/Publications

Publications

Primary LanguageTeX

Scientific publications by Werner Van Geit

Papers

  • Alessio Paolo Buccino, Tanguy Damart, Julian Bartram, Darshan Mandge, Xiaohan Xue, Mickael Zbili, Tobias Gänswein, Aurélien Jaquier, Vishalini Emmenegger, Henry Markram, Andreas Hierlemann, and Werner Van Geit. A Multimodal Fitting Approach to Construct Single-Neuron Models With Patch Clamp and High-Density Microelectrode Arrays. Neural Computation, 36(7):1286–1331, 06 2024. URL: https://doi.org/10.1162/neco\_a\_01672, doi:10.1162/neco_a_01672.

  • Konstantin Weise, Torge Worbs, Benjamin Kalloch, Victor H. Souza, Aurélien Tristan Jaquier, Werner Van Geit, Axel Thielscher, and Thomas R. Knösche. Directional Sensitivity of Cortical Neurons Towards TMS Induced Electric Fields. Imaging Neuroscience, 11 2023. doi:10.1162/imag_a_00036.

  • Alexis Arnaudon, Maria Reva, Mickael Zbili, Henry Markram, Werner Van Geit, and Lida Kanari. Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. iScience, 2023. doi:10.1016/j.isci.2023.108222.

  • Maria Reva, Christian Rössert, Alexis Arnaudon, Tanguy Damart, Darshan Mandge, Anıl Tuncel, Srikanth Ramaswamy, Henry Markram, and Werner Van Geit. A universal workflow for creation, validation, and generalization of detailed neuronal models. Patterns, 4(11):100855, 2023. doi:10.1016/j.patter.2023.100855.

  • Yina Wei, Anirban Nandi, Xiaoxuan Jia, Joshua H. Siegle, Daniel Denman, Soo Yeun Lee, Anatoly Buchin, Werner Van Geit, Clayton P. Mosher, Shawn Olsen, and Costas A. Anastassiou. Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex. Nature Communications, 14(1):2344, Apr 2023. doi:10.1038/s41467-023-37844-8.

  • Elisabetta Iavarone, Jane Simko, Ying Shi, Marine Bertschy, María García-Amado, Polina Litvak, Anna-Kristin Kaufmann, Christian O’Reilly, Oren Amsalem, Marwan Abdellah, Grigori Chevtchenko, Benoît Coste, Jean-Denis Courcol, András Ecker, Cyrille Favreau, Adrien Christian Fleury, Werner Van Geit, Michael Gevaert, Nadir Román Guerrero, Joni Herttuainen, Genrich Ivaska, Samuel Kerrien, James G. King, Pramod Kumbhar, Patrycja Lurie, Ioannis Magkanaris, Vignayanandam Ravindernath Muddapu, Jayakrishnan Nair, Fernando L. Pereira, Rodrigo Perin, Fabien Petitjean, Rajnish Ranjan, Michael Reimann, Liviu Soltuzu, Mohameth François Sy, M. Anıl Tuncel, Alexander Ulbrich, Matthias Wolf, Francisco Clascá, Henry Markram, and Sean L. Hill. Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep. Cell Reports, 42(3):112200, 2023. doi:10.1016/j.celrep.2023.112200.

  • Giuseppe Chindemi, Marwan Abdellah, Oren Amsalem, Ruth Benavides-Piccione, Vincent Delattre, Michael Doron, András Ecker, Aurélien T. Jaquier, James King, Pramod Kumbhar, Caitlin Monney, Rodrigo Perin, Christian Rössert, Anil M. Tuncel, Werner Van Geit, Javier DeFelipe, Michael Graupner, Idan Segev, Henry Markram, and Eilif B. Muller. A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex. Nature Communications, 13(1):3038, June 2022. doi:10.1038/s41467-022-30214-w.

  • Anirban Nandi, Thomas Chartrand, Werner Van Geit, Anatoly Buchin, Zizhen Yao, Soo Yeun Lee, Yina Wei, Brian Kalmbach, Brian Lee, Ed Lein, Jim Berg, Uygar Sümbül, Christof Koch, Bosiljka Tasic, and Costas A. Anastassiou. Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types. Cell Reports, 40(6):111176, 2022. doi:10.1016/j.celrep.2022.111176.

  • Lida Kanari, Hugo Dictus, Athanassia Chalimourda, Alexis Arnaudon, Werner Van Geit, Benoit Coste, Julian Shillcock, Kathryn Hess, and Henry Markram. Computational synthesis of cortical dendritic morphologies. Cell Reports, 39(1):110586, April 2022. doi:10.1016/j.celrep.2022.110586.

