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Department of Applied Mathematics and Theoretical Physics


  • 1997-2000 Wellcome Trust Fellow in Mathematical Biology, Edinburgh
  • 2000-2001 Lecturer, School of Informatics, Edinburgh
  • 2001-2004 Wellcome Trust Travelling Fellowship, St Louis and Edinburgh
  • 2004-2006 Lecturer, DAMTP
  • 2006-2015 Senior Lecturer, DAMTP
  • 2015- Reader. DAMTP


Stephen Eglen is a computational neuroscientist: he uses computational methods to study the development of the nervous system, using mostly the retina and other parts of the visual pathway as a model system. He is particularly interested in questions of structural and functional development:

Structural development: how do retinal neurons acquire their positional information within a circuit?

Functional development: what are the mechanisms by which neurons make contact with each other, to perform functioning circuits?

Selected Publications

Please see my publications page


DeepClean - self-supervised artefact rejection for intensive care waveform data using generative deep learning.
T Edinburgh, P Smielewski, M Czosnyka, M Cabeleira, SJ Eglen, A Ercole
Burst Detection Methods
E Cotterill, SJ Eglen
Recent developments in scholarly publishing to improve research practices in the life sciences
SJ Eglen, R Mounce, L Gatto, AM Currie, Y Nobis
– Emerging topics in life sciences
meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays
S Gelfman, Q Wang, Y-F Lu, D Hall, CD Bostick, R Dhindsa, M Halvorsen, KM McSweeney, E Cotterill, T Edinburgh, MA Beaumont, WN Frankel, S Petrovski, AS Allen, MJ Boland, DB Goldstein, SJ Eglen
– PLoS Comput Biol
Scholarly Publishing, Freedom of Information and Academic Self-Determination: The UNAM-Elsevier Case
E Priego, E McKiernan, A Posada, R Hartley, N Rodríguez-ortega, D Fiormonte, A Gil, C Logan, JP Alperin, R Mounce, S Eglen, EM Trigueros, S Lawson, L Gatto, A Ramos, N Pérez
Toward standard practices for sharing computer code and programs in neuroscience.
SJ Eglen, B Marwick, YO Halchenko, M Hanke, S Sufi, P Gleeson, RA Silver, AP Davison, L Lanyon, M Abrams, T Wachtler, DJ Willshaw, C Pouzat, J-B Poline
– Nature neuroscience
A molecular mechanism for the topographic alignment of convergent neural maps.
E Savier, SJ Eglen, A Bathélémy, M Perraut, FW Pfrieger, G Lemke, M Reber
– eLife
A comparison of computational methods for detecting bursts in neuronal spike trains and their application to human stem cell-derived neuronal networks
E Cotterill, P Charlesworth, CW Thomas, O Paulsen, SJ Eglen
– Journal of Neurophysiology
Ten Simple Rules for Taking Advantage of git and GitHub
Y Perez-Riverol, L Gatto, R Wang, T Sachsenberg, J Uszkoreit, FDV Leprevost, C Fufezan, T Ternent, SJ Eglen, DS Katz, TJ Pollard, A Konovalov, RM Flight, K Blin, JA Vizcaíno
– PLoS Computational Biology
Ten Simple Rules for Taking Advantage of git and GitHub
Y Perez-Riverol, L Gatto, R Wang, T Sachsenberg, J Uszkoreit, FD Veiga Leprevost, C Fufezan, T Ternent, S Eglen, D Katz, T Pollard, A Konovalov, R Flight, K Blin, JA Vizcaino
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Research Group

Computational Biology