Publications by Jay Coggan | EPFL Graph Search

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

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

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

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

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

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 UNIV PRESS2020

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

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

Pierre Magistretti, Renaud Jolivet, Henry Markram, Felix Schürmann, Corrado Cali, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Stefan Eilemann, Jay Coggan, Daniya Boges, Kalpana Kare, Markus Hadwiger, Marco Agus

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

Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate

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

Although efficient compared to computers, the human brain utilizes energy at 10-fold the rate of other organs by mass. How the brain is supplied with sufficient on-demand energy to support its activity in the absence of neuronal storage capacity remains un ...

2018

Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble

Pierre Magistretti, Renaud Jolivet, Igor Allaman, Jay Coggan

Glucose is the main energy substrate in the adult brain under normal conditions. Accumulating evidence, however, indicates that lactate produced in astrocytes (a type of glial cell) can also fuel neuronal activity. The quantitative aspects of this so-calle ...

2015