  • Gilad Shapira, Mira Marcus-Kalish, Oren Amsalem, Werner Van Geit, Idan Segev, and David M. Steinberg. Statistical Emulation of Neural Simulators: Application to Neocortical L2/3 Large Basket Cells. Frontiers in Big Data, 5:789962, March 2022. doi:10.3389/fdata.2022.789962.

  • Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Christian O'Reilly, Werner Van Geit, Christian Rössert, Henry Markram, and Sean L. Hill. Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons. PLOS Computational Biology, 15(5):e1006753, May 2019. doi:10.1371/journal.pcbi.1006753.

  • Sára Sáray, Christian A. Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen A. Lupascu, Luca L. Bologna, Werner Van Geit, Armando Romani, Andrew P. Davison, Eilif Muller, Tamás F. Freund, and Szabolcs Káli. HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data. PLOS Computational Biology, 17(1):e1008114, January 2021. doi:10.1371/journal.pcbi.1008114.

  • Kael Dai, Juan Hernando, Yazan N Billeh, Sergey L Gratiy, Judit Planas, Andrew P Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K Dichter, and others. The sonata data format for efficient description of large-scale network models. PLoS computational biology, 16(2):e1007696, 2020. doi:10.1371/journal.pcbi.1007696.

  • Padraig Gleeson, Matteo Cantarelli, Boris Marin, Adrian Quintana, Matt Earnshaw, Sadra Sadeh, Eugenio Piasini, Justas Birgiolas, Robert C Cannon, N Alex Cayco-Gajic, and others. Open source brain: a collaborative resource for visualizing, analyzing, simulating, and developing standardized models of neurons and circuits. Neuron, 103(3):395–411, 2019. doi:10.1016/j.neuron.2019.05.019.

  • Rosanna Migliore, Carmen A Lupascu, Luca L Bologna, Armando Romani, Jean-Denis Courcol, Stefano Antonel, Werner AH Van Geit, Alex M Thomson, Audrey Mercer, Sigrun Lange, and others. The physiological variability of channel density in hippocampal ca1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow. PLoS computational biology, 14(9):e1006423, 2018. doi:10.1371/journal.pcbi.1006423.

  • Stefano Masoli, Martina F. Rizza, Martina Sgritta, Werner Van Geit, Felix Schürmann, and Egidio D'Angelo. Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells. Frontiers in Cellular Neuroscience, March 2017. doi:10.3389/fncel.2017.00071.

  • Werner Van Geit, Michael Gevaert, Giuseppe Chindemi, Christian Rössert, Jean-Denis Courcol, Eilif Benjamin Muller, Felix Schürmann, Idan Segev, and Henry Markram. Bluepyopt: leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience. Frontiers in Neuroinformatics, 2016. URL: http://www.frontiersin.org/neuroinformatics/10.3389/fninf.2016.00017/abstract, doi:10.3389/fninf.2016.00017.

  • Oren Amsalem, Werner Van Geit, Eilif Muller, Henry Markram, and Idan Segev. From neuron biophysics to orientation selectivity in electrically coupled networks of neocortical l2/3 large basket cells. Cerebral Cortex, 26(8):3655–3668, 2016. doi:10.1093/cercor/bhw166.

  • Henry Markram, Eilif Muller, Srikanth Ramaswamy, Michael W Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean-Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul Druckmann, Raphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean-Pierre Ghobril, Albert Gidon, Joe W Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean-Vincent Le Bé, Bruno R C Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José-Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M Zaninetta, Javier DeFelipe, Sean L Hill, Idan Segev, and Felix Schürmann. Reconstruction and simulation of neocortical microcircuitry. Cell, 163(2):456–492, October 2015. doi:10.1016/j.cell.2015.09.029.

  • Srikanth Ramaswamy, Jean-Denis Courcol, Marwan Abdellah, Stanislaw R Adaszewski, Nicolas Antille, Selim Arsever, Guy Atenekeng, Ahmet Bilgili, Yury Brukau, Athanassia Chalimourda, and others. The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits, 9:44, 2015. doi:10.3389/fncir.2015.00044.

  • Werner Van Geit, Erik De Schutter, and Pablo Achard. Automated neuron model optimization techniques: a review. Biological cybernetics, 99(4-5):241–251, 2008. doi:10.1007/s00422-008-0257-6.

  • Werner Van Geit, Pablo Achard, and Erik De Schutter. Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models. Frontiers in neuroinformatics, 1:89, 2007. doi:10.3389/neuro.11.001.2007.

