Henry Markram
EPFL SV BMI LNMC
AAB 1 10 (Bâtiment AAB)
Station 15
CH-1015 Lausanne
Web site: Site web: https://markram-lab.epfl.ch
+41 21 693 95 36
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Web site: Site web: https://sv.epfl.ch/education
EPFL BBP-CORE
Campus Biotech
Bâtiment B1
Ch. des Mines 9
CH-1202 Genève
+41 21 693 95 36
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B1 5 282.040
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Web site: Site web: https://www.epfl.ch/research/domains/bluebrain/
Publications
Publications Infoscience
Infoscience
Thalamic control of sensory processing and spindles in a biophysical somatosensory thalamoreticular circuit model of wakefulness and sleep
Cell Reports. 2023. DOI : 10.1016/j.celrep.2023.112200.Blue Brain Nexus: An open, secure, scalable system for knowledge graph management and data-driven science
Semantic Web. 2023. DOI : 10.3233/SW-222974.Digital reconstruction of the mammalian spinal cord: from anatomical reference volume to cell type atlas of the mouse spinal cord
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-9198.Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons
Plos Computational Biology. 2023-01-01. DOI : 10.1371/journal.pcbi.1010058.Overexpression of UCP4 in astrocytic mitochondria prevents multilevel dysfunctions in a mouse model of Alzheimer's disease
Glia. 2022-12-20. DOI : 10.1002/glia.24317.A method to estimate the cellular composition of the mouse brain from heterogeneous datasets
Plos Computational Biology. 2022-12-01. DOI : 10.1371/journal.pcbi.1010739.Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience
Briefings In Bioinformatics. 2022-11-26. DOI : 10.1093/bib/bbac491.Optimum trajectory learning in musculoskeletal systems with model predictive control and deep reinforcement learning
Biological Cybernetics. 2022-08-11. DOI : 10.1007/s00422-022-00940-x.Strong and reliable synaptic communication between pyramidal neurons in adult human cerebral cortex
Cerebral Cortex. 2022-07-08. DOI : 10.1093/cercor/bhac246.A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex
Nature Communications. 2022-06-01. DOI : 10.1038/s41467-022-30214-w.Representing stimulus information in an energy metabolism pathway
Journal Of Theoretical Biology. 2022-05-07. DOI : 10.1016/j.jtbi.2022.111090.Computational synthesis of cortical dendritic morphologies
Cell Reports. 2022-04-05. DOI : 10.1016/j.celrep.2022.110586.Modeling and simulation of rat non-barrel somatosensory cortex. Part I: Modeling anatomy
bioRxiv. 2022. DOI : 10.1101/2022.08.11.503144.A multi-modal fitting approach to construct single-neuron models with patch clamp and high-density microelectrode arrays
2022. DOI : 10.1101/2022.08.03.502468.Reconstruction of the Hippocampus
Computational Modelling of the Brain: Modelling Approaches to Cells, Circuits and Networks; Springer, 2022. p. 361.Neuromodulatory organization in the developing rat somatosensory cortex
2022. DOI : 10.1101/2022.11.11.516108.A universal workflow for creation, validation and generalization of detailed neuronal models
2022. DOI : 10.1101/2022.12.13.520234.Data-driven whole mouse brain modeling for multi-scale simulations
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-8715.Extracellular stimulation and Local Field Potential recording in a L5 PC model with full axonal arbor
2021-12-01. p. S123-S124.Building somatosensory cortex neuron models using a workflow for the creation, validation and generalization of biophysically detailed cell models
2021-12-01. p. S122-S123.Computational modelling of a mouse layer 5 pyramidal neuron using genetic ion channels
2021-12-01. p. S123-S123.Digital Reconstruction of the Neuro-Glia-Vascular Architecture
Cerebral Cortex. 2021-12-01. DOI : 10.1093/cercor/bhab254.A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation
Frontiers In Molecular Neuroscience. 2021-11-10. DOI : 10.3389/fnmol.2021.604559.Morphology, physiology and synaptic connectivity of local interneurons in the mouse somatosensory thalamus
Journal Of Physiology. 2021-10-23. DOI : 10.1113/JP281711.The Role of Hub Neurons in Modulating Cortical Dynamics
Frontiers In Neural Circuits. 2021-09-24. DOI : 10.3389/fncir.2021.718270.Supervised Learning With Perceptual Similarity for Multimodal Gene Expression Registration of a Mouse Brain Atlas
Frontiers In Neuroinformatics. 2021-07-28. DOI : 10.3389/fninf.2021.691918.A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19
Frontiers In Public Health. 2021-07-28. DOI : 10.3389/fpubh.2021.695139.Metaball skinning of synthetic astroglial morphologies into realistic mesh models for visual analytics and in silico simulations
Bioinformatics. 2021-07-01. DOI : 10.1093/bioinformatics/btab280.In silico voltage-sensitive dye imaging reveals the emergent dynamics of cortical populations
