Stephen J Eglen Computational Neuroscience


After each reference, Paper links to papers; Info to further information about that paper, including code and data.


Akarca D, Dunn AWE, Hornauer PJ, Ronchi S, Fiscella M, Wang C, Terrigno M, Jagasia R, Vértes PE, Mierau SB, Paulsen O, Eglen SJ, Hierlemann A, Astle DE, Schröter M (2022) Homophilic wiring principles underpin neuronal network topology in vitro. bioRxiv:2022.03.09.483605 Paper Code.

Lyngholm D, Sterratt DC, Johannes Hjorth JJ, Willshaw DJ, Eglen SJ, Thompson ID (2019) Measuring and modelling the emergence of order in the mouse retinocollicular projection. bioRxiv:713628 Paper Info.

Lonborg AV, Eglen SJ (2017) A mechanistic model of the spatial interaction between blue cones and blue cone bipolar cells in macaque retina. bioRxiv:129643 Paper

Cutts CS, Eglen SJ (2016) A Bayesian framework for comparing the structure of spontaneous correlated activity recorded under different conditions. bioRxiv:037358 Paper

Reprints for papers already published are also available by searching on biorxiv.


N Gale, J Rodger, M Small, S Eglen (2022) Analysis of activity dependent development of topographic maps in neural field theory with short time scale dependent plasticity. Mathematical Neuroscience and Applications 2 Paper Code.

T Edinburgh, SJ Eglen, P Thoral, P Elbers, A Ercole (2022) Sepsis-3 criteria in AmsterdamUMCdb: open-source code implementation. Gigabyte 2022:1–7 Paper Code.


Edinburgh T, Eglen SJ, Ercole A (2021) Causality indices for bivariate time series data: A comparative review of performance. Chaos 31:083111 Paper Code.

Edinburgh T, Smielewski P, Czosnyka M, Cabeleira M, Eglen SJ, Ercole A (2021) DeepClean: Self-Supervised Artefact Rejection for Intensive Care Waveform Data Using Deep Generative Learning. In: Intracranial Pressure and Neuromonitoring XVII, pp 235–241 Acta Neurochirurgica Supplement. Paper.

Nüst D, Eglen SJ (2021) CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility. F1000Res 10:253 Paper.

Eglen SJ (2021) [Re] Spatial constraints underlying the retinal mosaics of two types of horizontal cells in cat and macaque. Rescience C 6:22 Paper.


Nüst D, Sochat V, Marwick B, Eglen SJ, Head T, Hirst T, Evans BD (2020) Ten simple rules for writing Dockerfiles for reproducible data science. PLoS Comput Biol 16:e1008316 Paper.

Keeley PW, Eglen SJ, Reese BE (2020) From Random to Regular: Variation in the Patterning of Retinal Mosaics. J Comp Neurol 528:2135-2160. Paper. Preprint.


Hyvärinen T, Hyysalo A, Kapucu FE, Aarnos L, Vinogradov A, Eglen SJ, Ylä-Outinen L, Narkilahti S (2019) Functional characterization of human pluripotent stem cell-derived cortical networks differentiated on laminin-521 substrate: comparison to rat cortical cultures. Sci Rep 9:17125 Paper.

Cotterill E, Eglen SJ (2019) Burst Detection Methods. In: In Vitro Neuronal Networks, From Culturing Methods to Neuro-Technological Applications, pp 185–206 Paper.


Eglen SJ, Mounce R, Gatto L, Currie AM, Nobis Y (2018) Recent developments in scholarly publishing to improve research practices in the life sciences. Emerg Top Life Sci 2:775–778 Paper

Gelfman S, Wang Q, Lu Y-F, Hall D, Bostick C, Dhindsa R, Halvorsen M, Melodi McSweeney K, Cotterill E, Edinburgh T, Petrovski S, Boland MJ, Allen AS, Goldstein DB, Eglen SJ (2018) meaRtools: an R package for the analysis of neuronal networks recorded on microelectrode arrays. PLOS Comput Biol 14:e1006506. Paper Code


Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Angus Silver R, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline J-B (2017) Toward standard practices for sharing computer code and programs in neuroscience. Nat Neurosci 20:770–773. Paper

Savier E, Eglen SJ, Bathélémy A, Perraut M, Pfrieger FW, Lemke G, Reber M (2017) A molecular mechanism for the topographic alignment of convergent neural maps. eLife Sciences 6:e20470. Paper Info


Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, da Veiga Leprevost F, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaino JA (2016) Ten simple rules for taking advantage of git and github. PLoS Comput Biol 12:e1004947. Paper Info

Cotterill E, Charlesworth P, Thomas CW, Paulsen O, Eglen SJ (2016) A comparison of computational methods for detecting bursts in neuronal spike trains and their application to human stem cell-derived neuronal networks. J Neurophysiol 116:306-321. Paper Info

Eglen SJ (2016) Bivariate spatial point patterns in the retina: a reproducible review. Journal de la Société Française de Statistique 157:33–48. Paper Info

Gjorgjieva J, Evers JF, Eglen SJ (2016) Homeostatic activity-dependent tuning of recurrent networks for robust propagation of activity. J Neurosci 36:3722–3734. Paper

Cotterill E, Hall D, Wallace K, Mundy WR, Eglen SJ, Shafer TJ (2016) Characterization of Early Cortical Neural Network Development in Multiwell Microelectrode Array Plates. J Biomol Screen 21:510-519 Paper Info

