Publications by Daniel Keller | EPFL Graph Search

A multiscale electro-metabolic model of a rat neocortical circuit reveals the impact of ageing on central cortical layers

Henry Markram, James Gonzalo King, Daniel Keller, Polina Shichkova, James Bryden Isbister, Darshan Mandge, Alessandro Cattabiani

The high energetic demands of the brain arise primarily from neuronal activity. Neurons consume substantial energy to transmit information as electrical signals and maintain their resting membrane potential. These energetic requirements are met by the neur ...

Public Library of Science (PLoS)2025

Seizure and redox rescue in a model of glucose transport deficiency

Henry Markram, Daniel Keller, Polina Shichkova

Disruptions of energy supply to the brain are associated with many neurodegenerative pathologies and are difficult to study due to numerous interlinked metabolic pathways. We explored the effects of diminished energy supply on brain metabolism using a comp ...

2025

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

Kathryn Hess Bellwald, Henry Markram, Felix Schürmann, James Gonzalo King, Srikanth Ramaswamy, Juan Bautista Hernando Vieites, Alexis Arnaudon, Eilif Benjamin Muller, Daniel Keller, Michael Reimann, Huanxiang Lu, Ying Shi, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Lida Kanari, Juan Luis Riquelme Roman, Ran Levi, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Liesbeth Maria L Vanherpe, Armando Romani, Cyrille Pierre Henri Favreau, Judit Planas Carbonell, Adrien Michel Achille Devresse, András Ecker, Nicolas René Jean Ninin, Daniela Egas Santander, Alexander Dietz, Benoît Jean-Albert Coste, Samuel Lieven D. Lapere, Matthias Wolf, Sirio Bolaños Puchet, Hugo Thabo Dictus, Thomas Brice Delemontex, James Bryden Isbister, Janis Lazovskis, Gianluca Ficarelli, Joni Henrikki Herttuainen,

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex

Henry Markram, Giovanna Ambrosini, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Romain Guiet, Nicolas René Chiaruttini, Elvis Boci

The relation of astrocytic endfeet to the vasculature plays a key functional role in the neuro‐glia‐vasculature unit. We characterize the spatial organization of astrocytes and the structural aspects that facilitate their involvement in molecular exchanges ...

Wiley2024

Modeling and simulation of neocortical micro- and mesocircuitry. Part II: Physiology and experimentation

Henry Markram, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Alexis Arnaudon, Eilif Benjamin Muller, Daniel Keller, Michael Reimann, Vishal Sood, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Giuseppe Chindemi, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Armando Romani, Christian Andreas Rössert, Judit Planas Carbonell, Genrich Ivaska, András Ecker, Daniela Egas Santander, Natali Barros Zulaica, Alexander Dietz, Omar Awile, Samuel Lieven D. Lapere, Matthias Wolf, Sirio Bolaños Puchet, Thomas Brice Delemontex, Jorge Blanco Alonso, Mustafa Anil Tuncel, Tanguy Pierre Louis Damart, Maria Reva, James Bryden Isbister, Darshan Mandge, Weina Ji, Aleksandra Zuzanna Teska, Polina Litvak, Gianluca Ficarelli, Joni Henrikki Herttuainen, ,

Cell density quantification of high resolution Nissl images of the juvenile rat brain

Henry Markram, Olivier Burri, Rodrigo de Campos Perin, Julie Meystre, Daniel Keller, Ying Shi

Copyright © 2024 Meystre, Jacquemier, Burri, Zsolnai, Frank, Vieira, Shi, Perin, Keller and Markram.Nissl histology underpins our understanding of brain anatomy and architecture. Despite its importance, no high-resolution datasets are currently available i ...

2024

Brain Metabolism in Health and Neurodegeneration: The Interplay Among Neurons and Astrocytes

Henry Markram, Daniel Keller, Jay Coggan, Polina Shichkova

The regulation of energy in the brain has garnered substantial attention in recent years due to its significant implications in various disorders and aging. The brain’s energy metabolism is a dynamic and tightly regulated network that balances energy deman ...

MDPI AG2024

Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling

Georges Khazen, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Adrien Christian Fleury, Jay Coggan, Judit Planas Carbonell, Juan José García Cantero, Alessandro Enrico Foni, Nadir Roman Guerrero, Elvis Boci

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuron ...

Oxford University Press (OUP)2024

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Eleftherios Zisis, Jay Coggan, Juan José García Cantero, Alessandro Enrico Foni, Nadir Roman Guerrero

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) ...

