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Publications that use or mention BluePyOpt

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Aurélien Jaquier edited this page Jun 13, 2022 · 6 revisions

Publications that use or mention BluePyOpt

Scientific papers that use BluePyOpt

  • 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.
  • 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.
  • 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.
  • 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.
  • 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, December 2022. doi:10.1038/s41467-022-30214-w.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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, December 2020. doi:10.1038/s42003-020-0953-x.
  • 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.
  • Mario Michiels. Electrophysiology prediction of single neurons based on their morphology. Preprint, Neuroscience, February 2020. doi:10.1101/2020.02.04.933697.
  • 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.
  • 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.
  • 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.
  • 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, Bosiljka Tasic, and Costas A. Anastassiou. Single-neuron models linking electrophysiology, morphology and transcriptomics across cortical cell types. Preprint, Neuroscience, April 2020. doi:10.1101/2020.04.09.030239.
  • 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.
  • 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, December 2021. doi:10.1038/s41598-021-83209-w.
  • Nadia Rosenberg, Maria Reva, Leonardo Restivo, 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. Preprint, Neuroscience, January 2022. doi:10.1101/2022.01.25.477694.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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 ca1 synaptic physiology in silico. Hippocampus, 30(11):1129–1145, 2020. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/hipo.23220, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/hipo.23220, doi:https://doi.org/10.1002/hipo.23220.
  • Géza Berecki, Alexander Bryson, Jan Terhag, Snezana Maljevic, Elena V. Gazina, Sean L. Hill, and Steven Petrou. Scn1a gain of function in early infantile encephalopathy. Annals of Neurology, 85(4):514–525, 2019. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/ana.25438, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/ana.25438, doi:https://doi.org/10.1002/ana.25438.

