Related papers: Inverted Repeats in Viral Genomes
This paper develops an analogy between the cycle structure of, on the one hand, random permutations with cycle lengths restricted to lie in an infinite set $S$ with asymptotic density $\sigma$ and, on the other hand, permutations selected…
We propose distribution-free runs-based control charts for detecting location shifts. Using the fact that given the number of total successes, the outcomes of a sequence of Bernoulli trials are random permutations, we are able to control…
Motivated by applications in mathematical biology concerning randomly alternating motion of micro-organisms, we analyze a generalized integrated telegraph process. The random times between consecutive velocity reversals are…
For a recently derived pairwise model of network epidemics with non-Markovian recovery, we prove that under some mild technical conditions on the distribution of the infectious periods, smaller variance in the recovery time leads to higher…
A common task in experimental sciences is to fit mathematical models to real-world measurements to improve understanding of natural phenomenon (reverse-engineering or inverse modeling). When complex dynamical systems are considered, such as…
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single…
The phenotype of any organism on earth is, in large part, the consequence of interplay between numerous gene products encoded in the genome, and such interplay between gene products affects the evolutionary fate of the genome itself through…
The use of genetic variants as instrumental variables - an approach known as Mendelian randomization - is a popular epidemiological method for estimating the causal effect of an exposure (phenotype, biomarker, risk factor) on a disease or…
Random Boolean networks (RBNs) have been a popular model of genetic regulatory networks for more than four decades. However, most RBN studies have been made with random topologies, while real regulatory networks have been found to be…
In this paper, we analyze the properties of invertible neural networks, which provide a way of solving inverse problems. Our main focus lies on investigating and controlling the Lipschitz constants of the corresponding inverse networks.…
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about…
Structural variation occurs in the genomes of individuals because of the different positions occupied by repetitive genome elements like endogenous retroviruses, or ERVs. The presence or absence of ERVs can be determined by identifying the…
This paper tackles the challenge of detecting unreliable behavior in regression algorithms, which may arise from intrinsic variability (e.g., aleatoric uncertainty) or modeling errors (e.g., model uncertainty). First, we formally introduce…
The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and…
In this paper, we propose and study several inverse problems of identifying/determining unknown coefficients for a class of coupled PDE systems by measuring the average flux data on part of the underlying boundary. In these coupled systems,…
Benchmark rankings are routinely used to justify scientific claims about method quality in gene regulatory network (GRN) inference, yet the stability of these rankings under plausible evaluation protocol choices is rarely examined. We…
We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the…
Regular variation of distributional tails is known to be preserved by various linear transformations of some random structures. An inverse problem for regular variation aims at understanding whether the regular variation of a transformed…
Genomic foundation models trained on DNA sequences have demonstrated remarkable capabilities across diverse biological tasks, from variant effect prediction to genome design. These models are typically trained on massive, publicly sourced…