Leiwe MN, Hendry AC, Bard AD, Eglen SJ, Lowe AS, Thompson ID (2016) Geniculo-cortical projection diversity revealed within the mouse visual thalamus. PLoS One 11:e0144846. Paper

Charlesworth P, Morton A, Eglen SJ, Komiyama NH, Grant SGN (2016) Canalization of genetic and pharmacological perturbations in developing primary neuronal activity patterns. Neuropharmacology 100:47–55. Paper Info


Hjorth JJJ, Savier E, Sterratt DC, Reber M, Eglen SJ (2015b) Estimating the location and size of retinal injections from orthogonal images of an intact retina. BMC Neurosci 16:80. Paper Info

Budd JML, Cuntz H, Eglen SJ, Krieger P (2015) Editorial: Quantitative Analysis of Neuroanatomy. Front Neuroanat 9:143. Paper

Hjorth JJJ, Sterratt DC, Cutts CS, Willshaw DJ, Eglen SJ (2015a) Quantitative assessment of computational models for retinotopic map formation. Dev Neurobiol 75:641–666. Paper Info

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


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 34:14288–14303. Paper Info

Eglen S (2014a) Open access: sharing your data is easier than you think. Nature 510:340. Paper

Maccione A, Hennig MH, Gandolfo M, Muthmann O, van Coppenhagen J, Eglen SJ, Berdondini L, Sernagor E (2014) Following the ontogeny of retinal waves: pan-retinal recordings of population dynamics in the neonatal mouse. J Physiol 592:1545–1563. Paper Info

Eglen SJ (2014b) Retinotopic Development, Models of. In: Encyclopedia of Computational Neuroscience, pp 1–4. Springer New York. Paper DOI

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:e86139. Paper

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 3:3. Paper Info


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. Paper


Hore VRA, Troy JB, Eglen SJ (2012) Parasol cell mosaics are unlikely to drive the formation of structured orientation maps in primary visual cortex. Vis Neurosci 29:283–299. Paper

Keeley PW, Sliff BJ, Lee SCS, Fuerst PG, Burgess RW, Eglen SJ, Reese BE (2012) Neuronal clustering and fasciculation phenotype in Dscam- and Bax-deficient mouse retinas. J Comp Neurol 520:1349–1364. Paper

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


Gjorgjieva J, Eglen SJ (2011) Modeling developmental patterns of spontaneous activity. Curr Opin Neurobiol 21:679–684. Paper


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:e1000618. Paper

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. Paper

Eglen SJ (2009) A Quick Guide to Teaching R Programming to Computational Biology Students. PLoS Comput Biol 5:e1000482. Paper


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. Paper

Eglen SJ, Wong JCT (2008) Spatial constraints underlying the retinal mosaics of two types of horizontal cells in cat and macaque. Vis Neurosci 25:209–214. Paper


Eglen SJ (2006) Development of regular cellular spacing in the retina: theoretical models. Math Med Biol 23:79–99. Paper

Sernagor E, Eglen SJ, Harris WA, Wong ROL eds. (2006) Retinal Development. Cambridge University Press.


Eglen SJ, Diggle PJ, Troy JB (2005) Homotypic constraints dominate positioning of on- and off-center beta retinal ganglion cells. Vis Neurosci 22:859–871. Paper

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 169:355–366. Paper


Eglen SJ, Raven MA, Tamrazian E, Reese BE (2003b) Dopaminergic amacrine cells in the inner nuclear layer and ganglion cell layer comprise a single functional retinal mosaic. J Comp Neurol 466:343–355. Paper

Sernagor E, Young C, Eglen SJ (2003) Developmental Modulation of Retinal Wave Dynamics: Shedding Light on the GABA Saga. J Neurosci 23:7621–7629. Paper

Raven MA, Eglen SJ, Ohab JJ, Reese BE (2003) Determinants of the exclusion zone in dopaminergic amacrine cell mosaics. J Comp Neurol 461:123–136. Paper

Eglen SJ, Galli-Resta L, Reese BE (2003a) Theoretical models of retinal mosaic formation. In: Modeling neural development (van Ooyen A, ed), pp 133–150. MIT Press.

Demas J, Eglen SJ, Wong ROL (2003) Developmental loss of synchronous spontaneous activity in the mouse retina is independent of visual experience. J Neurosci 23:2851–2860. Paper


Lee CW, Eglen SJ, Wong ROL (2002) Segregation of on and off Retinogeniculate Connectivity Directed by Patterned Spontaneous Activity. J Neurophysiol 88:2311–2321. Paper Info


Eglen SJ, van Ooyen A, Willshaw DJ (2000) Lateral cell movement driven by dendritic interactions is sufficient to form retinal mosaics. Network 11:103–118. Paper Info

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:RC56. Paper Info


Eglen SJ (1999) The role of retinal waves and synaptic normalization in retinogeniculate development. Philos Trans R Soc Lond B Biol Sci 354:497–506. Paper


Eglen S, Bray A, Stone J (1997) Unsupervised discovery of invariances. Network: Computation in Neural Systems 8:441–452. Paper


Tate AR, Watson D, Eglen S, Arvanitis TN, Thomas EL, Bell JD (1996) Automated feature extraction for the classification of human in vivo13C NMR spectra using statistical pattern recognition and wavelets. Magn Reson Med 35:834–840. Paper