Publications by David Gfeller | EPFL Graph Search

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

Julien Racle, David Gfeller, Philippe Guillaume Coune, Florence Pojer, Marta Andreia Da Silva Perez, George Coukos, Kelvin Ka Ching Lau, Amédé Noredine Larabi, Alexandre Harari

CD4+T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward ...

CELL PRESS2023

Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer

David Gfeller, Georg Alexander Rockinger, Pedro Romero, Amélie Cachot, Hatice Altug, Margaux Saillard, Xiaokang Li, George Coukos, Yen-Cheng Liu, Alexandre Harari, Alexander Mathis

CD4 T cells have been implicated in cancer immunity for their helper functions. Moreover, their direct cytotoxic potential has been shown in some patients with cancer. Here, by mining single-cell RNA-seq datasets, we identified CD4 T cell clusters displayi ...

2021

Tumor-Specific Cytolytic Cd4 T Cells Mediate Protective Immunity Against Human Cancer

David Gfeller, Pedro Romero, Amélie Cachot, Hatice Altug, Margaux Saillard, Xiaokang Li, George Coukos, Yen-Cheng Liu, Alexandre Harari, Alexander Mathis

BMJ PUBLISHING GROUP2020

Spectral coarse graining and synchronization in oscillator networks

Paolo De Los Rios, David Gfeller

Coarse graining techniques offer a promising alternative to large-scale simulations of complex dynamical systems, as long as the coarse-grained system is truly representative of the initial one. Here, we investigate how the dynamical properties of oscillat ...

American Physical Society2008

Spectral coarse graining of complex networks

Paolo De Los Rios, David Gfeller

Reducing the complexity of large systems described as complex networks is key to understanding them and a crucial issue is to know which properties of the initial system are preserved in the reduced one. Here we use random walks to design a coarse graining ...

American Physical Society2007

Uncovering the topology of configuration space networks

David Sébastien Morton de Lachapelle, Paolo De Los Rios, David Gfeller

The configuration space network (CSN) of a dynamical system is an effective approach to represent the ensemble of configurations sampled during a simulation and their dynamic connectivity. To elucidate the connection between the CSN topology and the underl ...

2007

Complex network analysis of free-energy landscapes

Paolo De Los Rios, David Gfeller

The kinetics of biomolecular isomerization processes, such as protein folding, is governed by a free-energy surface of high dimensionality and complexity. As an alternative to projections into one or two dimensions, the free-energy surface can be mapped in ...

National Academy of Sciences2007

Simplifying complex networks : from a clustering to a coarse graining strategy

David Gfeller

The framework of complex networks has been shown to describe adequately a wide class of complex systems made up of a large number of interacting units. In this framework, a node is associated to each unit and two nodes are connected by an edge if the two u ...

EPFL2007

Finding instabilities in the community structure of complex networks

Jean-Cédric Chappelier, Paolo De Los Rios, David Gfeller

2005