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Ulrich Egert


    egert.jpgProf. Dr. Ulrich Egert
    Director, Bernstein Center Freiburg

    Bernstein Center Freiburg &
    Biomicrotechnology, Dept. of Microsystems Engineering
    Faculty of Engineering
    Georges-Köhler-Allee 102
    79110 Freiburg i.Br.
    Tel.: +49 (0)761 203 7524
    Fax: +49 (0)761 203 97759


Research Topics

  • Mechanisms and functions underlying the spatial and temporal dynamics of activity in natural and artificial biological neuronal networks under physiological and pathophysiological conditions.
  • The influence of mesoscale network structure on dynamics and robustness of neuronal network activity
  • Mechanisms of epilepsy
  • Control of network dynamics and interaction of stimulation with ongoing activity
  • Neurotechnological hybrid systems
  • Recording and analysis of spatial and temporal structure of electrical activity in neuronal networks in slices and cell cultures


We are interested in processing and activity dynamics in generic neuronal networks, the role of a network's mesoscale structure on its properties and new techniques for neuronal network electrophysiology. This we investigate by recording and analyzing the spatial and temporal structure of electrical activity in neuronal networks in slices, cell cultures of cortical neurons and in mice, based on spontaneous and electrically, optogenetically or pharmacologically stimulated activity as well as pharmacological modulation of network structure. We use intracellular whole-cell patch clamp recordings to identify single neuron properties and pairwise connectivity, in conjunction with network activity recorded simultaneously with microelectrode arrays (MEA) and calcium imaging. The main perspective here is the embedding of individual neurons into neuronal network dynamics and the heterogeneity of this across neurons.

As a pathological aspect of changes to the structure of neuronal networks, we investigate mechanisms underlying epilepsy. Specifically, we are interested in how the restructuring of the hippocampal network is reflected in interictal activity seemingly without salient signs of epileptiform activity and how to reduce the propensity to develop seizures by neurotechnological means.

Much of our work involves developing new tools to analyze and interpret our data, e.g. to relate whole cell patch clamp data to network dynamics, analyse spatial activity patterns as a function of network architecture, new measures for time resolved severity analysis of epileptic episodes or current susceptibility for seizures,

In terms of technical aspects we collaborate with several engineering groups to develop new devices for high-density extracellular recording in vitro and in vivo, autonomous control of closed-loop stimulation, also based on machine-learning approaches.

In previous projects we investigated the differentiation and structure of electrical activity in cardiac networks, developed applications for biological neuronal networks in drug screening, and addressed the use of biosensors to identify molecular markers associated with changing states of neuronal activity.



  • Single- and multiple-neuron recordings in slices, neuronal networks in cell cultures and in vivo
  • Design and application of advanced data analysis techniques for electrophysiological data
  • Cell culture techniques
  • Neurotechnology
  • Optogenetic analysis
  • Calcium imaging
  • Microelectrode array recoding in vivo and in vitro



Academic Background

  • 2005: Habilitation at the Faculty of Biology, Univ. Freiburg
  • 1995: Dr. rer. nat. (PhD) in Biology, Thesis: Development of thin-film microelectrode arrays and their application in neurophysiology.
  • 1988 - 1995: PhD Studies, Eberhard-Karls University, Tübingen and Natural and Medical Sciences Institute, Reutlingen
  • 1987: Diploma in Biology; Thesis on the effects of anesthetics on cortical visual plasticity and memory consolidation in kittens.
  • 1983 - 1987: Graduate studies in biology, Eberhard-Karls University, Tübingen, Germany
  • 1982 - 1983: Graduate studies in zoology, Duke University, Durham, NC, (USA)
  • 1980 - 1982: Eberhard-Karls University Tübingen, Germany, Undergraduate studies in biology


Research Positions

  • 2008 - present: Professor for Biomicrotechnology, Dept. of Microsystems Engineering, Faculty of Applied Sciences, Univ. Freiburg
  • 2001 - 2007: Assistant Professor, Dept. Neurobiology and Biophysics, Faculty of Biology, Univ. Freiburg
  • 1996 - 2007: Head of the Applied Neuroscience Laboratory, Dept. Neurobiology and Biophysics, Faculty of Biology, Univ. Freiburg
  • 1988 - 1996: PhD-Student and Research Associate Position, Natural and Medical Sciences Institute, Reutlingen




