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Publications that use or mention BluePyOpt

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Aurélien Jaquier edited this page May 25, 2023 · 6 revisions

Publications that use or mention BluePyOpt

Scientific papers that use BluePyOpt

  • 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.
  • 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.
  • Alexandre Guet-McCreight, Homeira Moradi Chameh, Sara Mahallati, Margaret Wishart, Shreejoy J Tripathy, Taufik A Valiante, and Etay Hay. Age-dependent increased sag amplitude in human pyramidal neurons dampens baseline cortical activity. Cerebral Cortex, 33(8):4360–4373, April 2023. doi:10.1093/cercor/bhac348.
  • Francesco Cavarretta and Dieter Jaeger. Modeling synaptic integration of bursty and beta oscillatory inputs in ventromedial motor thalamic neurons in normal and parkinsonian states. Preprint, Neuroscience, April 2023. doi:10.1101/2023.04.14.536959.
  • Alexis Arnaudon, Maria Reva, Mickael Zbili, Henry Markram, Werner Van Geit, and Lida Kanari. Controlling morpho-electrophysiological variability of neurons with detailed biophysical models. Preprint, Neuroscience, April 2023. doi:10.1101/2023.04.06.535923.
  • Stefano Masoli, Diana Sanchez-Ponce, Nora Vrieler, Karin Abu-Haya, Vitaly Lerner, Tal Shahar, Hermina Nedelescu, Martina Francesca Rizza, Ruth Benavides-Piccione, Javier DeFelipe, Yosef Yarom, Alberto Munoz, and Egidio D'Angelo. Human outperform mouse Purkinje cells in dendritic complexity and computational capacity. Preprint, Neuroscience, March 2023. doi:10.1101/2023.03.08.531672.
  • Alexandre Guet-McCreight, Homeira Moradi Chameh, Frank Mazza, Thomas D. Prevot, Taufik A. Valiante, Etienne Sibille, and Etay Hay. In-silico testing of new pharmacology for restoring inhibition and human cortical function in depression. Preprint, Neuroscience, February 2023. doi:10.1101/2023.02.22.529541.
  • Nadia Rosenberg, Maria Reva, Francesca Binda, Leonardo Restivo, Pauline Depierre, Julien Puyal, Marc Briquet, Yann Bernardinelli, Anne-Bérengère Rocher, Henry Markram, and Jean-Yves Chatton. Overexpression of ucp4 in astrocytic mitochondria prevents multilevel dysfunctions in a mouse model of alzheimer's disease. Glia, 71(4):957–973, 2023. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/glia.24317, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/glia.24317, doi:https://doi.org/10.1002/glia.24317.
  • 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. Preprint, Neuroscience, December 2022. doi:10.1101/2022.12.13.520234.
  • René Wilbers, Anna A. Galakhova, Tim S. Heistek, Verjinia D. Metodieva, Jim Hagemann, Djai B. Heyer, Eline J. Mertens, Suixin Deng, Sander Idema, Philip C. de Witt Hamer, David P. Noske, Paul van Schie, Ivar Kommers, Guoming Luan, Tianfu Li, Yousheng Shu, Christiaan P.J. de Kock, Huibert D. Mansvelder, and Natalia A. Goriounova. Structural and functional specializations of human fast spiking neurons support fast cortical signaling. Preprint, Neuroscience, November 2022. doi:10.1101/2022.11.29.518193.
  • Zhenyang Sun, David Crompton, Milad Lankarany, and Frances K Skinner. Reduced oriens-lacunosum/moleculare (OLM) cell model identifies biophysical current balances for \emph in Vivo theta frequency spiking resonance. Preprint, Neuroscience, October 2022. doi:10.1101/2022.10.20.513073.
  • Luca Leonardo Bologna, Roberto Smiriglia, Carmen Alina Lupascu, Shailesh Appukuttan, Andrew P. Davison, Genrich Ivaska, Jean-Denis Courcol, and Michele Migliore. The EBRAINS Hodgkin-Huxley Neuron Builder: An online resource for building data-driven neuron models. Frontiers in Neuroinformatics, 16:991609, September 2022. doi:10.3389/fninf.2022.991609.
  • 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 multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays. Preprint, Neuroscience, August 2022. doi:10.1101/2022.08.03.502468.
  • Sarah Hunt, Yoni Leibner, Eline J Mertens, Natalí Barros-Zulaica, Lida Kanari, Tim S Heistek, Mahesh M Karnani, Romy Aardse, René Wilbers, Djai B Heyer, Natalia A Goriounova, Matthijs B Verhoog, Guilherme Testa-Silva, Joshua Obermayer, Tamara Versluis, Ruth Benavides-Piccione, Philip de Witt-Hamer, Sander Idema, David P Noske, Johannes C Baayen, Ed S Lein, Javier DeFelipe, Henry Markram, Huibert D Mansvelder, Felix Schürmann, Idan Segev, and Christiaan P J de Kock. Strong and reliable synaptic communication between pyramidal neurons in adult human cerebral cortex. Cerebral Cortex, pages bhac246, July 2022. doi:10.1093/cercor/bhac246.
