Dr Stephen Eglen

Stephen Eglen

University position


Dr Stephen Eglen is pleased to consider applications from prospective PhD students.


Department of Applied Mathematics and Theoretical Physics (DAMTP)


Cambridge Computational Biology Institute (CCBI)



Home page

http://www.damtp.cam.ac.uk/user/eglen (personal home page)

Research Themes

Systems and Computational Neuroscience

Developmental Neuroscience


I use computational tools to help investigate mechanisms of neural development.

In particular, I study the formation of retinotopic maps and retinal mosaics in vertebrate visual systems. In addition, I am interested in the analysis of large-scale neurophysiological datasets, such as those recorded using multi-electrode arrays or calcium imaging.

Research Focus


retinal development

retinotopic maps

hebbian learning

synaptic plasticity

neural circuit

Clinical conditions

No direct clinical relevance


Calcium imaging

Computational modelling



Seth Grant

Bill Harris

Ole Paulsen


Andrew Huberman Web: http://www.hubermanlab.com/

Michael Reber Web: http://reber2.wix.com/research

Timothy Shafer Web: http://www2.epa.gov/researc...

Associated News Items



Charlesworth P, Cotterill E, Morton A, Grant SG, Eglen SJ (2015), “Quantitative differences in developmental profiles of spontaneous activity in cortical and hippocampal cultures.” Neural Dev 10(1):1 Details

Hjorth JJ, Sterratt DC, Cutts CS, Willshaw DJ, Eglen SJ (2015), “Quantitative assessment of computational models for retinotopic map formation.” Dev Neurobiol 75(6):641-66 Details


Cutts CS, Eglen SJ (2014), “Detecting pairwise correlations in spike trains: an objective comparison of methods and application to the study of retinal waves.” J Neurosci 34(43):14288-303 Details

Eglen S (2014), “Open access: sharing your data is easier than you think.” Nature 509(7505):340 Details

Eglen SJ, Weeks M, Jessop M, Simonotto J, Jackson T, Sernagor E (2014), “A data repository and analysis framework for spontaneous neural activity recordings in developing retina.” Gigascience 3(1):3 Details

Schottdorf M, Eglen SJ, Wolf F, Keil W (2014), “Can retinal ganglion cell dipoles seed iso-orientation domains in the visual cortex?” PLoS One 9(1):e86139 Details


Gjorgjieva J, Berni J, Evers JF, Eglen SJ (2013), “Neural circuits for peristaltic wave propagation in crawling Drosophila larvae: analysis and modeling.” Front Comput Neurosci 7:24 Details

Maccione A, Hennig MH, Gandolfo M, Muthmann O, van Coppenhagen J, Eglen SJ, Berdondini L, Sernagor E (2013), “Following the Ontogeny of Retinal Waves: Pan-Retinal Recordings of Population Dynamics in the Neonatal Mouse.” J Physiol Details


Chabrol FP, Eglen SJ, Sernagor E (2012), “GABAergic control of retinal ganglion cell dendritic development.” Neuroscience 227:30-43 Details

Hore VR, Troy JB, Eglen SJ (2012), “Parasol cell mosaics are unlikely to drive the formation of structured orientation maps in primary visual cortex.” Vis Neurosci 29(6):283-99 Details

Keeley PW, Sliff BJ, Lee SC, Fuerst PG, Burgess RW, Eglen SJ, Reese BE (2012), “Neuronal clustering and fasciculation phenotype in Dscam- and Bax-deficient mouse retinas.” J Comp Neurol 520(7):1349-64 Details


Gjorgjieva J, Eglen SJ (2011), “Modeling developmental patterns of spontaneous activity.” Curr Opin Neurobiol Details

Keeley PW, Sliff B, Lee SC, Fuerst PG, Burgess RW, Eglen SJ, Reese BE (2011), “Neuronal clustering and fasciculation phenotype in dscam- and bax-deficient mouse retinas.” J Comp Neurol


Eglen SJ (2009), “A quick guide to teaching R programming to computational biology students.” PLoS Comput Biol 5(8):e1000482 Details

Eglen SJ, Gjorgjieva J (2009), “Self-organization in the developing nervous system: theoretical models.” HFSP J 3(3):176-85 Details