Nature Communications. 2021-06-15. DOI : 10.1038/s41467-021-23901-7.ARC: An Open Web-Platform for Request/Supply Matching for a Prioritized and Controlled COVID-19 Response
Frontiers In Public Health. 2021-02-16. DOI : 10.3389/fpubh.2021.607677.Synthesis of branching morphologies
US2022414436 ; EP4032103 ; CN114787939 ; KR20220084391 ; WO2021078588 . 2021.Thalamic microcircuitry: neurons, synapses, and circuit motifs in receptive field structure and sensory processing
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-7614.Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis
Bioinformatics. 2020-07-01. DOI : 10.1093/bioinformatics/btaa461.Excitation states of metabolic networks predict dose-response fingerprinting and ligand pulse phase signalling
Journal Of Theoretical Biology. 2020-02-21. DOI : 10.1016/j.jtbi.2019.110123.A Kinetic Map of the Homomeric Voltage-gated Potassium Channel (Kv) Family
2020-02-07. 64th Annual Meeting of the Biophysical-Society, San Diego, CA, Feb 15-19, 2020. p. 108A-108A. DOI : 10.1016/j.bpj.2019.11.739.Neuron Geometry Underlies Universal Network Features in Cortical Microcircuits
bioRxiv. 2020. DOI : 10.1101/656058.Dense Computer Replica of Cortical Microcircuits Unravels Cellular Underpinnings of Auditory Surprise Response
bioRxiv. 2020. DOI : 10.1101/2020.05.31.126466.Data driven building of realistic neuron model using IBEA and CMA evolution strategies
2020. GECCO '20: Genetic and Evolutionary Computation Conference, Cancún, Mexico, July 8 - 12, 2020. p. 35-36. DOI : 10.1145/3377929.3398161.Impact of higher order network structure on emergent cortical activity
Network Neuroscience. 2020-01-01. DOI : 10.1162/netn_a_00124.Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in the Neocortex
Frontiers In Synaptic Neuroscience. 2019-10-15. DOI : 10.3389/fnsyn.2019.00029.A null model of the mouse whole-neocortex micro-connectome
Nature Communications. 2019-08-29. DOI : 10.1038/s41467-019-11630-x.Caries Detection with Near-Infrared Transillumination Using Deep Learning
Journal of Dental Research. 2019-08-26. DOI : 10.1177/0022034519871884.Cortical reliability amid noise and chaos
Nature Communications. 2019-08-22. DOI : 10.1038/s41467-019-11633-8.A Kinetic Map of the Homomeric Voltage-Gated Potassium Channel (Kv) Family
Frontiers in Cellular Neuroscience. 2019-08-20. DOI : 10.3389/fncel.2019.00358.A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
Frontiers In Neuroanatomy. 2019-08-06. DOI : 10.3389/fnana.2019.00078.Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons
PLoS Computational Biology. 2019-05-16. DOI : 10.1371/journal.pcbi.1006753.A Brief History of Simulation Neuroscience
Frontiers In Neuroinformatics. 2019-05-07. DOI : 10.3389/fninf.2019.00032.Cellular, Synaptic and Network Effects of Acetylcholine in the Neocortex
Frontiers In Neural Circuits. 2019-04-12. DOI : 10.3389/fncir.2019.00024.Objective Morphological Classification of Neocortical Pyramidal Cells
Cerebral Cortex. 2019-04-01. DOI : 10.1093/cercor/bhy339.Individual differences in sensory sensitivity: Further lessons from an Autism model
Cognitive Neuroscience. 2019-03-30. DOI : 10.1080/17588928.2019.1592143.A Cell Atlas for the Mouse Brain (vol 12, 84, 2018)
Frontiers In Neuroinformatics. 2019-02-19. DOI : 10.3389/fninf.2019.00007.In Silico Voltage-Sensitive Dye Imaging: A Model-Based Approach for Bridging Scales of Cortical Activity
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9848.Reverse engineering the motor control system
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9599.Untangling emergent cortical dynamics: neurons from networks, noise from chaos
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9616.A Cell Atlas for the Mouse Brain
Frontiers In Neuroinformatics. 2018-11-28. DOI : 10.3389/fninf.2018.00084.Cell Densities in the Mouse Brain: A Systematic Review
Frontiers In Neuroanatomy. 2018-10-23. DOI : 10.3389/fnana.2018.00083.Data-Driven Modeling of Cholinergic Modulation of Neural Microcircuits: Bridging Neurons, Synapses and Network Activity
Frontiers In Neural Circuits. 2018-10-09. DOI : 10.3389/fncir.2018.00077.A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble
Frontiers In Neuroscience. 2018-09-25. DOI : 10.3389/fnins.2018.00664.The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow
Plos Computational Biology. 2018-09-01. DOI : 10.1371/journal.pcbi.1006423.Microcircuitry of the neocortex
Handbook of Brain Microcircuits; Oxford University Press, 2018. p. 35-46.Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate
PLOS Computational Biology. 2018. DOI : 10.1371/journal.pcbi.1006392.Reconstruction and simulation of neocortical microcircuitry
US2018101660 . 2018.Generating and identifying functional subnetworks within structural networks
US11615285 ; US2018197069 . 2018.Simplification of neural network models
