Publications related to Systems biology

Related publications (28)

Prolamins' 3D structure: A new insight into protein modeling using the language of numbers and shapes

This study combined protein modeling methods to generate the prolamins' fractions as precise as possible. Hence, gliadins, zeins, kafirins, hordeins, secalins, avenins and oryzins were generated based on their characteristics and disulfide mapping. Finding ...

Elsevier Sci Ltd2024

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

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Martin Peter Bircher, Justin Villard

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

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

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Hybrid Quadratic Programming - Pullback Bundle Dynamical Systems Control

Aude Billard, Bernardo Fichera

Dynamical System (DS)-based closed-loop control is a simple and effective way to generate reactive motion policies that well generalize to the robotic workspace, while retaining stability guarantees. Lately the formalism has been expanded in order to handl ...

SPRINGER INTERNATIONAL PUBLISHING AG2023

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

Backtracking Dynamical Cavity Method

Lenka Zdeborová, Freya Behrens, Barbora Hudcová

The cavity method is one of the cornerstones of the statistical physics of disordered systems such as spin glasses and other complex systems. It is able to analytically and asymptotically exactly describe the equilibrium properties of a broad range of mode ...

American Physical Society2023

Investigation of Carboxylic Acid Isosteres and Prodrugs for Inhibition of the Human SIRT5 Lysine Deacylase Enzyme

Alexander Lund Nielsen

Sirtuin 5 (SIRT5) is a protein lysine deacylase enzyme that regulates diverse biology by hydrolyzing epsilon-N-carboxyacyllysine posttranslational modifications in the cell. Inhibition of SIRT5 has been linked to potential treatment of several cancers but ...

Wiley-VCH Verlag GmbH2022

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Vassily Hatzimanikatis, Maria Masid Barcon, Georgios Fengos, Daniel Robert Weilandt, Pierre Guy Rémy Salvy, Zhaleh Hosseini

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

Oxford University Press2022

Bistable-Type Interactions Of Complex Systems In A Fractal Paradigm Of Motion

Maria-Alexandra Paun

In the present paper the "interface" dynamics in the case of two complex systems interaction, assimilated to fractal-type mathematical objects, are analyzed. In such context, fractal bistable-type behaviors as transitions in the scale space are obtained. O ...

UNIV POLITEHNICA BUCHAREST, SCI BULL2022

Bistable-Type Interactions Of Complex Systems In A Fractal Paradigm Of Motion

Maria-Alexandra Paun

In the present paper the "interface" dynamics in the case of two complex systems interaction, assimilated to fractal-type mathematical objects, are analyzed. In such context, fractal bistable-type behaviors as transitions in the scale space are obtained. O ...

UNIV POLITEHNICA BUCHAREST, SCI BULL2022

An integrative multi-omics approach reveals new central nervous system pathway alterations in Alzheimer's disease

Christopher Clark

Background Multiple pathophysiological processes have been described in Alzheimer's disease (AD). Their inter-individual variations, complex interrelations, and relevance for clinical manifestation and disease progression remain poorly understood. We hypot ...

2021

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

Daniel Keller

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

New and improved methods for integrated models of metabolism and gene expression

Pierre Guy Rémy Salvy

The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...

EPFL2021

Molecular physiology of bile acid signaling in health, disease, and aging

Kristina Schoonjans, Alessia Perino, Hadrien Charles Edouard Demagny, Laura Alejandra Velazquez Villegas

Over the last two decades, bile acids (BAs) have become established as important signaling molecules that enable fine-tuned inter-tissue communication from the liver, their site of production, over the intestine, where they are modified by the gut microbio ...

2021

Applying Peptide and Protein Synthesis to Study Post-translational Modifications in Epigenetics and Beyond

Beat Fierz

Epigenetics research focuses on the study of heritable gene regulatory mechanisms that do not involve changes of the DNA sequence. Such mechanisms include post-translational modifications of histone proteins that organize the genome in the nucleus into a n ...

2021

Developing new tools to study and program cell fate at the single-cell level

Marjan Biocanin

Single-cell transcriptomics (scRNA-seq) started a technological revolution in biology by enabling through the plethora of methods to assess a molecular state of the cell on systems level without the strict necessity of the prior knowledge of the cell state ...

EPFL2021