  • Alexander Ladd, Kyung Geun Kim, Jan Balewski, Kristofer Bouchard, and Roy Ben-Shalom. Scaling and Benchmarking an Evolutionary Algorithm for Constructing Biophysical Neuronal Models. Frontiers in Neuroinformatics, 16:882552, June 2022. doi:10.3389/fninf.2022.882552.
  • 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.
  • Daniele Linaro, Matthew J. Levy, and David L. Hunt. Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons. PLOS Computational Biology, 18(4):e1010071, April 2022. doi:10.1371/journal.pcbi.1010071.
  • 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 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 enhancement and sleep spindle properties in a biophysical model of thalamoreticular microcircuitry. Preprint, Neuroscience, March 2022. doi:10.1101/2022.02.28.482273.
  • Heng Kang Yao, Alexandre Guet-McCreight, Frank Mazza, Homeira Moradi Chameh, Thomas D. Prevot, John D. Griffiths, Shreejoy J. Tripathy, Taufik A. Valiante, Etienne Sibille, and Etay Hay. Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits. Cell Reports, 38(2):110232, January 2022. doi:10.1016/j.celrep.2021.110232.
  • András Ecker, Bence Bagi, Eszter Vértes, Orsolya Steinbach-Németh, Mária R Karlócai, Orsolya I Papp, István Miklós, Norbert Hájos, Tamás F Freund, Attila I Gulyás, and Szabolcs Káli. Hippocampal sharp wave-ripples and the associated sequence replay emerge from structured synaptic interactions in a network model of area CA3. eLife, 11:e71850, January 2022. doi:10.7554/eLife.71850.
  • Roy Ben-Shalom, Alexander Ladd, Nikhil S. Artherya, Christopher Cross, Kyung Geun Kim, Hersh Sanghevi, Alon Korngreen, Kristofer E. Bouchard, and Kevin J. Bender. NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs. Journal of Neuroscience Methods, 366:109400, January 2022. doi:10.1016/j.jneumeth.2021.109400.
  • Anirban Nandi, Tom 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, and Costas A Anastassiou. Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types. Cell Reports, 2022. doi:10.1016/j.celrep.2022.111176.
  • Felix Schürmann, Jean-Denis Courcol, and Srikanth Ramaswamy. Computational Concepts for Reconstructing and Simulating Brain Tissue. In Michele Giugliano, Mario Negrello, and Daniele Linaro, editors, Computational Modelling of the Brain, volume 1359, pages 237–259. Springer International Publishing, Cham, 2022. doi:10.1007/978-3-030-89439-9_10.
  • Armando Romani, Felix Schürmann, Henry Markram, and Michele Migliore. Reconstruction of the Hippocampus. In Michele Giugliano, Mario Negrello, and Daniele Linaro, editors, Computational Modelling of the Brain, volume 1359, pages 261–283. Springer International Publishing, Cham, 2022. doi:10.1007/978-3-030-89439-9_11.
  • Casey M Schneider-Mizell, Agnes L Bodor, Forrest Collman, Derrick Brittain, Adam Bleckert, Sven Dorkenwald, Nicholas L Turner, Thomas Macrina, Kisuk Lee, Ran Lu, Jingpeng Wu, Jun Zhuang, Anirban Nandi, Brian Hu, JoAnn Buchanan, Marc M Takeno, Russel Torres, Gayathri Mahalingam, Daniel J Bumbarger, Yang Li, Thomas Chartrand, Nico Kemnitz, William M Silversmith, Dodam Ih, Jonathan Zung, Aleksandar Zlateski, Ignacio Tartavull, Sergiy Popovych, William Wong, Manuel Castro, Chris S Jordan, Emmanouil Froudarakis, Lynne Becker, Shelby Suckow, Jacob Reimer, Andreas S Tolias, Costas A Anastassiou, H Sebastian Seung, R Clay Reid, and Nuno Maçarico da Costa. Structure and function of axo-axonic inhibition. eLife, 10:e73783, December 2021. doi:10.7554/eLife.73783.
  • Sushmita L. Allam, Timothy H. Rumbell, Tuan Hoang-Trong, Jaimit Parikh, and James R. Kozloski. Neuronal population models reveal specific linear conductance controllers sufficient to rescue preclinical disease phenotypes. iScience, 24(11):103279, November 2021. doi:10.1016/j.isci.2021.103279.
  • J. J. Johannes Hjorth, Jeanette Hellgren Kotaleski, and Alexander Kozlov. Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda. Neuroinformatics, 19(4):685–701, October 2021. doi:10.1007/s12021-021-09531-w.
