
Schnorrer F, Dickson BJ (2004) Axon guidance: morphogens show the way. Curr Biol 14:R19-21 [PubMed]
Sergi PN, Morana Roccasalvo I, Tonazzini I, Cecchini M, Micera S (2013) Cell guidance on nanogratings: a computational model of the interplay between PC12 growth cones and nanostructures. PLoS One 8:e70304 [Journal] [PubMed]
Shimozono S, Iimura T, Kitaguchi T, Higashijima S, Miyawaki A (2013) Visualization of an endogenous retinoic acid gradient across embryonic development. Nature 496:363-6 [Journal] [PubMed]
Shirasaki R, Lewcock JW, Lettieri K, Pfaff SL (2006) FGF as a target-derived chemoattractant for developing motor axons genetically programmed by the LIM code. Neuron 50:841-53 [Journal] [PubMed]
Shirasaki R, Murakami F (2001) Crossing the floor plate triggers sharp turning of commissural axons. Dev Biol 236:99-108 [Journal] [PubMed]
Song H, Poo M (2001) The cell biology of neuronal navigation. Nat Cell Biol 3:E81-8 [Journal] [PubMed]
SPERRY RW (1963) CHEMOAFFINITY IN THE ORDERLY GROWTH OF NERVE FIBER PATTERNS AND CONNECTIONS. Proc Natl Acad Sci U S A 50:703-10 [PubMed]
Strogatz SH (1994) Nonlinear Dynamics And Chaos With Applications To Physics, Biology, Chemistry, And Engineering
Tessier-Lavigne M, Goodman CS (1996) The molecular biology of axon guidance. Science 274:1123-33 [PubMed]
van Ooyen A (2011) Using theoretical models to analyse neural development. Nat Rev Neurosci 12:311-26 [Journal] [PubMed]
Yamamoto N, Tamada A, Murakami F (2002) Wiring of the brain by a range of guidance cues. Prog Neurobiol 68:393-407 [PubMed]
Zou Y, Lyuksyutova AI (2007) Morphogens as conserved axon guidance cues. Curr Opin Neurobiol 17:22-8 [Journal] [PubMed]
Zubler F, Douglas R (2009) A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 3:25 [Journal] [PubMed]
Ferrario A, Merrison-Hort R, Soffe SR, Borisyuk R (2018) Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network. Elife [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
(58 refs)

Ferrario A, Merrison-Hort R, Soffe SR, Borisyuk R (2018) Structural and functional properties of a probabilistic model of neuronal connectivity in a simple locomotor network. Elife [PubMed]

