Publications related to Reconstruction and systems analysis of metabolism in apicomplexan parasites Toxoplasma gondii and Plasmodium falciparum

Related publications (29)

Live-cell imaging powered by computation

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

Nature Portfolio2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

A Combination Technique for Optimal Control Problems Constrained by Random PDEs

Fabio Nobile, Tommaso Vanzan

We present a combination technique based on mixed differences of both spatial approximations and quadrature formulae for the stochastic variables to solve efficiently a class of optimal control problems (OCPs) constrained by random partial differential equ ...

2024

Orchestrating chromosome conformation capture analysis with Bioconductor

Cyril Matthey-Doret

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Seeking the new, learning from the unexpected: Computational models of surprise and novelty in the brain

Alireza Modirshanechi

Human babies have a natural desire to interact with new toys and objects, through which they learn how the world around them works, e.g., that glass shatters when dropped, but a rubber ball does not. When their predictions are proven incorrect, such as whe ...

EPFL2024

Hausdorff dimension of fermions on a random lattice

Mattia Guerino Varrone

Geometric properties of lattice quantum gravity in two dimensions are studied numerically via Monte Carlo on Euclidean Dynamical Triangulations. A new computational method is proposed to simulate gravity coupled with fermions, which allows the study of int ...

Elsevier2024

The role of computational methods in cardiovascular medicine: a narrative review

Alfio Quarteroni, Luca Dede', Christian Vergara, Stefano Pagani

Background and Objective: Computational models of the cardiovascular system allow for a detailed and quantitative investigation of both physiological and pathological conditions, thanks to their ability to combine clinical-possibly patient-specific-data wi ...

Ame Publishing Company2024

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

Butterfly effects in perceptual development: A review of the 'adaptive initial degradation' hypothesis

Lukas Vogelsang

Human perceptual development evolves in a stereotyped fashion, with initially limited perceptual capabilities maturing over the months or years following the commencement of sensory experience into robust proficiencies. This review focuses on the functiona ...

Academic Press Inc Elsevier Science2024

Thermal conductivity of Li 3 PS 4 solid electrolytes with ab initio accuracy

Michele Ceriotti, Federico Grasselli, Davide Tisi, Lorenzo Gigli

The vast amount of computational studies on electrical conduction in solid-state electrolytes is not mirrored by comparable efforts addressing thermal conduction, which has been scarcely investigated despite its relevance to thermal management and (over)he ...

Amer Physical Soc2024

Hardware-Software co-design Methodologies for Edge AI Optimization

Flavio Ponzina

ML-based edge devices may face memory and computational errors that affect applications' reliability and performance. These errors can be the result of particular working conditions (e.g., radiation areas in physical experiments or avionics) or could be th ...

EPFL2023

Molecular reconstruction and simulation of the Neuron-Glia-Vasculature system

Polina Shichkova

The outstanding information processing capacity of the brain relies on numerous molecular mechanisms. It is an extremely energy-expensive function, which involves specialization and collaboration of different cell types. A common framework to study the com ...

EPFL2023

PROBING INTRACELLULAR ELASTICITY WITH MINIMAL-HESSIAN REGISTRATION

Michaël Unser

We propose an image-based elastography method to measure the heterogeneous stiffness inside a cell and its nucleus. It uses a widely accessible setup consisting of plate compression imaged with fluorescence microscopy. Our framework recovers a spatial map ...

IEEE2023

Fast in vivo assay of creatine kinase activity in the human brain by P-31 magnetic resonance fingerprinting

Lijing Xin, Mark Stephan Widmaier, Songi Lim, Daniel Wenz

A new and efficient magnetisation transfer P-31 magnetic resonance fingerprinting (MT-P-31-MRF) approach is introduced to measure the creatine kinase metabolic rate kCK

{k}_{\mathrm{CK}}

between phosphocreatine (PCr) and adenosine triphosphate (ATP) i ...

WILEY2023

3DHumanGAN: 3D-Aware Human Image Generation with 3D Pose Mapping

Zhuoqian Yang

We present 3DHumanGAN, a 3D-aware generative adversarial network that synthesizes photo-like images of fullbody humans with consistent appearances under different view-angles and body-poses. To tackle the representational and computational challenges in sy ...

Ieee Computer Soc2023

From Automated Bootstrapping to Collaborative Editing: A Framework for 4D City Reconstruction

Rémi Guillaume Petitpierre, Paul Robert Guhennec, Beatrice Vaienti, Didier Louis Dupertuis

We propose a framework for the construction of 4D scientific models for cities of the past. It leverages both the use of computational methods for bootstrapping, and a collaborative interface for visualisation and edition. This permits to continuously enri ...

Zenodo2023

Different responses of mice and rats hippocampus CA1 pyramidal neurons to in vitro and in vivo-like inputs

Ying Shi, Armando Romani, Maurizio Ferdinando Pezzoli

The fundamental role of any neuron within a network is to transform complex spatiotemporal synaptic input patterns into individual output spikes. These spikes, in turn, act as inputs for other neurons in the network. Neurons must execute this function acro ...

2023

Robust optimization of control parameters for WEC arrays using stochastic methods

Tommaso Vanzan

This work presents a new computational optimization framework for the robust control of parks of Wave Energy Converters (WEC) in irregular waves. The power of WEC parks is maximized with respect to the individual control damping and stiffness coefficients ...

Journal of Computational Physics2023

Encoding and Decoding Narratives: Datafication and Alternative Access Models for Audiovisual Archives

Yuchen Yang

Situated in the intersection of audiovisual archives, computational methods, and immersive interactions, this work probes the increasingly important accessibility issues from a two-fold approach. Firstly, the work proposes an ontological data model to hand ...

ACM2023

Modeling high-entropy transition metal alloys with alchemical compression

Michele Ceriotti, Sandip De, Guillaume André Jean Fraux, Nataliya Lopanitsyna

Alloys composed of several elements in roughly equimolar composition, often referred to as high-entropy alloys, have long been of interest for their thermodynamics and peculiar mechanical properties, and more recently for their potential application in cat ...

AMER PHYSICAL SOC2023