  • Johanna Frost Nylén, Ilaria Carannante, Sten Grillner, and Jeanette Hellgren Kotaleski. Reciprocal interaction between striatal cholinergic and low-threshold spiking interneurons — A computational study. European Journal of Neuroscience, 53(7):2135–2148, April 2021. doi:10.1111/ejn.14854.
  • Martina Francesca Rizza, Francesca Locatelli, Stefano Masoli, Diana Sánchez-Ponce, Alberto Muñoz, Francesca Prestori, and Egidio D'Angelo. Stellate cell computational modeling predicts signal filtering in the molecular layer circuit of cerebellum. Scientific Reports, 11(1):3873, February 2021. doi:10.1038/s41598-021-83209-w.
  • Willem AM Wybo, Jakob Jordan, Benjamin Ellenberger, Ulisses Marti Mengual, Thomas Nevian, and Walter Senn. Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses. eLife, 10:e60936, January 2021. doi:10.7554/eLife.60936.
  • 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.
  • Stefano Masoli, Alessandra Ottaviani, Stefano Casali, and Egidio D'Angelo. Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity. PLOS Computational Biology, 16(12):e1007937, December 2020. doi:10.1371/journal.pcbi.1007937.
  • Ulisses Marti Mengual, Willem A.M. Wybo, Lotte J.E. Spierenburg, Mirko Santello, Walter Senn, and Thomas Nevian. Efficient Low-Pass Dendro-Somatic Coupling in the Apical Dendrite of Layer 5 Pyramidal Neurons in the Anterior Cingulate Cortex. The Journal of Neuroscience, 40(46):8799–8815, November 2020. doi:10.1523/JNEUROSCI.3028-19.2020.
  • András Ecker, Armando Romani, Sára Sáray, Szabolcs Káli, Michele Migliore, Joanne Falck, Sigrun Lange, Audrey Mercer, Alex M. Thomson, Eilif Muller, Michael W. Reimann, and Srikanth Ramaswamy. Data-driven integration of hippocampal \textsc CA1 synaptic physiology \emph in Silico. Hippocampus, 30(11):1129–1145, November 2020. doi:10.1002/hipo.23220.
  • Daniele Linaro, Federico Bizzarri, Angelo Brambilla, Alberto Granato, and Michele Giugliano. Modelling the Effects of Early Exposure to Alcohol on the Excitability of Cortical Neurons. In 2020 IEEE International Symposium on Circuits and Systems (ISCAS), 1–5. Seville, Spain, October 2020. IEEE. doi:10.1109/ISCAS45731.2020.9180633.
  • Vladislav Sekulić, Feng Yi, Tavita Garrett, Alexandre Guet-McCreight, J. Josh Lawrence, and Frances K. Skinner. Integration of Within-Cell Experimental Data With Multi-Compartmental Modeling Predicts H-Channel Densities and Distributions in Hippocampal OLM Cells. Frontiers in Cellular Neuroscience, 14:277, September 2020. doi:10.3389/fncel.2020.00277.
  • Pedro J Gonçalves, Jan-Matthis Lueckmann, Michael Deistler, Marcel Nonnenmacher, Kaan Öcal, Giacomo Bassetto, Chaitanya Chintaluri, William F Podlaski, Sara A Haddad, Tim P Vogels, David S Greenberg, and Jakob H Macke. Training deep neural density estimators to identify mechanistic models of neural dynamics. eLife, 9:e56261, September 2020. doi:10.7554/eLife.56261.
  • Mate Mohacsi, Mark Patrik Torok, Sara Saray, and Szabolcs Kali. A unified framework for the application and evaluation of different methods for neural parameter optimization. In 2020 International Joint Conference on Neural Networks (IJCNN), 1–7. Glasgow, United Kingdom, July 2020. IEEE. doi:10.1109/IJCNN48605.2020.9206692.
  • Tanguy Damart, Werner Van Geit, and Henry Markram. Data driven building of realistic neuron model using IBEA and CMA evolution strategies. In Proceedings of the 2020 Genetic and Evolutionary Computation Conference Companion, 35–36. Cancún Mexico, July 2020. ACM. doi:10.1145/3377929.3398161.
  • Stefano Masoli, Marialuisa Tognolina, Umberto Laforenza, Francesco Moccia, and Egidio D'Angelo. Parameter tuning differentiates granule cell subtypes enriching transmission properties at the cerebellum input stage. Communications Biology, 3(1):222, May 2020. doi:10.1038/s42003-020-0953-x.
  • Casey M. Schneider-Mizell, Agnes L. Bodor, Forrest Collman, Derrick Brittain, Adam A. Bleckert, Sven Dorkenwald, Nicholas L. Turner, Thomas Macrina, Kisuk Lee, Ran Lu, Jingpeng Wu, Jun Zhuang, Anirban Nandi, Brian Hu, JoAnn Buchanan, Marc M. Takeno, Russel Torres, Gayathri Mahalingam, Daniel J. Bumbarger, Yang Li, Tom Chartrand, Nico Kemnitz, William M. Silversmith, Dodam Ih, Jonathan Zung, Aleksandar Zlateski, Ignacio Tartavull, Sergiy Popovych, William Wong, Manuel Castro, Chris S. Jordan, Emmanouil Froudarakis, Lynne Becker, Shelby Suckow, Jacob Reimer, Andreas S. Tolias, Costas Anastassiou, H. Sebastian Seung, R. Clay Reid, and Nuno Maçarico da Costa. Chandelier cell anatomy and function reveal a variably distributed but common signal. Preprint, Neuroscience, April 2020. doi:10.1101/2020.03.31.018952.
