相关论文: What can be observed in real time PCR and when doe…

Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive…

We propose a one mutation model for cancer with a mutation rate that increases with time. Under rather general hypotheses the number of mutations is necessarily a (non homogeneous) Poisson process with the prescribed mutation rate. We show…

Early diagnosis of treatable diseases is essential for improving healthcare, and many diseases' onsets are predictable from annual lab tests and their temporal trends. We introduce a multi-resolution convolutional neural network for early…

As the first step in an investigation of the origin of genetic information, we study how some species of molecules are preserved over cell generations and play an important role in controlling the growth of a cell. We consider a model…

The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely…

This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…

Many populations, e.g. of cells, bacteria, viruses, or replicating DNA molecules, start small, from a few individuals, and grow large into a noticeable fraction of the environmental carrying capacity $K$. Typically, the elements of the…

New experimental methods make it possible to measure the expression levels of many genes, simultaneously, in snapshots from thousands or even millions of individual cells. Current approaches to analyze these experiments involve clustering…

Detection of extremely rare variant alleles, such as tumour DNA, within a complex mixture of DNA molecules is experimentally challenging due to sequencing errors. Barcoding of target DNA molecules in library construction for next-generation…

DNA labeling is a powerful tool in molecular biology and biotechnology that allows for the visualization, detection, and study of DNA at the molecular level. Under this paradigm, a DNA molecule is being labeled by specific k patterns and is…

Coalescent processes, including mutation, are derived from Moran type population models admitting large offspring numbers. Including mutation in the coalescent process allows for quantifying the turnover of alleles by computing the…

When a defendant's DNA matches a sample found at a crime scene, how compelling is the match? To answer this question, DNA analysts typically use relative frequencies, random-match probabilities or likelihood ratios. They compute these…

In this work, we investigate the population dynamics of tumor cells under therapeutic pressure. Although drug treatment initially induces a reduction in tumor burden, treatment failure frequently occurs over time due to the emergence of…

In this study, we develop consistent estimators for key parameters that govern the dynamics of tumor cell populations when subjected to pharmacological treatments. While these treatments often lead to an initial reduction in the abundance…

In this work we implement the so-called matching time estimators for estimating the entropy rate as well as the entropy production rate for symbolic sequences. These estimators are based on recurrence properties of the system, which have…

DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…

We define data analyses to monitor a change in R, the average number of secondary cases caused by a typical infected individual. The input dataset consists of incident cases partitioned into outbreaks, each initiated from a single index…

In this paper, we develop an explicit formula allowing to compute the first k moments of the random count of a pattern in a multi-states sequence generated by a Markov source. We derive efficient algorithms allowing to deal both with low or…

Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…

Initiation and development of a malignant tumor is a complex phenomenon that has critical stages determining its long time behavior. This phenomenon is mathematically described by means of various models: from simple heuristic models to…