US2022230052 ; US11301750 ; US2018285716 . 2018.Data-driven reconstruction of a point neuron mouse brain
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8962.NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks
BIOINFORMATICS. 2018. DOI : 10.1093/bioinformatics/bty231.A Topological Representation of Branching Neuronal Morphologies
NEUROINFORMATICS. 2018. DOI : 10.1007/s12021-017-9341-1.Neuronal morphologies: the shapes of thoughts
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8255.Towards a unified understanding of synaptic plasticity
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8186.A Physically Plausible Model for Rendering Highly Scattering Fluorescent Participating Media
2017Timed Synaptic Inhibition Shapes NMDA Spikes, Influencing Local Dendritic Processing and Global I/O Properties of Cortical Neurons
Cell Reports. 2017. DOI : 10.1016/j.celrep.2017.10.035.In Silico Brain Imaging Physically-plausible Methods for Visualizing Neocortical Microcircuitry
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8161.Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies
Bmc Bioinformatics. 2017. DOI : 10.1186/s12859-017-1788-4.Using the Green's function to simplify and understand dendrites
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7869.Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity
Cerebral Cortex. 2017. DOI : 10.1093/cercor/bhx150.Modeling the metabolic response of astrocytes to neuronal activity
2017. 13th European Meeting on Glial Cells in Health and Disease, Edinburgh, SCOTLAND, JUL 08-11, 2017. p. E280-E280.Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function
Frontiers In Computational Neuroscience. 2017. DOI : 10.3389/fncom.2017.00048.Rich cell-type-specific network topology in neocortical microcircuitry
Nature Neuroscience. 2017. DOI : 10.1038/nn.4576.Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation
Bmc Bioinformatics. 2017. DOI : 10.1186/s12859-016-1444-4.From Neuron Biophysics to Orientation Selectivity in Electrically Coupled Networks of Neocortical L2/3 Large Basket Cells
Cerebral Cortex. 2016-06-09. DOI : 10.1093/cercor/bhw166.Automated point-neuron simplification of data-driven microcircuit models
2016Tight Coupling of Astrocyte pH Dynamics to Epileptiform Activity Revealed by Genetically Encoded pH Sensors
Journal Of Neuroscience. 2016. DOI : 10.1523/Jneurosci.0664-16.2016.BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience
Frontiers In Neuroinformatics. 2016. DOI : 10.3389/fninf.2016.00017.Agile in-litero experiments
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6809.Structural to functional synaptic conversion
US9165244 ; US2014108315 . 2015.Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
BMC bioinformatics. 2015. DOI : 10.1186/1471-2105-16-S11-S8.The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex
Frontiers In Neural Circuits. 2015. DOI : 10.3389/fncir.2015.00044.An algorithm to predict the connectome of neural microcircuits
Frontiers In Computational Neuroscience. 2015. DOI : 10.3389/fncom.2015.00120.Reconstruction and Simulation of Neocortical Microcircuitry
Cell. 2015. DOI : 10.1016/j.cell.2015.09.029.Anatomy and physiology of the thick-tufted layer 5 pyramidal neuron
Frontiers In Cellular Neuroscience. 2015. DOI : 10.3389/fncel.2015.00233.An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
PLoS computational biology. 2015. DOI : 10.1371/journal.pcbi.1004253.Network-timing-dependent plasticity
Frontiers in cellular neuroscience. 2015. DOI : 10.3389/fncel.2015.00220.Predictable enriched environment prevents development of hyper-emotionality in the VPA rat model of autism
Frontiers in Neuroscience. 2015. DOI : 10.3389/fnins.2015.00127.Cell-type- and activity-dependent extracellular correlates of intracellular spiking
Journal of Neurophysiology. 2015. DOI : 10.1152/jn.00628.2014.A versatile clearing agent for multi-modal brain imaging
Scientific Reports. 2015. DOI : 10.1038/srep09808.The future of human cerebral cartography: a novel approach
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 2015. DOI : 10.1098/rstb.2014.0171.Large Volume Imaging of Rodent Brain Anatomy with Emphasis on Selective Plane Illumination Microscopy
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6533.Anti-Obesity and Anti-Hyperglycemic Effects of Cinnamaldehyde via altered Ghrelin Secretion and Functional impact on Food Intake and Gastric Emptying
Scientific Reports. 2015. DOI : 10.1038/srep07919.Distributor of neurons in a neocortical column
US2014107992 . 2014.Single-cell RT-PCR, a technique to decipher the electrical, anatomical, and genetic determinants of neuronal diversity
Methods in molecular biology (Clifton, N.J.). 2014. DOI : 10.1007/978-1-4939-1096-0_8.Enseignement & Phd
Enseignement
Life Sciences Engineering