  • Anatoly Buchin, Rebecca de Frates, Anirban Nandi, Rusty Mann, Peter Chong, Lindsay Ng, Jeremy Miller, Rebecca Hodge, Brian Kalmbach, Soumita Bose, Ueli Rutishauser, Stephen McConoughey, Ed Lein, Jim Berg, Staci Sorensen, Ryder Gwinn, Christof Koch, Jonathan Ting, and Costas A. Anastassiou. Multi-modal characterization and simulation of human epileptic circuitry. Preprint, Neuroscience, April 2020. doi:10.1101/2020.04.24.060178.
  • Clayton P. Mosher, Yina Wei, Jan Kamiński, Anirban Nandi, Adam N. Mamelak, Costas A. Anastassiou, and Ueli Rutishauser. Cellular Classes in the Human Brain Revealed In Vivo by Heartbeat-Related Modulation of the Extracellular Action Potential Waveform. Cell Reports, 30(10):3536–3551.e6, March 2020. doi:10.1016/j.celrep.2020.02.027.
  • Mario Michiels. Electrophysiology prediction of single neurons based on their morphology. Preprint, Neuroscience, February 2020. doi:10.1101/2020.02.04.933697.
  • Alexander Bryson, Robert John Hatch, Bas-Jan Zandt, Christian Rossert, Samuel F. Berkovic, Christopher A. Reid, David B. Grayden, Sean L. Hill, and Steven Petrou. GABA-mediated tonic inhibition differentially modulates gain in functional subtypes of cortical interneurons. Proceedings of the National Academy of Sciences, 117(6):3192–3202, February 2020. doi:10.1073/pnas.1906369117.
  • Timothy Rumbell and James Kozloski. Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons. PLOS Computational Biology, 15(9):e1007375, September 2019. doi:10.1371/journal.pcbi.1007375.
  • Michael Doron, Idan Segev, and Dafna Shahaf. Discovering Unexpected Local Nonlinear Interactions in Scientific Black-box Models. In Proceedings of the 25th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, 425–435. Anchorage AK USA, July 2019. ACM. doi:10.1145/3292500.3330886.
  • Richard C. Gerkin, Justas Birgiolas, Russell J. Jarvis, Cyrus Omar, and Sharon M. Crook. NeuronUnit: A package for data-driven validation of neuron models using SciUnit. Preprint, Neuroscience, June 2019. doi:10.1101/665331.
  • J. Christopher Octeau, Mohitkumar R. Gangwani, Sushmita L. Allam, Duy Tran, Shuhan Huang, Tuan M. Hoang-Trong, Peyman Golshani, Timothy H. Rumbell, James R. Kozloski, and Baljit S. Khakh. Transient, Consequential Increases in Extracellular Potassium Ions Accompany Channelrhodopsin2 Excitation. Cell Reports, 27(8):2249–2261.e7, May 2019. doi:10.1016/j.celrep.2019.04.078.
  • 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.
  • Géza Berecki, Alexander Bryson, Jan Terhag, Snezana Maljevic, Elena V. Gazina, Sean L. Hill, and Steven Petrou. \emph SCN1A gain of function in early infantile encephalopathy. Annals of Neurology, 85(4):514–525, April 2019. doi:10.1002/ana.25438.
  • Brian E. Kalmbach, Anatoly Buchin, Brian Long, Jennie Close, Anirban Nandi, Jeremy A. Miller, Trygve E. Bakken, Rebecca D. Hodge, Peter Chong, Rebecca de Frates, Kael Dai, Zoe Maltzer, Philip R. Nicovich, C. Dirk Keene, Daniel L. Silbergeld, Ryder P. Gwinn, Charles Cobbs, Andrew L. Ko, Jeffrey G. Ojemann, Christof Koch, Costas A. Anastassiou, Ed S. Lein, and Jonathan T. Ting. H-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex. Neuron, 100(5):1194–1208.e5, December 2018. doi:10.1016/j.neuron.2018.10.012.
  • Rosanna Migliore, Carmen A. Lupascu, Luca L. Bologna, Armando Romani, Jean-Denis Courcol, Stefano Antonel, Werner A. H. Van Geit, Alex M. Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Christian A. Rössert, Ying Shi, Olivier Hagens, Maurizio Pezzoli, Tamas F. Freund, Szabolcs Kali, Eilif B. Muller, Felix Schürmann, Henry Markram, and Michele Migliore. 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, September 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.
  • Jan-Matthis Lueckmann, Pedro J. Gonçalves, Giacomo Bassetto, Kaan Öcal, Marcel Nonnenmacher, and Jakob H. Macke. Flexible statistical inference for mechanistic models of neural dynamics. In Proceedings of the 31st International Conference on Neural Information Processing Systems, NIPS'17, 1289–1299. Red Hook, NY, USA, 2017. Curran Associates Inc.