  • Wülfing JM, Kumar SS, Boedecker J, Riedmiller M, Egert U (2019) Adaptive long-term control of biological neural networks with deep reinforcement learning. Neurocomputing 342:66–74, DOI:10.1016/j.neucom.2018.10.084.
  • Okujeni S, Egert U (2019) Self-organization of modular network architecture by activity-dependent neuronal migration and outgrowth. Elife 8:e47966, DOI:10.7554/eLife.47996.
  • Heining K, Kilias A, Janz P, Häussler U, Kumar A, Haas CA, Egert U (2019) Bursts with high and low load of epileptiform spikes show context-dependent correlations in epileptic mice. eNeuro:10.1523/ENEURO.0299-18.2019, DOI:10.1523/ENEURO.0299-18.2019.
  • Okujeni S, Egert U (2019) Inhomogeneities in network structure and excitability govern initiation and propagation of spontaneous burst activity. Front Neurosci 13:543, DOI:10.3389/fnins.2019.00543.
  • Janz P, Hauser P, Heining K, Nestel S, Kirsch M, Egert U, Haas CA (2018) Position- and time-dependent arc expression links neuronal activity to synaptic plasticity during epileptogenesis. Front Cell Neurosci 12:244, DOI:10.3389/fncel.2018.00244.
  • Kilias A, Canales A, Froriep UP, Park S, Egert U, Anikeeva P (2018) Optogenetic entrainment of neural oscillations with hybrid fiber probes. J Neural Eng 15:056006, DOI:10.1088/1741-2552/aacdb9.
  • Wülfing J, Kumar SS, Boedecker J, Riedmiller M, Egert U (2018) Controlling biological neural networks with deep reinforcement learning. In: Proceedings of ESANN 2018, pp ES2018-128. Bruges, Belgium.
  • Heizmann S, Kilias A, Ruther P, Egert U, Asplund M (2018) Active control of dye release for neuronal tracing using pedot-pss coated electrodes. IEEE Trans Neural Syst Rehabil Eng 26:299–306, DOI:10.1109/TNSRE.2016.2606559.
  • Kilias A, Häussler U, Heining K, Froriep UP, Haas CA, Egert U (2018) Theta frequency decreases throughout the hippocampal formation in a focal epilepsy model. Hippocampus 28:375–391, DOI:10.1002/hipo.22838.
  • Janz P, Schwaderlapp N, Heining K, Häussler U, Korvink JG, von Elverfeldt D, Hennig J, Egert U, LeVan P, Haas CA (2017) Early tissue damage and microstructural reorganization predict disease severity in experimental epilepsy. Elife 6:e25742, DOI:10.7554/eLife.25742.
  • Okujeni S, Kandler S, Egert U (2017) Mesoscale architecture shapes initiation and richness of spontaneous network activity. J Neurosci 37:3972–3987. doi: 10.1523/JNEUROSCI.2552-16.2017
  • Janz P, Savanthrapadian S, Häussler U, Kilias A, Nestel S, Kretz O, Kirsch M,  Bartos M, Egert U, Haas CA. (2017) Synaptic remodeling of entorhinal input contributes to an aberrant hippocampal network in temporal lobe epilepsy. Cereb Cortex. 27:2348-2364. doi: 10.1093/cercor/bhw093
  • Orcinha C, Münzner G, Gerlach J, Kilias A, Follo M, Egert U, Haas CA (2016) Seizure-Induced Motility of Differentiated Dentate Granule Cells Is Prevented by the Central Reelin Fragment. Front Cell Neurosci. 2016 Jul 28;10:183. doi: 10.3389/fncel.2016.00183.
  • Häussler U, Rinas K, Kilias A, Egert U, Haas CA (2016) Mossy fiber sprouting and pyramidal cell dispersion in the hippocampal CA2 region in a mouse model of temporal lobe epilepsy.
    Hippocampus. 2016 May;26(5):577-88. doi: 10.1002/hipo.22543
  • Kumar SS, Wülfing J, Okujeni S, Boedecker J, Riedmiller M, Egert U. (2016) Autonomous Optimization of Targeted Stimulation of Neuronal Networks. PLoS Comput Biol. 12(8):e1005054. doi: 10.1371/journal.pcbi.1005054.
