NEMo: An Evolutionary Model with Modularity for PPI Networks

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Host-Pathogen Interactions Through the Genomic Lens

Zhi Ming Xu

Hosts and pathogens are involved in a long-standing evolutionary arms race characterized by successive rounds of evolution. Specifically, while hosts evolve resistance against infections, pathogens adapt to re-establish virulence. Since the signatures of t ...

EPFL2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Genetic features and genomic targets of human KRAB-zinc finger proteins

Didier Trono, Jacques Fellay, Priscilla Turelli, Christian Axel Wandall Thorball, Sandra Eloise Kjeldsen, Evaristo Jose Planet Letschert, Julien Léonard Duc, Cyril David Son-Tuyên Pulver, Romain Forey, Bara Khubieh

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

2023

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Opinion Formation over Adaptive Networks

Virginia Bordignon

An adaptive network consists of multiple communicating agents, equipped with sensing and learning abilities that allow them to extract meaningful information from measurements. The objective of the network is to solve a global inference problem in a decent ...

EPFL2022

Applicability of the landscape evolution model in the absence of rills

David Andrew Barry, Andrea Rinaldo, Paolo Perona, Seifeddine Jomaa, Mohsen Cheraghi, Andrea Cimatoribus

Despite numerous applications of physically-based models for incised landscapes, their applicability for overland flow on unchanneled surfaces is not known. This work challenges a widely used landscape evolution model for the case of non-uniform rainfall a ...

2022

Investigating cognitive ability using action-based models of structural brain networks

Enrico Amico

Recent developments in network neuroscience have highlighted the importance of developing techniques for analysing and modelling brain networks. A particularly powerful approach for studying complex neural systems is to formulate generative models that use ...

OXFORD UNIV PRESS2022

The kinectome: A comprehensive kinematic map of human motion in health and disease

Enrico Amico, Antonella Romano, Emahnuel Troisi Lopez

Human voluntary movement stems from the coordinated activations in space and time of many musculoskeletal segments. However, the current methodological approaches to study human movement are still limited to the evaluation of the synergies among a few body ...

WILEY2022

The influence of human genetic variation on Epstein–Barr virus sequence diversity

Jacques Fellay, Olivier Noël Marie Naret, Christian Hammer, Dylan Lawless, Sina Rüeger

Epstein–Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imp ...

Nature Research2021

True scale-free networks hidden by finite size effects

Andrea Rinaldo, Samir Suweis, Amos Maritan

We analyze about 200 naturally occurring networks with distinct dynamical origins to formally test whether the commonly assumed hypothesis of an underlying scale-free structure is generally viable. This has recently been questioned on the basis of statisti ...

National Academy of Sciences2021

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