2023

Cell-type-specific densities in mouse somatosensory cortex derived from scRNA-seq and in situ RNA hybridization

Henry Markram, Daniel Keller

Cells in the mammalian cerebral cortex exhibit layer-dependent patterns in their distribution. Classical methods of determining cell type distributions typically employ a painstaking process of large-scale sampling and characterization of cellular composit ...

FRONTIERS MEDIA SA2023

Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons

Henry Markram, Srikanth Ramaswamy, Daniel Keller, Michael Reimann, Yann Roussel, Dimitri Bruno Marie Rodarie, Tanguy Pierre Louis Damart

Author summaryThe computational abilities of the brain arise from its organization principles at the cellular level. One of these principles is the neuronal type composition over different regions. Since computational functions of neurons are best describe ...

2023

A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience

Daniel Keller, Andrii Stepaniuk

Neuroscience incorporates knowledge from a range of scales, from single molecules to brain wide neural networks. Modeling is a valuable tool in understanding processes at a single scale or the interactions between two adjacent scales and researchers use a ...

HUMANA PRESS INC2022

A method to estimate the cellular composition of the mouse brain from heterogeneous datasets

Henry Markram, Srikanth Ramaswamy, Daniel Keller, Michael Reimann, Marc-Oliver Gewaltig, Yann Roussel, Dimitri Bruno Marie Rodarie

The mouse brain contains a rich diversity of inhibitory neuron types that have been characterized by their patterns of gene expression. However, it is still unclear how these cell types are distributed across the mouse brain. We developed a computational m ...

2022

Representing stimulus information in an energy metabolism pathway

Henry Markram, Felix Schürmann, Daniel Keller, Jay Coggan

We explored a computational model of astrocytic energy metabolism and demonstrated the theoretical plausibility that this type of pathway might be capable of coding information about stimuli in addition to its known functions in cellular energy and carbon ...

2022

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

Daniel Keller

Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system work ...

2022

A Machine-Generated View of the Role of Blood Glucose Levels in the Severity of COVID-19

Henry Markram, Daniel Keller, Emmanuelle Logette, Francesco Casalegno, Jay Coggan, Cyrille Pierre Henri Favreau, Mohameth François Sy, Samuel Claude Kerrien, Anna-Kristin Kaufmann, Pierre-Alexandre Fonta, Enrico Scantamburlo, Marine Laure Bertschy

SARS-CoV-2 started spreading toward the end of 2019 causing COVID-19, a disease that reached pandemic proportions among the human population within months. The reasons for the spectrum of differences in the severity of the disease across the population, an ...

FRONTIERS MEDIA SA2021

Metaball skinning of synthetic astroglial morphologies into realistic mesh models for visual analytics and in silico simulations

Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Eleftherios Zisis, Jay Coggan, Samuel Lieven D. Lapere, Alessandro Enrico Foni, Nadir Roman Guerrero

Motivation: Astrocytes, the most abundant glial cells in the mammalian brain, have an instrumental role in developing neuronal circuits. They contribute to the physical structuring of the brain, modulating synaptic activity and maintaining the blood-brain ...

OXFORD UNIV PRESS2021

A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation

Henry Markram, Daniel Keller, Jay Coggan, Polina Shichkova

Accurate molecular concentrations are essential for reliable analyses of biochemical networks and the creation of predictive models for molecular and systems biology, yet protein and metabolite concentrations used in such models are often poorly constraine ...

FRONTIERS MEDIA SA2021

Supervised Learning With Perceptual Similarity for Multimodal Gene Expression Registration of a Mouse Brain Atlas

Henry Markram, Felix Schürmann, Csaba Erö, Daniel Keller, Huanxiang Lu, Francesco Casalegno, Dimitri Bruno Marie Rodarie

The acquisition of high quality maps of gene expression in the rodent brain is of fundamental importance to the neuroscience community. The generation of such datasets relies on registering individual gene expression images to a reference volume, a task en ...

FRONTIERS MEDIA SA2021

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

Kathryn Hess Bellwald, Henry Markram, Felix Schürmann, Corrado Cali, Alexis Arnaudon, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Lida Kanari, Eleftherios Zisis, Michael Emiel Gevaert, Benoît Jean-Albert Coste, Thomas Brice Delemontex, Alessandro Enrico Foni

Astrocytes connect the vasculature to neurons mediating the supply of nutrients and biochemicals. They are involved in a growing number of physiological and pathophysiological processes that result from biophysical, physiological, and molecular interaction ...

OXFORD UNIV PRESS INC2021