  • Heizmann S, Kilias A, Okujeni S, Boehler C, Ruther P, Egert U, Asplund M (2015) Accurate neuronal tracing of microelectrodes based on PEDOT-dye coatings. In: 7th International IEEE/EMBS Conference on Neural Engineering (NER), pp 22–24. IEEE. doi: 10.1109/NER.2015.7146640
  • Weihberger O, Okujeni S, Mikkonen JE, Egert U (2013) Quantitative examination of stimulus-response relations in cortical networks in vitro. J Neurophysiol 109:1764-1774
  • Froriep UP, Kumar A, Cosandier-Rimele D, Haussler U, Kilias A, Haas CA, Egert U (2012) Altered theta coupling between medial entorhinal cortex and dentate gyrus in temporal lobe epilepsy. Epilepsia 53:1937-1947
  • Tetzlaff C, Okujeni S, Egert U, Wörgötter F, Butz M (2010) Self-organized criticality in developing neuronal networks. PLoS Comput Biol 6(12): e1001013. doi:10.1371/journal.pcbi.1001013
  • Jarvis S, Rotter S, Egert U (2010) Aiming for stable instability: introducing hierarchy to reservoir networks. Frontiers in Neuroinformatics 4:11. doi: 10.3389/fninf.2010.00011
  • Frey, U., Egert, U., Heer, F., Hafizovic, S. & Hierlemann, A. (2009) Microelectronic system for high-resolution mapping of extracellular electric fields applied to brain slices. Biosens. Bioelectron., 24, 2191-2198
  • Frey U, Egert U, Jackel D, Sedivy J, Ballini M, Livi P, Faraci F, Heer F, Hafizovic S, Roscic B, and Hierlemann A (2009) Depth recording capabilities of planar high-density microelectrode arrays. Proc.of the 4th International IEEE EMBS Conference on Neural Engineering, 207-210
  • Gürel T, Rotter S, Egert U (2009) Functional identification of biological neural networks using reservoir adaptation for point processes. J.Comp.Neurosci. DOI 10.1007/s10827-009-0176-0
  • Meier R, Egert U, Aertsen A, Nawrot MP (2008) FIND — A unified framework for neural data analysis. Neural Networks 21:1085-1093
  • Wörz A, Berchtold M, Kandler S, Prucker O, Egert U, Aertsen A, and Rühe J (2007) Tailormade surfaces for a guided adhesion and outgrowth of cells. Proc. MST Conference 2007
  • Gürel T, Egert U, Kandler S, De Raedt L, Rotter S (2007) Predicting Spike Activity in Neuronal Cultures. IEEE International Joint Conference on Neural Networks: 2942-2947
  • Meier R, Häussler U, Aertsen A, Deransart C, Depaulis A, Egert U (2007): Short term changes in bilateral hippocampal coherence precede epileptiform events. Neuroimage 38:138-149
  • Frey U, Sanchez-Bustamante CD, Ugniwenko T, Heer F, Sedivy J, Hafizovic S, Roscic B, Fussenegger M, Blau A, Egert U, Hierlemann A (2007) Cell recordings with a CMOS high-density microelectrode array, Conf Proc IEEE Eng Med Biol Soc. 2007;2007:167-170
  • Egert U, Okujeni S, Nisch W, Boven KH, Rudorf R, Gottschlich N and Stett A. Optimized Oxygen Availability and Signal-to-Noise Ratio in Brain Slice Recordings with Perforated Microelectrode Arrays. 5th International Meeting on Substrate-Integrated Micro Electrode Arrays Reutlingen 2006
  • Kandler S, Reinartz S, and Egert U. Towards a functional classification of neuroleptics: identifying drug classes from population response profiles. 5^th International Meeting on Substrate-Integrated Micro Electrode Arrays Reutlingen 2006
  • Egert U, Banach K, Meyer T (2006) Analysis of cardiac myocyte activity dynamics with microelectrode arrays. In: Taketani M and Baudry M (eds) Advances in network electrophysiology using multi electrode arrays, Springer Vlg., Dordrecht, NL
  • Egert U, (2006) Networks on Chips: Spatial and temporal activity dynamics of functional networks in brain slices and cardiac tissue. In: Urban G, (ed) BioMEMS, Springer Vlg., Dordrecht, NL
