相关论文: Revisiting Waiting Times in DNA evolution

In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…

Motivated by recent single molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of N particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target…

We consider a multi-type Moran model (in continuous time) with selection and type-dependent mutation. This paper is concerned with the evolution of genealogical information forward in time. For this purpose we define and analytically…

We study the eigenvalue distributions for sums of independent rank-one $k$-fold tensor products of large $n$-dimensional vectors. Previous results in the literature assume that $k=o(n)$ and show that the eigenvalue distributions converge to…

Motivation:Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We demonstrate the usefulness of (nonmetric) multidimensional scaling (MDS) method in analyzing a…

Given a non-deterministic finite automaton (NFA) A with m states, and a natural number n (presented in unary), the #NFA problem asks to determine the size of the set L(A_n) of words of length n accepted by A. While the corresponding…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…

Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection…

Clustering is a fundamental problem in unsupervised machine learning with many applications in data analysis. Popular clustering algorithms such as Lloyd's algorithm and $k$-means++ can take $\Omega(ndk)$ time when clustering $n$ points in…

In Soda'06, Chaudhuri, Chen, Mihaescu and Rao study algorithmic properties of the tandem duplication - random loss model of genome rearrangement, well-known in evolutionary biology. In their model, the cost of one step of duplication-loss…

Probabilistic distributions over spanning trees in directed graphs are a fundamental model of dependency structure in natural language processing, syntactic dependency trees. In NLP, dependency trees often have an additional root…

PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We…

Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…

A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…

Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…

Language evolves over time in many ways relevant to natural language processing tasks. For example, recent occurrences of tokens 'BERT' and 'ELMO' in publications refer to neural network architectures rather than persons. This type of…

Motivated by experiments in which single-stranded DNA with a short hairpin loop at one end undergoes unforced diffusion through a narrow pore, we study the first passage times for a particle, executing one-dimensional brownian motion in an…

This work proposes a markovian memoryless model for the DNA that simplifies enormously the complexity of it. We encode nucleotide sequences into symbolic sequences, called words, from which we establish meaningful length of words and group…

A fundamental characteristic of natural language is the high rate at which speakers produce novel expressions. Because of this novelty, a heavy-tail of rare events accounts for a significant amount of the total probability mass of…