References and models cited by this paper

References and models that cite this paper

Barabasi AL, Albert R (1999) Emergence of scaling in random networks Science 286:509-12 [PubMed]
Bauer R, Zubler F, Hauri A, Muir DR, Douglas RJ (2014) Developmental origin of patchy axonal connectivity in the neocortex: a computational model. Cereb Cortex 24:487-500 [Journal] [PubMed]
Binzegger T, Douglas RJ, Martin KA (2004) A quantitative map of the circuit of cat primary visual cortex. J Neurosci 24:8441-53 [Journal] [PubMed]
Borisyuk R, Al Azad AK, Conte D, Roberts A, Soffe SR (2011) Modeling the connectome of a simple spinal cord. Front Neuroinform 5:20 [Journal] [PubMed]
Borisyuk R, Al Azad AK, Conte D, Roberts A, Soffe SR (2014) A developmental approach to predicting neuronal connectivity from small biological datasets: a gradient-based neuron growth model. PLoS One 9:e89461 [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
Buhl E, Soffe SR, Roberts A (2015) Sensory initiation of a co-ordinated motor response: synaptic excitation underlying simple decision-making. J Physiol 593:4423-37 [Journal] [PubMed]
Bullmore E, Sporns O (2009) Complex brain networks: graph theoretical analysis of structural and functional systems. Nat Rev Neurosci 10:186-98 [Journal] [PubMed]
Clauset A,Shalizi CR,Newman ME (2009) "Power-law distributions in empirical data SIAM Review 51(4):661-703
Flycircuit 1p1 (2018) Flycircuit Database Http://Wwwflycircuittw/
Hu HB,Wang XF (2008) Unified index to quantifying heterogeneity of complex networks Physica A: Statistical Mechanics and its Applications 387(14):3769-3780
Hull MJ, Soffe SR, Willshaw DJ, Roberts A (2015) Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity. PLoS Comput Biol 11:e1004240 [Journal] [PubMed]
Hull MJ, Soffe SR, Willshaw DJ, Roberts A (2016) Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity. PLoS Comput Biol 12:e1004702 [Journal] [PubMed]
Humphries MD, Gurney K, Prescott TJ (2006) The brainstem reticular formation is a small-world, not scale-free, network. Proc Biol Sci 273:503-11 [Journal] [PubMed]
   Medial reticular formation of the brainstem: anatomy and dynamics (Humphries et al. 2006, 2007) [Model]
Kaiser M, Hilgetag CC (2006) Nonoptimal component placement, but short processing paths, due to long-distance projections in neural systems. PLoS Comput Biol 2:e95 [Journal] [PubMed]
Li WC, Cooke T, Sautois B, Soffe SR, Borisyuk R, Roberts A (2007) Axon and dendrite geography predict the specificity of synaptic connections in a functioning spinal cord network. Neural Dev 2:17 [Journal] [PubMed]
Li WC, Higashijima S, Parry DM, Roberts A, Soffe SR (2004) Primitive roles for inhibitory interneurons in developing frog spinal cord. J Neurosci 24:5840-8 [Journal] [PubMed]
Li WC, Merrison-Hort R, Zhang HY, Borisyuk R (2014) The generation of antiphase oscillations and synchrony by a rebound-based vertebrate central pattern generator. J Neurosci 34:6065-77 [Journal] [PubMed]
Li WC, Roberts A, Soffe SR (2009) Locomotor rhythm maintenance: electrical coupling among premotor excitatory interneurons in the brainstem and spinal cord of young Xenopus tadpoles. J Physiol 587:1677-93 [Journal] [PubMed]
Li WC, Roberts A, Soffe SR (2010) Specific brainstem neurons switch each other into pacemaker mode to drive movement by activating NMDA receptors. J Neurosci 30:16609-20 [Journal] [PubMed]
Li WC, Sautois B, Roberts A, Soffe SR (2007) Reconfiguration of a vertebrate motor network: specific neuron recruitment and context-dependent synaptic plasticity. J Neurosci 27:12267-76 [Journal] [PubMed]
Li WC, Soffe SR, Wolf E, Roberts A (2006) Persistent responses to brief stimuli: feedback excitation among brainstem neurons. J Neurosci 26:4026-35 [Journal] [PubMed]
Lin CW, Lin HW, Chiu MT, Shih YH, Wang TY, Chang HM, Chiang AS (2015) Automated in situ brain imaging for mapping the Drosophila connectome. J Neurogenet 29:157-68 [Journal] [PubMed]
Marder E, Calabrese RL (1996) Principles of rhythmic motor pattern generation. Physiol Rev 76:687-717 [Journal] [PubMed]
Roberts A, Conte D, Hull M, Merrison-Hort R, al Azad AK, Buhl E, Borisyuk R, Soffe SR (2014) Can simple rules control development of a pioneer vertebrate neuronal network generating behavior? J Neurosci 34:608-21 [Journal] [PubMed]
   Model of the Xenopus tadpole swimming spinal network (Roberts et al. 2014) [Model]
Roberts A, Li WC, Soffe SR (2010) How neurons generate behavior in a hatchling amphibian tadpole: an outline. Front Behav Neurosci 4:16 [Journal] [PubMed]
Rubinov M, Sporns O (2010) Complex network measures of brain connectivity: uses and interpretations. Neuroimage 52:1059-69 [Journal] [PubMed]
Sautois B, Soffe SR, Li WC, Roberts A (2007) Role of type-specific neuron properties in a spinal cord motor network. J Comput Neurosci 23:59-77 [Journal] [PubMed]
Seung HS, Sümbül U (2014) Neuronal cell types and connectivity: lessons from the retina. Neuron 83:1262-72 [Journal] [PubMed]
Seung S (2012) Connectome: how the brain's wiring makes us who we are
Shih CT, Sporns O, Yuan SL, Su TS, Lin YJ, Chuang CC, Wang TY, Lo CC, Greenspan RJ, Chiang AS (2015) Connectomics-based analysis of information flow in the Drosophila brain. Curr Biol 25:1249-58 [Journal] [PubMed]
Soffe SR (1989) Roles of Glycinergic Inhibition and N-Methyl-D-Aspartate Receptor Mediated Excitation in the Locomotor Rhythmicity of One Half of the Xenopus Embryo Central Nervous System. Eur J Neurosci 1:561-571 [PubMed]
Soffe SR (1993) Two distinct rhythmic motor patterns are driven by common premotor and motor neurons in a simple vertebrate spinal cord. J Neurosci 13:4456-69 [PubMed]
Sporns O, Honey CJ, Kötter R (2007) Identification and classification of hubs in brain networks. PLoS One 2:e1049 [Journal] [PubMed]
Sporns O, Tononi G, Kötter R (2005) The human connectome: A structural description of the human brain. PLoS Comput Biol 1:e42 [Journal] [PubMed]
Sporns O, Zwi JD (2004) The small world of the cerebral cortex. Neuroinformatics 2:145-62 [Journal] [PubMed]
Sprott DA (1958) The Method of Maximum Likelihood Applied to the Poisson Binomal Distribution Biometrics 14(1):97-106
Stobb M, Peterson JM, Mazzag B, Gahtan E (2012) Graph theoretical model of a sensorimotor connectome in zebrafish. PLoS One 7:e37292 [Journal] [PubMed]
Towlson EK, Vértes PE, Ahnert SE, Schafer WR, Bullmore ET (2013) The rich club of the C. elegans neuronal connectome. J Neurosci 33:6380-7 [Journal] [PubMed]
Varier S, Kaiser M (2011) Neural development features: spatio-temporal development of the Caenorhabditis elegans neuronal network. PLoS Comput Biol 7:e1001044 [Journal] [PubMed]
Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB (2011) Structural properties of the Caenorhabditis elegans neuronal network. PLoS Comput Biol 7:e1001066 [Journal] [PubMed]
Wolf E, Soffe SR, Roberts A (2009) Longitudinal neuronal organization and coordination in a simple vertebrate: a continuous, semi-quantitative computer model of the central pattern generator for swimming in young frog tadpoles. J Comput Neurosci 27:291-308 [Journal] [PubMed]
Zubler F, Douglas R (2009) A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 3:25 [Journal] [PubMed]
(44 refs)