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Almost all viruses, regardless of their genomic material, produce defective viral genomes (DVG) as an unavoidable byproduct of their error-prone replication. Defective interfering (DI) elements are a subgroup of DVGs that have been shown to…
We analyze 14,651 HIV1 reverse transcriptase (HIV RT) sequences from the Stanford HIV Drug Resistance Database labeled with treatment regimen in order to study the evolution this enzyme under drug selection in the clinic. Our goal is to…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
The aetiology of polygenic obesity is multifactorial, which indicates that life-style and environmental factors may influence multiples genes to aggravate this disorder. Several low-risk single nucleotide polymorphisms (SNPs) have been…
Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53…
A Constraint Satisfaction Problem (CSP) is a framework used for modeling and solving constrained problems. Tree-search algorithms like backtracking try to construct a solution to a CSP by selecting the variables of the problem one after…
In this review, we focus on the kinesin-3 family molecular motor protein UNC-104 and its regulatory protein ARL-8. UNC-104, originally identified in Caenorhabditis elegans (C. elegans), has a primary role transporting synaptic vesicle…
Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human…
Tremendous effort has been given to the development of diagnostic tests, preventive vaccines, and therapeutic medicines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Much of…
We describe the evolution of macromolecules as an information transmission process and apply tools from Shannon information theory to it. This allows us to isolate three independent, competing selective pressures that we term compression,…
We study Sr$_2$(Ba$_2$)VO$_4$ under high pressure by means of the local density approximation + dynamical mean field theory method. While Sr$_2$VO$_4$ is a 1/6-filling three-band system at ambient pressure with a small level splitting…
Vehicle movements, including vehicle cabs and trailers, play a role in disseminating disease in swine production. However, there are many information gaps about vehicle movements patterns that increase the probability of disease…
By deploying myelofibrosis as the disease context, I wish to propose that increased availability of Tmp21 (an NFAT gene target) induces aberrant protein secretion from the ER contributing to pathological consequences, which has not been…
Respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection worldwide, resulting in approximately sixty thousand annual hospitalizations of <5-year-olds in the United States alone and three million annual…
Prion is a misfolded protein found in mammals that causes infectious diseases of the nervous system in humans and animals. Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of…
A feed-forward loop (FFL) is a common gene-regulatory motif in which usually the upstream regulator is a protein, a transcription factor, that regulates the expression of the target protein in two parallel pathways. Here, we study a…
The spike protein (SP) of SARS-CoV-2 is the major molecular target for making diagnostic tests, vaccines, and therapeutic development. We used a combination of transmission electron microscopy (TEM) and surface enhanced Raman microscopy…
The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow collective motions governing the long-time conformational…
Modern high-scoring models of vision in the brain score competition do not stem from Vision Transformers. However, in this paper, we provide evidence against the unexpected trend of Vision Transformers (ViT) being not perceptually aligned…
RNA protein Interactions (RPIs) play an important role in biological systems. Recently, we have enumerated the RPIs at the residue level and have elucidated the minimum structural unit (MSU) in these interactions to be a stretch of five…