Preprints

  • James B Isbister, András Ecker, Christoph Pokorny, Sirio Bolaños-Puchet, Daniela Egas Santander, Alexis Arnaudon, Omar Awile, Natali Barros-Zulaica, Jorge Blanco Alonso, Elvis Boci, Giuseppe Chindemi, Jean-Denis Courcol, Tanguy Damart, Thomas Delemontex, Alexander Dietz, Gianluca Ficarelli, Mike Gevaert, Joni Herttuainen, Genrich Ivaska, Weina Ji, Daniel Keller, James King, Pramod Kumbhar, Samuel Lapere, Polina Litvak, Darshan Mandge, Eilif B. Muller, Fernando Pereira, Judit Planas, Rajnish Ranjan, Maria Reva, Armando Romani, Christian Rössert, Felix Schürmann, Vishal Sood, Aleksandra Teska, Anil Tuncel, Werner Van Geit, Matthias Wolf, Henry Markram, Srikanth Ramaswamy, and Michael W. Reimann. Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part II: Physiology and Experimentation. Preprint, Neuroscience, May 2023. doi:10.1101/2023.05.17.541168.

  • Armando Romani, Alberto Antonietti, Davide Bella, Julian Budd, Elisabetta Giacalone, Kerem Kurban, Sára Sáray, Marwan Abdellah, Alexis Arnaudon, Elvis Boci, Cristina Colangelo, Jean-Denis Courcol, Thomas Delemontex, András Ecker, Joanne Falck, Cyrille Favreau, Michael Gevaert, Juan B. Hernando, Joni Herttuainen, Genrich Ivaska, Lida Kanari, Anna-Kristin Kaufmann, James Gonzalo King, Pramod Kumbhar, Sigrun Lange, Huanxiang Lu, Carmen Alina Lupascu, Rosanna Migliore, Fabien Petitjean, Judit Planas, Pranav Rai, Srikanth Ramaswamy, Michael W. Reimann, Juan Luis Riquelme, Nadir Román Guerrero, Ying Shi, Vishal Sood, Mohameth François Sy, Werner Van Geit, Liesbeth Vanherpe, Tamás F. Freund, Audrey Mercer, Eilif Muller, Felix Schürmann, Alex M. Thomson, Michele Migliore, Szabolcs Káli, and Henry Markram. Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus. Preprint, Neuroscience, May 2023. doi:10.1101/2023.05.17.541167.

  • Michael W Reimann, Sirio Bolaños-Puchet, Jean-Denis Courcol, Daniela Egas Santander, Alexis Arnaudon, Benoît Coste, Thomas Delemontex, Adrien Devresse, Hugo Dictus, Alexander Dietz, and others. Modeling and simulation of rat non-barrel somatosensory cortex. part i: modeling anatomy. Preprint, Neuroscience, 2022. doi:10.1101/2022.08.11.503144.

Book chapters

  • Erik De Schutter and Werner Van Geit. Modeling complex neurons. In Computational modeling methods for neuroscientists, pages 259–84. MIT Press Cambridge, 2009. doi:10.7551/mitpress/7543.003.0013.

  • Pablo Achard, Werner Van Geit, Gwendal LeMasson, and Erik De Schutter. Parameter searching. In Computational modeling methods for neuroscientists, pages 31–60. MIT Press Cambridge, 2009. doi:https://doi.org/10.7551/mitpress/7543.003.0004.

Software

  • Werner Van Geit, Michael Gevaert, Tanguy Damart, Christian Rössert, Jean-Denis Courcol, Guiseppe Chindemi, Aurélien Jaquier, and Eilif Muller. BluePyOpt. doi:10.5281/zenodo.8135890.

  • Werner Van Geit, Anil Tuncel, Mike Gevaert, Benjamin Torben-Nielsen, and Eilif Muller. BlueCelluLab. doi:10.5281/zenodo.8113483.

  • Rajnish Ranjan, Werner Van Geit, Ruben Moor, Christian Rössert, Juan Luis Riquelme, Tanguy Damart, Aurélien Jaquier, and Anil Tuncel. eFEL. doi:10.5281/zenodo.593869.

  • Roessert Christian, Damart Tanguy, and Van Geit Werner. BluePyEfe. doi:10.5281/zenodo.3728191.

  • Werner Van Geit, Liesbeth Vanherpe, Christian Rössert, Michael Gevaert, Jean-Denis Courcol, James Gonzalo King, and Aurélien Jaquier. BluePyMM. doi:10.5281/zenodo.8146238.

  • Tanguy Pierre Louis Damart, Aurélien Jaquier, Alexis Arnaudon, Darshan Mandge, Werner Van Geit, and Ilkan Kilic. BluePyEModel. doi:10.5281/zenodo.8283490.

  • Aurélien Jaquier, Anil Tuncel, and Werner Van Geit. EModelRunner. doi:10.5281/zenodo.8116075.

  • Aurélien Jaquier, Anil Tuncel, Werner Van Geit, Leandro M Alonso, and Eve Marder. Currentscape. doi:10.5281/zenodo.8046373.

  • Werner Van Geit, Pablo Achard, and Erik De Schutter. Neurofitter. URL: https://neurofitter.sourceforge.net/.