Scientific papers that mention BluePyOpt

  • Oren Amsalem, James King, Michael Reimann, Srikanth Ramaswamy, Eilif Muller, Henry Markram, Israel Nelken, and Idan Segev. Dense Computer Replica of Cortical Microcircuits Unravels Cellular Underpinnings of Auditory Surprise Response. Preprint, Neuroscience, June 2020. doi:10.1101/2020.05.31.126466.
  • 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, December 2020. doi:10.1038/s41467-019-13932-6.
  • 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. Preprint, Neuroscience, March 2022. doi:10.1101/2022.03.03.482816.
  • Marcel Beining, Lucas Alberto Mongiat, Stephan Wolfgang Schwarzacher, Hermann Cuntz, and Peter Jedlicka. T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells. eLife, 6:e26517, November 2017. doi:10.7554/eLife.26517.
  • Roy Ben-Shalom, Jan Balewski, Anand Siththaranjan, Vyassa Baratham, Henry Kyoung, Kyung Geun Kim, Kevin J. Bender, and Kristofer E. Bouchard. Inferring neuronal ionic conductances from membrane potentials using CNNs. Preprint, Neuroscience, August 2019. doi:10.1101/727974.
  • Luca L. Bologna, Roberto Smiriglia, Dario Curreri, and Michele Migliore. The EBRAINS NeuroFeatureExtract: An Online Resource for the Extraction of Neural Activity Features From Electrophysiological Data. Frontiers in Neuroinformatics, 15:713899, August 2021. doi:10.3389/fninf.2021.713899.
  • Richard R. Carrillo, Francisco Naveros, Eduardo Ros, and Niceto R. Luque. A Metric for Evaluating Neural Input Representation in Supervised Learning Networks. Frontiers in Neuroscience, 12:913, December 2018. doi:10.3389/fnins.2018.00913.
  • Antonio Díaz-Parra, Zachary Osborn, Santiago Canals, David Moratal, and Olaf Sporns. Structural and functional, empirical and modeled connectivity in the cerebral cortex of the rat. NeuroImage, 159:170–184, October 2017. doi:10.1016/j.neuroimage.2017.07.046.
  • Salvador Dura-Bernal, Benjamin A Suter, Padraig Gleeson, Matteo Cantarelli, Adrian Quintana, Facundo Rodriguez, David J Kedziora, George L Chadderdon, Cliff C Kerr, Samuel A Neymotin, Robert A McDougal, Michael Hines, Gordon MG Shepherd, and William W Lytton. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. eLife, 8:e44494, April 2019. doi:10.7554/eLife.44494.
  • Georgia Economides, Svenja Falk, and Audrey Mercer. Biocytin Recovery and 3D Reconstructions of Filled Hippocampal CA2 Interneurons. Journal of Visualized Experiments, pages 58592, November 2018. doi:10.3791/58592.
  • Jorgen Jensen Farner, Hakon Weydahl, Ruben Jahren, Ola Huse Ramstad, Stefano Nichele, and Kristine Heiney. Evolving spiking neuron cellular automata and networks to emulate in vitro neuronal activity. In 2021 IEEE Symposium Series on Computational Intelligence (SSCI), 1–10. Orlando, FL, USA, December 2021. IEEE. doi:10.1109/SSCI50451.2021.9660185.
  • Johanna Frost Nylen, Jarl Jacob Johannes Hjorth, Sten Grillner, and Jeanette Hellgren Kotaleski. Dopaminergic and Cholinergic Modulation of Large Scale Networks in silico Using Snudda. Frontiers in Neural Circuits, 15:748989, October 2021. doi:10.3389/fncir.2021.748989.
  • Sergio E. Galindo, Pablo Toharia, Óscar D. Robles, Eduardo Ros, Luis Pastor, and Jesús A. Garrido. Simulation, visualization and analysis tools for pattern recognition assessment with spiking neuronal networks. Neurocomputing, 400:309–321, August 2020. doi:10.1016/j.neucom.2020.02.114.
  • Eyal Gal, Oren Amsalem, Alon Schindel, Michael London, Felix Schürmann, Henry Markram, and Idan Segev. The Role of Hub Neurons in Modulating Cortical Dynamics. Frontiers in Neural Circuits, 15:718270, September 2021. doi:10.3389/fncir.2021.718270.
  • Nathan W. Gouwens, Jim Berg, David Feng, Staci A. Sorensen, Hongkui Zeng, Michael J. Hawrylycz, Christof Koch, and Anton Arkhipov. Systematic generation of biophysically detailed models for diverse cortical neuron types. Nature Communications, 9(1):710, December 2018. doi:10.1038/s41467-017-02718-3.
  • Robin Gutzen, Michael von Papen, Guido Trensch, Pietro Quaglio, Sonja Grün, and Michael Denker. Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data. Frontiers in Neuroinformatics, 12:90, December 2018. doi:10.3389/fninf.2018.00090.
  • 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.
  • Zbigniew J\c edrzejewski-Szmek, Karina P. Abrahao, Joanna J\c edrzejewska-Szmek, David M. Lovinger, and Kim T. Blackwell. Parameter Optimization Using Covariance Matrix Adaptation—Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Frontiers in Neuroinformatics, 12:47, July 2018. doi:10.3389/fninf.2018.00047.
  • 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.
  • 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.
