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Daniel Keller

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Related publications (36)

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Excitation states of metabolic networks predict dose-response fingerprinting and ligand pulse phase signalling

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Jay Coggan

With a computational model of energy metabolism in an astrocyte, we show how a system of enzymes in a cascade can act as a functional unit of interdependent reactions, rather than merely a series of independent reactions. These systems may exist in multipl ...

2020

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

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

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

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

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

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

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

Cortical dynamics underlie many cognitive processes and emerge from complex multi-scale interactions, which are challenging to study in vivo. Large-scale, biophysically detailed models offer a tool which can complement laboratory approaches. We present a m ...

2024

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

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

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

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

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

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

Cell Densities in the Mouse Brain: A Systematic Review

Henry Markram, Daniel Keller, Csaba Erö

The mouse brain is the most extensively studied brain of all species. We performed an exhaustive review of the literature to establish our current state of knowledge on cell numbers in mouse brain regions, arguably the most fundamental property to measure ...

2018

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue

Daniel Keller

Recorded potentials in the extracellular space (ECS) of the brain is a standard measure of population activity in neural tissue. Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes a ...

Public Library of Science2016

Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis

Snigdha Dagar, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Jean-Denis Georges Emile Courcol, Jay Coggan, Nadir Roman Guerrero, Benoît Jean-Albert Coste, Samuel Lieven D. Lapere

Motivation: Accurate morphological models of brain vasculature are key to modeling and simulating cerebral blood flow in realistic vascular networks. This in silico approach is fundamental to revealing the principles of neurovascular coupling. Validating t ...

Oxford University Press2020

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

Henry Markram, Daniel Keller, Csaba Verasztó

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

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

Csaba Zsolnai, Henry Markram, Daniel Keller, Olivier Burri, Rodrigo de Campos Perin, Ying Shi, Julie Meystre, João Luís Prado Vieira, Jean Nicolas Jacquemier

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

A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Renaud Jolivet, Stefan Eilemann, Jay Coggan, Corrado Cali

One will not understand the brain without an integrated exploration of structure and function, these attributes being two sides of the same coin: together they form the currency of biological computation. Accordingly, biologically realistic models require ...

2018

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, Jay Coggan, Nadir Roman Guerrero, Alessandro Enrico Foni, Samuel Lieven D. Lapere, Eleftherios Zisis

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 University Press2021

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

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

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, hierarchical, interregional structure with a highly specific laminar architecture. The last decade has seen the emergence of extensive new ...

2024

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

Stanislav Schmidt, Henry Markram, Daniel Keller, Jay Coggan, Mohameth François Sy, Cyrille Pierre Henri Favreau, Anna-Kristin Kaufmann, Emmanuelle Logette, Francesco Casalegno, Samuel Claude Kerrien, Enrico Scantamburlo, Charlotte Lorin, Marine Laure Bertschy, Pierre-Alexandre Fonta, Jan Krepl, Emilie Delattre, Caitlin Claire Monney

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

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

Digital Reconstruction of the Neuro-Glia-Vascular Architecture

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

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

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

Henry Markram, Felix Schürmann, Eilif Benjamin Muller, Sean Lewis Hill, Idan Segev, Srikanth Ramaswamy, Michael Reimann, Daniel Keller, Werner Alfons Hilda Van Geit, Marwan Muhammad Ahmed Abdellah, James Gonzalo King, Lida Kanari, Julian Charles Shillcock, Ying Shi, Jean-Denis Georges Emile Courcol, Rajnish Ranjan, Juan Bautista Hernando Vieites, Stefan Eilemann, Michael Emiel Gevaert, Giuseppe Chindemi, Nicolas Antille, Jeffrey Christopher Muller, Ahmet Bilgili

We have established a multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data. We applied this process to reconstruct the microcircuitry of the somatosensory corte ...

Frontiers Research Foundation2015