Related papers: SSCU: an R/Bioconductor package for analyzing sele…
The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…
The R package ecosystem is expanding fast and dependencies among packages in the ecosystem are becoming more complex. In this study, we explored the package dependencies from a new aspect. We applied a new metric named "dependency…
Spiking Neural Networks (SNNs) have received widespread attention due to their unique neuronal dynamics and low-power nature. Previous research empirically shows that SNNs with Poisson coding are more robust than Artificial Neural Networks…
Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise. Here we carry out the first experimental study of SR in…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to…
SDRcausal is a package that implements sufficient dimension reduction methods for causal inference as proposed in Ghosh, Ma, and de Luna (2021). The package implements (augmented) inverse probability weighting and outcome regression…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Optimal subset selection is an important task that has numerous algorithms designed for it and has many application areas. STPGA contains a special genetic algorithm supplemented with a tabu memory property (that keeps track of previously…
Quantum nuclear effects and anharmonicity impact a wide range of functional materials and their properties. One of the most powerful techniques to model these effects is the Stochastic Self-Consistent Harmonic Approximation (SSCHA).…
Computer Science course instructors routinely have to create comprehensive test suites to assess programming assignments. The creation of such test suites is typically not trivial as it involves selecting a limited number of tests from a…
Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However,…
The choice of crossover and mutation strategies plays a crucial role in the searchability, convergence efficiency and precision of genetic algorithms. In this paper, a novel improved genetic algorithm is proposed by improving the crossover…
In this paper, a robust weighted score for unbalanced data (ROWSU) is proposed for selecting the most discriminative feature for high dimensional gene expression binary classification with class-imbalance problem. The method addresses one…
Modern biotechnologies often result in high-dimensional data sets with much more variables than observations (n $\ll$ p). These data sets pose new challenges to statistical analysis: Variable selection becomes one of the most important…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen…
N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering.…
In meta-analysis of diagnostic test accuracy, summary receiver operating characteristic (SROC) is a recommended method to summarize the discriminant capacity of a diagnostic test in the presence of study-specific cutoff values and the area…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…