Gjorgjieva J, Toyoizumi T, Eglen SJ (2009), “Burst-time-dependent plasticity robustly guides ON/OFF segregation in the lateral geniculate nucleus.” PLoS Comput Biol 5(12):e1000618 Details

Godfrey KB, Eglen SJ (2009), “Theoretical models of spontaneous activity generation and propagation in the developing retina.” Mol Biosyst 5(12):1527-35 Details

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(12):e1000600 Details


Eglen SJ, Lofgreen DD, Raven MA, Reese BE (2008), “Analysis of spatial relationships in three dimensions: tools for the study of nerve cell patterning.” BMC Neurosci 9:68 Details

Eglen SJ, Wong JC (2008), “Spatial constraints underlying the retinal mosaics of two types of horizontal cells in cat and macaque.” Vis Neurosci 25(2):209-14 Details


Eglen SJ (2006), “Development of regular cellular spacing in the retina: theoretical models.” Math Med Biol 23(2):79-99 Details


Eglen SJ, Diggle PJ, Troy JB (2005), “Homotypic constraints dominate positioning of on- and off-center beta retinal ganglion cells.” Vis Neurosci 22(6):859-71 Details

Kishi M, Kummer TT, Eglen SJ, Sanes JR (2005), “LL5beta: a regulator of postsynaptic differentiation identified in a screen for synaptically enriched transcripts at the neuromuscular junction.” J Cell Biol 169(2):355-66 Details


Demas J, Eglen SJ, Wong RO (2003), “Developmental loss of synchronous spontaneous activity in the mouse retina is independent of visual experience.” J Neurosci 23(7):2851-60 Details

Eglen SJ, Demas J, Wong ROL (2003), “Mapping by waves: patterned spontaneous activity regulates retinotopic map refinement” Neuron 40:1053-1055

Eglen SJ, Demas J, Wong RO (2003), “Mapping by waves. Patterned spontaneous activity regulates retinotopic map refinement.” Neuron 40(6):1053-5 Details

Eglen SJ, Raven MA, Tamrazian E, Reese BE (2003), “Dopaminergic amacrine cells in the inner nuclear layer and ganglion cell layer comprise a single functional retinal mosaic.” J Comp Neurol 466(3):343-55 Details

Raven MA, Eglen SJ, Ohab JJ, Reese BE (2003), “Determinants of the exclusion zone in dopaminergic amacrine cell mosaics.” J Comp Neurol 461(1):123-36 Details

Sernagor E, Young C, Eglen SJ (2003), “Developmental modulation of retinal wave dynamics: shedding light on the GABA saga.” J Neurosci 23(20):7621-9 Details


Eglen SJ, Willshaw DJ (2002), “Influence of cell fate mechanisms upon retinal mosaic formation: a modelling study.” Development 129(23):5399-408 Details

Lee CW, Eglen SJ, Wong RO (2002), “Segregation of ON and OFF retinogeniculate connectivity directed by patterned spontaneous activity.” J Neurophysiol 88(5):2311-21 Details


Sernagor E, Eglen SJ, Wong RO (2001), “Development of retinal ganglion cell structure and function.” Prog Retin Eye Res 20(2):139-74 Details


Eglen SJ, van Ooyen A, Willshaw DJ (2000), “Lateral cell movement driven by dendritic interactions is sufficient to form retinal mosaics.” Network 11(1):103-18 Details

Sernagor E, Eglen SJ, O'Donovan MJ (2000), “Differential effects of acetylcholine and glutamate blockade on the spatiotemporal dynamics of retinal waves.” J Neurosci 20(2):RC56 Details


Eglen SJ (1999), “The role of retinal waves and synaptic normalization in retinogeniculate development.” Philos Trans R Soc Lond B Biol Sci 354(1382):497-506 Details


Collin C, Eglen S (1998), “An introduction to natural computation.” Trends Cogn Sci 2(6):235-6 Details


Tate AR, Watson D, Eglen S, Arvanitis TN, Thomas EL, Bell JD (1996), “Automated feature extraction for the classification of human in vivo 13C NMR spectra using statistical pattern recognition and wavelets.” Magn Reson Med 35(6):834-40 Details