Related papers: Inverted Repeats in Viral Genomes
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been…
A primary goal of computational phenotype research is to conduct medical diagnosis. In hospital, physicians rely on massive clinical data to make diagnosis decisions, among which laboratory tests are one of the most important resources.…
Cardiac development is complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory…
In the first part of the paper, we study the inversion statistic of random permutations under the family $(\mathbb{P}_\theta^{(n)})_{\theta \ge 0}$ of Ewens sampling distributions on $S_n$. We obtain a rather simple exact formula for the…
This work proposes a statistical model for crossover trials with multiple skewed responses measured in each period. A 3 $\times$ 3 crossover trial data where different drug doses were administered to subjects with a history of seasonal…
Computer malware and biological pathogens often use similar mechanisms of infections. For this reason, it has been suggested to model malware spread using epidemiological models developed to characterize the spread of biological pathogens.…
Neural networks are known to be vulnerable to adversarial attacks, which are small, imperceptible perturbations that can significantly alter the network's output. Conversely, there may exist large, meaningful perturbations that do not…
Electronic health records contain valuable information for monitoring patients' health trajectories over time. Disease progression models have been developed to understand the underlying patterns and dynamics of diseases using these data as…
The inverse problem is studied in multi-body systems with nonlinear dynamics representing, e.g., phase-locked wave systems, standard multimode and random lasers. Using a general model for four-body interacting complex-valued variables we…
The collection of immunoglobulin genes in an individual's germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of…
Much of neuroscience aims at reverse engineering the brain, but we only record a small number of neurons at a time. We do not currently know if reverse engineering the brain requires us to simultaneously record most neurons or if multiple…
The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain…
In computational inverse problems, it is common that a detailed and accurate forward model is approximated by a computationally less challenging substitute. The model reduction may be necessary to meet constraints in computing time when…
Inferring concerted changes among biological traits along an evolutionary history remains an important yet challenging problem. Besides adjusting for spurious correlation induced from the shared history, the task also requires sufficient…
Recent advances in genotyping technology have delivered a wealth of genetic data, which is rapidly advancing our understanding of the underlying genetic architecture of complex diseases. Mendelian Randomization (MR) leverages such genetic…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation…
Iterative learning to infer approaches have become popular solvers for inverse problems. However, their memory requirements during training grow linearly with model depth, limiting in practice model expressiveness. In this work, we propose…
Motivated by recent studies of large Mallows$(q)$ permutations, we propose a class of random permutations of $\mathbb{N}_{+}$ and of $\mathbb{Z}$, called regenerative permutations. Many previous results of the limiting Mallows$(q)$…
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…