  • Stett A, Rudorf R, Egert U, Boven K-H, Gottschlich N, and Nisch W (2005) Perforated Polyimide Microelectrode Arrays for single-cell and tissue recording. Mikrosystemtechnik Kongress 2005, 427-430
  • Egert U, Okujeni S, Nisch W, Boven K-H, Rudolf R, Gottschlich N, and Stett A. (2005) Perforated microelectrode arrays optimize oxygen availability and signal-to-noise ratio in brain slice recordings. Mikrosystemtechnik Kongress 2005, 431-434
  • Egert U, Meyer T K (2005) Heart on a chip. In: Dhein S, Mohr F-W, Delmar M (eds) Practical Methods in Cardiovascular Research. Springer Vlg., Stuttgart, pp 431-453
  • Hescheler J, Halbach M, Egert U, Lu ZJ, Bohlen H, Fleischmann BK, Reppel M (2004) Determination of electrical properties of ES cell-derived cardiomyocytes using MEAs. Electrocardiol 37, Supplement 1:110-116
  • Egert U, Buchner M, Okujeni S, and Nisch W (2004) Oxygen availability in acute brain slices on solid and perforated MEAs. SIMEA 2004, Reutlingen, Germany
  • Banach K, Halbach M, Hescheler J, Egert U (2003) Development of electrical activity in cardiac myocyte aggregates derived from mouse embryonic stem cells. Am J Physiol 284:H2114-H2123
  • Halbach M, Egert U, Hescheler J, Banach K (2003) Estimation of action potential changes from field potential recordings in multicellular mouse cardiac myocyte cultures. Cell Physiol Biochem 13:271-284
  • Stett A, Egert U, Guenther E, Hofmann F, Meyer Th, Nisch W, Haemmerle H (2003): Biological applications of micro electrode arrays in drug discovery and basic research. Anal Bioanal Chem 377:486-495
  • Egert U, Knott Th, Schwarz C, Nawrot M, Brandt A, Rotter S, Diesmann M (2002) MEA-tools: an open source toolbox for the analysis of multielectrode-data with MATLAB. J Neurosci Meth. 177, 33-42
  • Egert U, Heck D, Aertsen, A (2002) 2-dimensional monitoring of spiking networks in acute brain slices. Exp Brain Res, 142:268-274
  • Egert U, Haemmerle H (2002) Application of the microelectrode-array (MEA) technology in pharmaceutical drug research. In: Baselt JP, Gerlach G (eds) Sensoren im Fokus neuer Anwendungen. w.e.b. Universitätsverlag, Dresden, pp 51-54
  • Banach K, Egert U, Hescheler J (2000) Excitation spread between heart cells derived form embryonic stem (ES) cells. Pflügers Archiv 439, Suppl.:13-19
  • Banach, K., Egert, U., Juchelka, F., Bahr, M., and Hescheler, J.(2000) Pacemaker activity and excitation spread in cardiac myocytes differentiated from embryonic stem (ES) cells: wildtype versus Cx43 (-/-) cells. International Meeting on Subtrate-Integrated Microelectrode Arrays: Hard-, Soft-, and Wetware 54
  • Drobinskaia, I., Egert, U., Juchelka, F., and Hescheler, J.(2000) Effects of cardioactive drugs on action potential generation and propagation in embryonic stem cell derived aggregates. International Meeting on Subtrate-Integrated Microelectrode Arrays: Hard-, Soft-, and Wetware 45
  • Egert U, Schrenk K, Kapfhammer J, Metzger F (2000) Electrophysiological characterization of long and short-term drug effects in acute slices and organotypic cultures of the cerebellum. Naunyn-Schmiedebergs's Archives of Pharmacology 361:359
  • Egert U, Heck D, Aertsen A (1999) Spatio–temporal aspects of neuronal spike activity recorded with 2–D microelectrode arrays in acute brain slices. Soc Neurosci Abstr 1:368.3
  • Egert U, Aertsen A (1999) Nutzung der Mikroelektroden-Array-Technik (MEA) in der pharmazeutischen Biotechnologie - Teilprojekt Netzwerkanalyse. BrainWorks 1999-01:1-41 (in German with English summary)