Scientific papers that mention BluePyOpt

  • Manuel Reyes-Sanchez, Rodrigo Amaducci, Pablo Sanchez-Martin, Irene Elices, Francisco B. Rodriguez, and Pablo Varona. Automatized offline and online exploration to achieve a target dynamics in biohybrid neural circuits built with living and model neurons. Neural Networks, 164:464–475, July 2023. doi:10.1016/j.neunet.2023.04.034.
  • Branden D. Sanabria, Sindhuja S. Baskar, Alex J. Yonk, Christian R. Lee, and David J. Margolis. Cell-Type Specific Connectivity of Whisker-Related Sensory and Motor Cortical Input to Dorsal Striatum. Preprint, Neuroscience, March 2023. doi:10.1101/2023.03.06.531405.
  • Huaqing Jin, Parul Verma, Fei Jiang, Srikantan Nagarajan, and Ashish Raj. Bayesian Inference of a Spectral Graph Model for Brain Oscillations. Preprint, Neuroscience, March 2023. doi:10.1101/2023.03.01.530704.
  • Michalis Pagkalos, Spyridon Chavlis, and Panayiota Poirazi. Introducing the Dendrify framework for incorporating dendrites to spiking neural networks. Nature Communications, 14(1):131, January 2023. doi:10.1038/s41467-022-35747-8.
  • Darrell Haufler, Shinya Ito, Christof Koch, and Anton Arkhipov. Simulations of cortical networks using spatially extended conductance-based neuronal models. The Journal of Physiology, pages JP284030, January 2023. doi:10.1113/JP284030.
  • Michael Deistler, Pedro J. Goncalves, and Jakob H. Macke. Truncated proposals for scalable and hassle-free simulation-based inference. November 2022. arXiv:arXiv:2210.04815.
  • Rituparna Roy and Rishikesh Narayanan. Ion-channel degeneracy and heterogeneities in the emergence of complex spike bursts in CA3 pyramidal neurons. The Journal of Physiology, pages JP283539, October 2022. doi:10.1113/JP283539.
  • Stefano Masoli, Martina Francesca Rizza, Marialuisa Tognolina, Francesca Prestori, and Egidio D'Angelo. Computational models of neurotransmission at cerebellar synapses unveil the impact on network computation. Frontiers in Computational Neuroscience, 16:1006989, October 2022. doi:10.3389/fncom.2022.1006989.
  • Olivia Eriksson, Upinder Singh Bhalla, Kim T Blackwell, Sharon M Crook, Daniel Keller, Andrei Kramer, Marja-Leena Linne, Ausra Saudargienė, Rebecca C Wade, and Jeanette Hellgren Kotaleski. Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows. eLife, 11:e69013, July 2022. doi:10.7554/eLife.69013.
  • Omar Awile, Pramod Kumbhar, Nicolas Cornu, Salvador Dura-Bernal, James Gonzalo King, Olli Lupton, Ioannis Magkanaris, Robert A. McDougal, Adam J. H. Newton, Fernando Pereira, Alexandru Săvulescu, Nicholas T. Carnevale, William W. Lytton, Michael L. Hines, and Felix Schürmann. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Frontiers in Neuroinformatics, 16:884046, June 2022. doi:10.3389/fninf.2022.884046.
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  • Elishai Ezra-Tsur, Oren Amsalem, Lea Ankri, Pritish Patil, Idan Segev, and Michal Rivlin-Etzion. Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity. PLOS Computational Biology, 17(12):e1009754, December 2021. doi:10.1371/journal.pcbi.1009754.
