Related papers: Group A Rotavirus NSP4 is Under Negative Selective…
The importance of understanding SARS-CoV-2 evolution cannot be overemphasized. Recent studies confirm that natural selection is the dominating mechanism of SARS-CoV-2 evolution, which favors mutations that strengthen viral infectivity. We…
We study the problem of nonparametric regression when the regressor is endogenous, which is an important nonparametric instrumental variables (NPIV) regression in econometrics and a difficult ill-posed inverse problem with unknown operator…
Single nucleotide polymorphisms (SNPs) are variations at specific locations in DNA. Sequence responsible for marking genes associated with diseases or tracking inherited diseases within The family. These variations in the Rb1 gene can cause…
Cancer is one of the leading causes of human death. Many efforts have made to understand its mechanism and have further identified many proteins and DNA sequence variations as suspected targets for therapy. However, drugs targeting these…
The SARS-CoV-2 RNA pseudoknot is a promising target for antiviral intervention, as it regulates the efficiency of $-$1 programmed ribosomal frameshifting ($-$1 PRF), a mechanism that is essential for viral protein synthesis. The pseudoknot…
Background: Two strains of the endoparasitoid Cotesia typhae present a differential parasitism success on the host, Sesamia nonagrioides. One is virulent on both permissive and resistant host populations, and the other only on the…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the…
Background: Creeping bentgrass (Agrostis soionifera) is a perennial grass of Gramineae, belonging to cold season turfgrass, but has poor disease resistance. Up to now, little is known about the induced systemic resistance (ISR) mechanism,…
In this paper, we present the empirical investigation results on the neuroendocrine system by bipartite graphs. This neuroendocrine network model can describe the structural characteristic of neuroendocrine system. The act degree…
HIV virus replication is a time-related process that includes several stages. Focusing on the core steps, RNA polymerase II transcripts in an early stage pre-mRNA containing regulator proteins (i.e nef,tat,rev,vif,vpr,vpu), which are…
Intrapatient HIV-1 evolution is dominated by selection on the protein level in the arms race with the adaptive immune system. When cytotoxic CD8+ T-cells or neutralizing antibodies target a new epitope, the virus often escapes via…
Respondent-driven sampling (RDS) is an approach to sampling design and analysis which utilizes the networks of social relationships that connect members of the target population, using chain-referral methods to facilitate sampling. RDS…
Deep neural networks such as AlphaFold and RoseTTAFold predict remarkably accurate structures of proteins compared to other algorithmic approaches. It is known that biologically small perturbations in the protein sequence do not lead to…
Reinforcement learning from verifiable rewards (RLVR) produces strong reasoning models, yet they can fail catastrophically when the conditioning context is fallible (e.g., corrupted chain-of-thought, misleading partial solutions, or mild…
Reinforcement learning with verifiable rewards (RLVR) has become a highly effective method for improving the reasoning abilities of Large Language Models (LLMs). Recent research shows that Negative Sample Reinforcement (NSR) -- which…
Kidney stones are a common and debilitating health issue, and genetic factors play a crucial role in determining susceptibility. While Genome-Wide Association Studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs)…
A convolutional neural network strongly robust to adversarial perturbations at reasonable computational and performance cost has not yet been demonstrated. The primate visual ventral stream seems to be robust to small perturbations in…
In this paper, we present NSGA-II-SVM (Non-dominated Sorting Genetic Algorithm with Support Vector Machine Guidance), a novel learnable evolutionary and search-based testing algorithm that leverages Support Vector Machine (SVM)…