Publications associées à Modelling biological systems

Information Theory in Transmembrane Transport

The past decades have seen the advent of information theory in various fields, from quantum physics to cosmology. At an intermediary scale between atomic and cosmological scales are biological systems and in particular the cell, as a constitutive element o ...

EPFL2023

Advancing first principle-based molecular dynamics of biological systems with machine learning

François Louis Mouvet

Molecular dynamics (MD) simulations have emerged as a transformative approach to analyse molecular systems at the atomic level, offering valuable insights into complex biological processes. Many biological phenomena can only accurately be described by inco ...

EPFL2023

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Philippe Abdel Sayed, Corinne Scaletta, Lee Ann Laurent-Applegate, Nathalie Hirt-Burri, Laurent Alexis Clément Vannay, Alexis Laurent

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 degrees C) a ...

MDPI2023

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

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

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 UNIV PRESS2022

Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications

Sebastian Maerkl, Ragunathan Bava Ganesh

Cell-free biology is increasingly utilized for engineering biological systems, incorporating novel functionality, and circumventing many of the complications associated with cells. The central dogma describes the information flow in biology consisting of t ...

FRONTIERS MEDIA SA2022

Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types

Werner Alfons Hilda Van Geit, Anatoly Buchin

Which cell types constitute brain circuits is a fundamental question, but establishing the correspondence across cellular data modalities is challenging. Bio-realistic models allow probing cause-and-effect and linking seemingly disparate modalities. Here, ...

2022

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri

Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...

BMC2021

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

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

Daniel Keller, Andrii Stepaniuk

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

High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

Maxim Norkin, Jörg Hülsken, Paloma Ordonez Moran

Organoids allow the recapitulation of intestinal homeostasis and cancerogenesis in vitro; however, RNA sequencing (RNA-seq)-based methods for drug screens are missing. We develop targeted organoid sequencing (TORNADO-seq), a high-throughput, high-content d ...

2021

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

The emergence and promise of single-cell temporal-omics approaches

Gioele La Manno, Alex Russell Lederer

Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes ...

CURRENT BIOLOGY LTD2020

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

Monobodies as enabling tools for structural and mechanistic biology

Oliver Hantschel

Monobodies, built with the scaffold of the fibronectin type III domain, are among the most well-established synthetic binding proteins. They promote crystallization of challenging molecular systems. They have strong tendency to bind to functional sites and ...

CURRENT BIOLOGY LTD2020

Algorithms and flowchart for the design of synthetic biochemical networks

Homa Mohammadi Peyhani

New drugs are needed to assure effective therapies for previously untreated diseases, emerging diseases, and personalized medicine, but the process of drug development is complex, costly, and time-consuming. This is especially problematic considering that ...

EPFL2020

Inexpensive modeling of quantum dynamics using path integral generalized Langevin equation thermostats

Michele Ceriotti, David Mark Wilkins, Venkat Kapil, Jinggang Lan

The properties of molecules and materials containing light nuclei are affected by their quantum mechanical nature. Accurate modeling of these quantum nuclear effects requires computationally demanding path integral techniques. Considerable success has been ...

2020

Parallel and Scalable Bioinformatics

Stuart Anthony Byma

The field of genomics is likely to become the largest producer of data as a consequence of the large-scale application of next-generation sequencing technology for biological research and personalized medical treatments. The raw sequence data produced by t ...

EPFL2020

Neuronal morphologies: the shapes of thoughts

Lida Kanari

The mammalian brain, one of the most fascinating systems in nature, is a complex biological structure that has kept scientists busy for over a century. Many of the brain's mysteries have been unraveled due to the enormous efforts of the scientific communit ...

EPFL2018

Scanning Probe Microscopy Characterization of Organic Self-Assembled Monolayers

Evangelia-Nefeli Athanasopoulou

As technology advances, surface coatings become more and more important to assure materials performances. In recent years, molecular coatings have found larger acceptance and uses. Among them, self-assembled monolayers (SAMs) are attractive because they ar ...

EPFL2018

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Duccio Malinverni

Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly o ...

EPFL2018