Publications associées à Metabolic pathway and distribution of superparamagnetic iron oxide nanoparticles: in vivo study

Predicting the long-term collective behaviour of fish pairs with deep learning

Francesco Mondada, Alexandre Massoud Alahi, Vaios Papaspyros

Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social in ...

2024

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

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Enabling Stroke Theranostics with Hyperpolarized Magnetic Resonance

Thanh Phong Kevin Lê

The severe social and economic burden of stroke is a strong motivation for the exploration of innovative medical approaches. In this context, magnetic resonance (MR) of hyperpolarized (HP) molecular agents via dissolution dynamic nuclear polarization (dDNP ...

EPFL2023

Modulation of the nanoscale motion rate of Candida albicans by X-rays

Sandor Kasas, María Inés Villalba

IntroductionPatients undergoing cancer treatment by radiation therapy commonly develop Candida albicans infections (candidiasis). Such infections are generally treated by antifungals that unfortunately also induce numerous secondary effects in the patient. ...

Frontiers Media SA2023

Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex

Werner Alfons Hilda Van Geit, Anatoly Buchin

The brain consists of many cell classes yet in vivo electrophysiology recordings are typically unable to identify and monitor their activity in the behaving animal. Here, we employed a systematic approach to link cellular, multi-modal in vitro properties f ...

Nature Research2023

Multi-animal pose estimation, identification and tracking with DeepLabCut

Tanmay Nath, Mackenzie Mathis, Alexander Mathis, Shaokai Ye, Jessy Lauer, Steffen Schneider

Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that ...

NATURE PORTFOLIO2022

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Victor Luc Etienne Viterbo, Anastasia Sveshnikova

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

In vivo and ex vivo range of motion in the fire salamander Salamandra salamandra

Joint range of motion (RoM) analyses are fundamental to our understanding of how an animal moves throughout its ecosystem. Recent technological advances allow for more detailed quantification of this RoM (e.g. including interaction of degrees of freedom) b ...

2022

Radical-free hyperpolarized MRI using endogenously occurring pyruvate analogues and UV-induced nonpersistent radicals

Rolf Gruetter, Josefina Adriana Maria Bastiaansen, Lionel Pierre Arn, Andrea Capozzi, Hikari Ananda Infinity Yoshihara, Claudia Christina Zanella, Alice Radaelli

It was recently demonstrated that nonpersistent radicals can be generated in frozen solutions of metabolites such as pyruvate by irradiation with UV light, enabling radical-free dissolution dynamic nuclear polarization. Although pyruvate is endogenous, the ...

WILEY2021

Methods to Enhance Nuclear Magnetic Resonance Sensitivity at High Magnetic Field

Claudia Christina Zanella

MR is a well-established technique routinely used in preclinical and clinical studies. This thesis focussed on the improvement of sensitivity of different methods in MR. Hyperpolarized 129Xe gas is used for studying pulmonary disease or cerebral perfusion ...

EPFL2021

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

OXFORD UNIV PRESS2021

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

HP agents and biochemical interactions

Hikari Ananda Infinity Yoshihara

The intense but transient increase in nuclear magnetic resonance signal provided by dynamic nuclear polarization (DNP) has enabled a range of new applications, including rapid, minimally-invasive metabolic imaging at the second timescale. This chapter prov ...

Academic Press2021

Mechanistic studies of DNP and applications of hyperpolarized probes to study renal physiology and metabolism

Alice Radaelli

Dissolution dynamic nuclear polarization (dDNP) is a powerful technique that enhances the magnetic resonance signal of nuclear spins by several orders of magnitude. DNP relies on the principle of cross-relaxation by electron spins driven out of equilibrium ...

EPFL2021

A hybrid erbium(III)-bacteriochlorin near-infrared probe for multiplexed biomedical imaging

Jean-Claude Bünzli, Zhiyong Liu, Fan Zhang, Ting Wang

Spectrally distinct fluorophores are desired for multiplexed bioimaging. In particular, monitoring biological processes in living mammals needs fluorophores that operate in the 'tissue-transparent' near-infrared (NIR) window, that is, between 700 and 1,700 ...

NATURE RESEARCH2021

Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks

Robin Alexander Denhardt-Eriksson

Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour. The importance of modelling in systems biology becomes even more evident when tackling complex, large systems. Approaches that rely on ...

EPFL2021

Development of novel tools for imaging of metabolic fluxes in vivo

Tamara Maric

Bioluminescent imaging is a powerful technique that enables imaging in living organisms with high sensitivity, low background signal, low cost and without the need for radioactivity. The emitted photons are produced in the oxidation reaction of luciferin c ...

EPFL2020

Modeling metabolic and signaling pathways in cancer cells

Maria Masid Barcon

Cancer is a leading cause of death in the world, and the mechanisms that underlie this disease are still not completely understood. As cancer develops and progresses, cells undergo a diversity of mutations that sustain their rapid proliferation and the eva ...

EPFL2020