Publications associées à About the need to make computational models of biological macromolecules available and discoverable

Publications associées (10)

lifex-fiber: an open tool for myofibers generation in cardiac computational models

Background: Modeling the whole cardiac function involves the solution of several complex multi-physics and multi-scale models that are highly computationally demanding, which call for simpler yet accurate, high-performance computational tools. Despite the ...

BMC2023

Modernizing the NEURON Simulator for Sustainability, Portability, and Performance

Nicolas Pierre Jean Cornu, Alexandru Savulescu, Oliver James Lupton, Felix Schürmann, James Gonzalo King, Pramod Shivaji Kumbhar, Fernando Joaquim Leite Pereira, Omar Awile, Ioannis Magkanaris

The need for reproducible, credible, multiscale biological modeling has led to the development of standardized simulation platforms, such as the widely-used NEURON environment for computational neuroscience. Developing and maintaining NEURON over several d ...

2022

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples

Loïc Dayon

Background: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinica ...

ELSEVIER SCI LTD2022

Editorial Overview: Mathematical modeling: It's a matter of scale

Vassily Hatzimanikatis

ELSEVIER2021

A New Lighting on Analytical Discrete Sensitivities in the Context of IsoGeometric Shape Optimization

Thibaut Hirschler

Isogeometric shape optimization has been now studied for over a decade. This contribution aims at compiling the key ingredients within this promising framework, with a particular attention to sensitivity analysis. Based on all the researches related to iso ...

2021

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

Jaume Bonet Martinez

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict ...

OXFORD UNIV PRESS2020

Spatiotemporal Maps of Proprioceptive Inputs to the Cervical Spinal Cord During Three-Dimensional Reaching and Grasping

Auke Ijspeert, Marco Capogrosso, Nathan Antoine Greiner, Shravan Tata Ramalingasetty, Pierre Charles Marie Kibleur

Proprioceptive feedback is a critical component of voluntary movement planning and execution. Neuroprosthetic technologies aiming at restoring movement must interact with it to restore accurate motor control. Optimization and design of such technologies de ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2020

Optimal Stimulation Protocol in a Bistable Synaptic Consolidation Model

Wulfram Gerstner, Chiara Gastaldi, Samuel Pavio Muscinelli

Synaptic changes induced by neural activity need to be consolidated to maintain memory over a timescale of hours. In experiments, synaptic consolidation can be induced by repeating a stimulation protocol several times and the effectiveness of consolidation ...

2019

How single neuron properties shape chaotic dynamics and signal transmission in random neural networks

Wulfram Gerstner, Tilo Schwalger, Samuel Pavio Muscinelli

While most models of randomly connected neural networks assume single-neuron models with simple dynamics, neurons in the brain exhibit complex intrinsic dynamics over multiple timescales. We analyze how the dynamical properties of single neurons and recurr ...

2019

Integrating computational methods to retrofit enzymes to synthetic pathways

Ursula Röthlisberger, Vassily Hatzimanikatis, Ivano Tavernelli, Marilisa Neri, Elizabeth Claire Brunk

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

Wiley-Blackwell2012