  • Marja-Leena Linne. Neuroinformatics and Computational Modelling as Complementary Tools for Neurotoxicology Studies. Basic & Clinical Pharmacology & Toxicology, 123:56–61, September 2018. doi:10.1111/bcpt.13075.
  • Tuomo Mäki-Marttunen, Geir Halnes, Anna Devor, Christoph Metzner, Anders M. Dale, Ole A. Andreassen, and Gaute T. Einevoll. A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. Journal of Neuroscience Methods, 293:264–283, January 2018. doi:10.1016/j.jneumeth.2017.10.007.
  • Milagros Marín, Nicolás C. Cruz, Eva M. Ortigosa, María J. Sáez-Lara, Jesús A. Garrido, and Richard R. Carrillo. On the Use of a Multimodal Optimizer for Fitting Neuron Models. Application to the Cerebellar Granule Cell. Frontiers in Neuroinformatics, 15:663797, June 2021. doi:10.3389/fninf.2021.663797.
  • Robert Meyer and Klaus Obermayer. Pypet: A Python Toolkit for Data Management of Parameter Explorations. Frontiers in Neuroinformatics, August 2016. doi:10.3389/fninf.2016.00038.
  • Samuel A. Neymotin, Benjamin A. Suter, Salvador Dura-Bernal, Gordon M. G. Shepherd, Michele Migliore, and William W. Lytton. Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. Journal of Neurophysiology, 117(1):148–162, January 2017. doi:10.1152/jn.00570.2016.
  • 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, December 2019. doi:10.1038/s41467-019-11633-8.
  • Srikanth Ramaswamy, Cristina Colangelo, and Henry Markram. Data-Driven Modeling of Cholinergic Modulation of Neural Microcircuits: Bridging Neurons, Synapses and Network Activity. Frontiers in Neural Circuits, 12:77, October 2018. doi:10.3389/fncir.2018.00077.
  • 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.
  • Gopal P. Sarma, Adam Safron, and Nick J. Hay. Integrative Biological Simulation, Neuropsychology, and AI Safety. January 2019. arXiv:1811.03493.
  • Jiamin Shen, Ye Wang, and Lihong Cao. Automatic fitting of neuron parameters. In 2018 IEEE 3rd International Conference on Cloud Computing and Big Data Analysis (ICCCBDA), 558–562. Chengdu, April 2018. IEEE. doi:10.1109/ICCCBDA.2018.8386578.
  • Manisha Sinha and Rishikesh Narayanan. Active Dendrites and Local Field Potentials: Biophysical Mechanisms and Computational Explorations. Neuroscience, 489:111–142, May 2022. doi:10.1016/j.neuroscience.2021.08.035.
  • Subhashini Sivagnanam, Kenneth Yoshimoto, Nicholas T. Carnevale, and Amit Majumdar. The Neuroscience Gateway: Enabling Large Scale Modeling and Data Processing in Neuroscience. In Proceedings of the Practice and Experience on Advanced Research Computing, 1–7. Pittsburgh PA USA, July 2018. ACM. doi:10.1145/3219104.3219139.
  • David B. Stockton and Fidel Santamaria. Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow. Neuroinformatics, 15(4):333–342, October 2017. doi:10.1007/s12021-017-9337-x.
  • Alper Yegenoglu, Anand Subramoney, Thorsten Hater, Cristian Jimenez-Romero, Wouter Klijn, Aaron Perez Martin, Michiel van der Vlag, Michael Herty, Abigail Morrison, and Sandra Diaz-Pier. Exploring hyper-parameter spaces of neuroscience models on high performance computers with Learning to Learn. February 2022. arXiv:2202.13822.
  • Jan-Matthis Lueckmann, Giacomo Bassetto, Theofanis Karaletsos, and Jakob H. Macke. Likelihood-free inference with emulator networks. In Francisco Ruiz, Cheng Zhang, Dawen Liang, and Thang Bui, editors, Proceedings of The 1st Symposium on Advances in Approximate Bayesian Inference, volume 96 of Proceedings of Machine Learning Research, 32–53. PMLR, 02 Dec 2019. URL: https://proceedings.mlr.press/v96/lueckmann19a.html.
  • Shailesh Appukuttan, Lungsi Sharma, Pedro Garcia-Rodriguez, and Andrew Davison. A Software Framework for Validating Neuroscience Models. working paper or preprint, February 2022. URL: https://hal.archives-ouvertes.fr/hal-03586825.
  • Peter Jedlicka, Alex Bird, and Hermann Cuntz. Pareto optimality, economy-effectiveness trade-offs and ion channel degeneracy: improving population models of neurons. 2022. URL: https://arxiv.org/abs/2203.06391, doi:10.48550/ARXIV.2203.06391.

Theses that use BluePyOpt

  • 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.
  • 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.

Theses that mention BluePyOpt

  • 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.
  • Oscar Johansson. Weight estimation and evaluation of user suggestions in mobile browsing. Master's thesis, Linköping University, Department of Computer and Information Science, 2019.
  • David N. Silverstein. Investigations of neural attractor dynamics in human visual awareness. PhD thesis, KTH, Computational Science and Technology (CST), 2018. QC 20180305.
  • 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.

Posters that use BluePyOpt

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