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The emergence and survival of cooperation is one of the hardest problems still open in science. Several factors such as the existence of punishment, fluctuations in finite systems, repeated interactions and the formation of prestige may all…
The emerging field of immunometabolism has underscored the central role of metabolic pathways in orchestrating immune cell function. Far from being passive background processes, metabolic activities actively regulate key immune responses.…
Cascading failures and epidemic dynamics, as two successful application realms of network science, are usually investigated separately. How do they affect each other is still one open, interesting problem. In this letter, we couple both…
Human skeletons and RGB sequences are both widely-adopted input modalities for human action recognition. However, skeletons lack appearance features and color data suffer large amount of irrelevant depiction. To address this, we introduce…
The goal of this study is to develop a computational model of the progression of changes in mitochondrial phenotype resulting from infection with pathogenic mycobacteria. This ultimately will enable a large-scale virulence screen of mutant…
During embryonic development, regeneration and homeostasis, cells have to physically integrate into their target tissues, where they ultimately execute their function. Despite a significant body of research on how mechanical forces instruct…
Collective rhythmic dynamics from neurons is vital for cognitive functions such as memory formation but how neurons self-organize to produce such activity is not well understood. Attractor-based models have been successfully implemented as…
Motivation: With the aim to amplify and make sense of interactions of virus-human proteins in the case of SARS-CoV-2, we performed a structural analysis of the network of protein interactions obtained from the integration of three sources:…
Information dissemination intricately intertwines with the dynamics of infectious diseases in the contemporary interconnected world. Recognizing the critical role of public awareness, individual vaccination choices appear to be an essential…
T lymphocytes (T cells) orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors (TCRs) on their surface to short peptides (p) derived from foreign proteins, which are…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
Network inference, the task of reconstructing interactions in a complex system from experimental observables, is a central yet extremely challenging problem in systems biology. While much progress has been made in the last two decades,…
The Integration Host Factor (IHF) is a nucleoid-associated protein critical for both DNA compaction and biofilm stability. While its role in DNA packaging within the cell is well understood, its structural role in scaffolding biofilms is…
Semantic segmentation of electron microscopy (EM) is an essential step to efficiently obtain reliable morphological statistics. Despite the great success achieved using deep convolutional neural networks (CNNs), they still produce coarse…
It is generally difficult to predict the positions of mutations in genomic DNA at the nucleotide level. Retroviral DNA insertion is one mode of mutation, resulting in host infections that are difficult to treat. This mutation process…
The symmetrical network theory is a framework for understanding the immune system, that dates back to the mid 1970s. The symmetrical network theory is based on symmetrical stimulatory, inhibitory and killing interactions between clones that…
Epidemic spreading on complex networks depends on the topological structure as well as on the dynamical properties of the infection itself. Generally speaking, highly connected individuals play the role of hubs and are crucial to channel…
We study numerically how the structures of distinct networks influence the epidemic dynamics in contact process. We first find that the variability difference between homogeneous and heterogeneous networks is very narrow, although the…
Extreme enrichment of the human immunodeficiency virus (HIV-1) RNA genome for the purine A parallels the mild purine-loading of the RNAs of most organisms. This should militate against loop-loop "kissing" interactions between the structured…
Inclusion of high throughput technologies in the field of biology has generated massive amounts of biological data in the recent years. Now, transforming these huge volumes of data into knowledge is the primary challenge in computational…