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Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep, goats, mice, humans, chimpanzees, hamsters, cattle, elks, deer, minks, cats, chicken, pigs,…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…
The multidomain protein gelsolin (GSN) is composed of six homologous modules, sequentially named G1 to G6. Single point substitutions in this protein are responsible for AGel amyloidosis, a hereditary disease characterized by progressive…
Sensory prediction (SP) is a fundamental mechanism of perception that supports cognitive development. Atypical SP has been reported across multiple neurodevelopmental disorders (ND), suggesting it may constitute an early cross-syndromic…
Pulmonary embolus (PE) refers to obstruction of pulmonary arteries by blood clots. PE accounts for approximately 100,000 deaths per year in the United States alone. The clinical presentation of PE is often nonspecific, making the diagnosis…
We analyse the impact of the selective pressure for the global optimisation capabilities of steady-state EAs. For the standard bimodal benchmark function \twomax we rigorously prove that using uniform parent selection leads to exponential…
We propose an effective way to create interpretable control agents, by re-purposing the function of a biological neural circuit model, to govern simulated and real world reinforcement learning (RL) test-beds. We model the tap-withdrawal…
Preliminary epidemiologic, phylogenetic and clinical findings suggest that several novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have increased transmissibility and decreased efficacy of several existing…
Transcription factors (TF) play an essential role in the cell as locus- and condition-specific recruiters of transcriptional machinery or chromatin-modifying complexes. However, predicting the in vivo profile of TF occupancy along the…
The wide spread of coronavirus disease 2019 (COVID-19) has declared a global health emergency. As one of the most important targets for antibody and drug developments, Spike RBD-ACE2 interface has received extensive attention. Here, using…
The SARS CoV-2 virus emerged at the end of 2019 and rapidly developed several mutated variants, specifically the Delta and Omicron, which demonstrate higher infectivity and escalating infection cases worldwide. The dominant transmission…
Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2500 coronaviruses and computed >100000 human protein interactions with severe acute respiratory syndrome…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
The heat shock protein 90 (Hsp90) is a molecular chaperone that controls the folding and activation of client proteins using the free energy of ATP hydrolysis. The Hsp90 active site is in its N-terminal domain (NTD). Our goal is to…
The convolutional neural network (CNN) is vulnerable to degraded images with even very small variations (e.g. corrupted and adversarial samples). One of the possible reasons is that CNN pays more attention to the most discriminative…
RNA interference (RNAi) is a mechanism whereby small RNAs (siRNAs) directly control gene expression without assistance from proteins. This mechanism consists of interactions between RNAs and small RNAs both of which may be single or double…
The emerging global infectious COVID-19 coronavirus disease by novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats to global public health and the economy since it was identified in late December…
We present preliminary results that quantify network robustness and fragility of Ewing sarcoma (ES), a rare pediatric bone cancer that often exhibits de novo or acquired drug resistance. By identifying novel proteins or pathways susceptible…
Most non-synonymous mutations are thought to be deleterious because of their effect on protein sequence. These polymorphisms are expected to be removed or kept at low frequency by the action of natural selection, and rare deleterious…
The domestication and subsequent selection by humans to create breeds of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability,…