  • Brandt A, Heck D, Aertsen A, Egert U (1999) Spatio-temporal structure of cerebellar responses to 'tidal-wave' stimuli 2. Stuttgart, Thieme. Proceedings of the 27th Göttingen Neurobiology Conference. 99. (abstract - PDF 27 kB , poster - zipped PDF 15 MB)
  • Egert U, Heck D, Aertsen A (1999) Spike activity in MEA recordings of acute slices 2. Stuttgart, Thieme. Proceedings of the 27th Göttingen Neurobiology Conference. 99. (abstract - PDF 80 kB, poster - zipped PDF 3.3 MB)
  • Hofmann F, Fejtl M, Egert U, Hämmerle H (1999) Analysis of multisite activity in organotypic hippocampal slices evoked by electrical stimulation using a microelectrode-array 2. Stuttgart, Thieme. Proceedings of the 27th Göttingen Neurobiology Conference. 99. (abstract (PDF, 8kB)
  • Knott Th, Fejtl M, Egert U, Schlosshauer B, Hämmerle H, Aertsen A (1999) Propagation of epileptic activity in organotypic hippocampal slices is accompanied by wave-form sharpening of the population spike 2. Stuttgart, Thieme. Proceedings of the 27th Göttingen Neurobiology Conference. 99. (abstract, zipped PDF, 9 kB)
  • Egert U, Brandt A, Aertsen A (1998) Analysis and visualization of multi-electrode recordings in-vitro with MEA-technology , 15. Reutlingen. International meeting on substrate-integrated microelectrode arrays - Technology and applications.
  • Egert U, Fejtl M, Knott Th, Schlosshauer B, Weiss S, Aertsen A, Hämmerle H (1998) Observing the activity of neurons in their network environment – Multielectrode recordings in excitable tissues Symposium on 'In vitro models for neuroprotective drug discovery'. 98.
  • Egert U, Heck D, Aertsen A (1998) Multielectrode recordings in acute slices - spike activity in the cerebellum in vitro , 494. Stuttgart, Thieme. Proceedings of the 26th Göttingen Neurobiology
  • Egert U, Schlosshauer B, Fennrich S, Nisch W, Fejtl M, Knott Th, Müller T, Hämmerle H (1998) A novel organotypic long-term culture of the rat hippocampus on substrate-integrated multielectrode arrays. Brain Res Prot 2:229-242 (PDF-file 1.5 MB)
  • Fejtl M, Knott Th, Leibrock C, Schlosshauer B, Nisch W, Egert U, Müller T, Hämmerle H (1998) Multi-site recording as a new tool to study epileptogenesis in organotypic hippocampal slices. Europ J Neurosci 10:44
  • Knott Th, Fejtl M, Egert U, Müller T, Schlosshauer B, Hämmerle H (1998) Spatio-temporal dynamics of bicuculline induced epileptiform activity in organotypic hippocampal slices 2, 509. Stuttgart, Thieme. Proceedings of the 26th Göttingen Neurobiology Conference.
  • Manuccia TJ, Dobbs LM (1998) The optically switched microelectrode array (OSMA) . Reutlingen, NMI Reutlingen. Substrate-integrated microelectrode arrays: technology and applications. 6-23-1998.
  • Egert U, Weiss S, Nisch W, Hämmerle H (1997) Temporal and spatial structure of spike activity and the ERG in a chicken retina preparation 1. Stuttgart, Thieme. Proceedings of the 25th Göttingen Neurobiology Conference.
  • Fejtl M, Egert U, Fennrich S, Nisch W, Hämmerle H (1997) Local stimulation and simultaneous recording of field and action potentials at multiple sites in organotypic hippocampal slices 1, 636-636. Stuttgart, Thieme. Proceedings of the 25th Göttingen Neurobiology Conference.
  • Nisch W, Stelzle M, Egert U, Stett A (3-24-1997) Mikroelementanordnung, Verfahren zum Kontaktieren von in einer flüssigen Umgebung befindlichen Zellen und Verfahren zum Herstellen einer Mikroelementanordnung DE 196 47 525.2 / DE 197 12 309.0. Germany. Patent Application