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  • Oren Amsalem, Guy Eyal, Noa Rogozinski, Michael Gevaert, Pramod Kumbhar, Felix Schürmann, and Idan Segev. An efficient analytical reduction of detailed nonlinear neuron models. Nature Communications, 11(1):288, January 2020. doi:10.1038/s41467-019-13932-6.
  • Kyesam Jung, Jiyoung Kang, Seungsoo Chung, and Hae-Jeong Park. Dynamic causal modeling for calcium imaging: Exploration of differential effective connectivity for sensory processing in a barrel cortical column. NeuroImage, 201:116008, November 2019. doi:10.1016/j.neuroimage.2019.116008.
  • Max Nolte, Michael W. Reimann, James G. King, Henry Markram, and Eilif B. Muller. Cortical reliability amid noise and chaos. Nature Communications, 10(1):3792, August 2019. doi:10.1038/s41467-019-11633-8.
  • Raghu Sesha Iyengar, Madhav Vinodh Pithapuram, Avinash Kumar Singh, and Mohan Raghavan. Curated Model Development Using NEUROiD: A Web-Based NEUROmotor Integration and Design Platform. Frontiers in Neuroinformatics, 13:56, August 2019. doi:10.3389/fninf.2019.00056.
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Theses that use BluePyOpt

  • Johanna Frost Nylén. On Striatum in Silico Thesis for Doctoral Degree (Ph.D.). PhD thesis, Karolinska Institutet, 2023.
  • Jan-Matthis Lückmann. Simulation-Based Inference for Neuroscience and Beyond. PhD thesis, Eberhard Karls Universität Tübingen, 2022.
  • Sára Sáray. Systematic Validation of Detailed Models of Hippocampal Neurons Based on Electrophysiological Data. PhD thesis, Pázmány Péter Catholic University, 2021.
  • Yadeesha Deerasooriya. Dynamic Clamp Analysis of Ion Channel Function. PhD thesis, The University Of Melbourne, 2019.
  • Martina Francesca Rizza. A Biophysically Detailed Cerebellar Stellate Neuron Model Optimized with Particle Swarm Optimization Algorithm. PhD thesis, Università Degli Studi Di Milano-Bicocca, 2017.

Theses that mention BluePyOpt

  • Milagros Marín Alejo. Estudio del impacto de la dinámica neuronal en el procesamiento de información en la capa granular del cerebelo. 2021. URL: http://hdl.handle.net/10481/70162.
  • Abdulrahman Alqahtani. A multi-domain continuum model of electrical stimulation of healthy and degenerate retina. PhD thesis, School of Biomedical Engineering, UNSW, 2019.
  • Oscar Johansson. Weight estimation and evaluation of user suggestions in mobile browsing. Master's thesis, Linköping University, Department of Computer and Information Science, 2019.
  • Francesco Cremonesi. Computational characteristics and hardware implications of brain tissue simulations. PhD thesis, École Polytechnique Fédérale de Lausanne, Lausanne, 2019. URL: http://infoscience.epfl.ch/record/271927, doi:10.5075/epfl-thesis-9767.
  • David N. Silverstein. Investigations of neural attractor dynamics in human visual awareness. PhD thesis, KTH, Computational Science and Technology (CST), 2018. QC 20180305.

Posters that use BluePyOpt

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