NEMo: An Evolutionary Model with Modularity for PPI Networks

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Designing optimal soft modular robots is difficult, due to non-trivial interactions between morphology and controller. Evolutionary algorithms (EAs), combined with physical simulators, represent a valid tool to overcome this issue. In this work, we investi ...

Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have docume ...

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 ...

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, a ...

The type VI secretion system (T6SS) is a nanomachine used by many bacteria to drive a toxin-laden needle into other bacterial cells. Although the potential to influence bacterial competition is clear, the fitness impacts of wielding a T6SS are not well und ...

By combining well-established population genetic theory with high-throughput sequencing data from natural populations, major strides have recently been made in understanding how, why, and when vertebrate populations evolve crypsis. Here, we focus on backgr ...

We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g., protein interaction networks involving complex formation and dissociation reactions. We propose the use of model reduction strategies t ...

The regulation of several processes inside and outside the cell depends on the action of a particular class of enzymes, called allosteric. In allosteric macromolecules, binding a ligand at one site affects the binding activity at a distal functional site, ...

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...

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 ...

Comparative genomics is a field of research that compares genomes of different organisms to identify common patterns. It is a powerful method used to identify the genetic diseases that cause mutations. Multiple Sequence Alignment (MSA) is an intermediate s ...

NEMo: An Evolutionary Model with Modularity for PPI Networks

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Host-Pathogen Interactions Through the Genomic Lens

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

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

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

Applicability of the landscape evolution model in the absence of rills

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

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

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

True scale-free networks hidden by finite size effects

Seeking Quality Diversity in Evolutionary Co-design of Morphology and Control of Soft Tensegrity Modular Robots

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

MPGM: Scalable and Accurate Multiple Network Alignment

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

The evolution of the type VI secretion system as a disintegration weapon

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks

Mechanics and co-evolution of allosteric materials and proteins

Optimization methods and objective functions for analysis of metabolic network models

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

An Interactive Gameplay to Crowdsource Multiple Sequence Alignment of Genome Sequences: Genenigma