  • Schlosshauer B, Egert U, Hämmerle H, Nisch W, Fennrich S (1997) Interphase-Kultur auf Multifunktionsarray (MFA) (DE 195 28 662 A1). Germany. 8-4-1995. Patent Application
  • Egert U, Nisch W, Hämmerle H (1996) Simultaneous recording of the electroretinogram and spike activity with a microelectrode array , 54-54. Bridging Disciplines for Biomedicine,,Proceedings of the 18th Annual Conference of the IEEE Engineering in Medicine and Biology Society.
  • Janders M, Egert U, Stelzle M, Nisch W (1996) Novel thin film titanium nitride micro-electrodes with excellent charge transfer capability for cell stimulation and sensing applications. 48-48. Bridging Disciplines for Biomedicine, Proceedings of the 18th Annual Conference of the IEEE Engineering in Medicine and Biology Society. Conference Proceeding
  • Egert U, Knott Th, Mohr A, Nisch W, Hämmerle W (1995) An in vitro model system for studies of horizontal interaction in excised retina segments with a multielectrode-array , 449. Stuttgart, Thieme. Proceedings of the 23rd Göttingen Neurobiology Conference. Conference Proceeding
  • Egert U (1995) Entwicklung und Erprobung eines Multielektroden-Ableitsystems auf der Basis eines photolithographisch hergestellten Mikroelektroden-Arrays . Universität Tübingen. Thesis/Dissertation
  • Egert U, Knott Th, Hämmerle H (1995) Multielectrode studies of neurotransmitter function in chicken retina whole-mounts , 16.20. Ann.Meeting of the European Neuroscience Assoc.
  • Knott Th, Egert U, Hämmerle H (1995) Neurotransmitter induced retinal spreading depressions - concentration ranges and functional relevance. 23rd Göttingen Neurobiology Conference , 450. Stuttgart, Thieme. Proceedings of the 23rd Göttingen Neurobiology Conference.
  • Hämmerle H, Egert U, Mohr A, Nisch W (1994) Extracellular recording in neuronal networks with substrate integrated microelectrode arrays. Biosens Bioelectron 9:691-696
  • Nisch W, Böck J, Egert U, Hämmerle H, Mohr A (1994) A thin film microelectrode array for monitoring extracellular neuronal activity in vitro. Biosens Bioelectron 9:737-741
  • Hämmerle H, Egert U, Mohr A, Nisch W (1993) Natürliche neuronale Netze auf Mikro-Elektroden-Arrays; Biohybride Funktionselemente für medizinische und pharmazeutische Fragestellungen . Dresden Sensor Symposion.
  • Schlosshauer B, Stier H, Egert U (1993) Graded distribution of the neural 2A10 antigen in the developing chicken retina. Brain Res Dev Brain Res 76:13-22
  • Rauschecker JP, Tian B, Korte M, Egert U (1992) Crossmodal Changes in the Somatosensory Vibrissa/Barrel System of Visually Deprived Animals. Proc Natl Acad Sci U S A 89:5063-5067
  • Rauschecker JP, Egert U, Kossel A (1990) Effects of competitive and non-competitive NMDA-antagonists on developmental plasticity in kitten visual cortex. Int J Dev Neurosci 8:425-435
  • Kossel A, Egert U, Rauschecker JP (1987) Ketamine but not xylazine impairs consolidation of plastic changes in kitten visual cortex Society for Neuroscience Abstracts 13. Soc.Neurosci.Abstr.
  • Rauschecker JP, Egert U, Hahn S (1987) Compensatory whisker growth in visually deprived cats. Neuroscience 22S:665P-665P
  • Egert U, Kalko E, Stuermer CAO (1984) Retinotopic termination and abnormal pathways of regenerating optic axons in the goldfish tectum 10, 143-143. Soc.Neurosci.Abstr.


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