相关论文: Waiting for regulatory sequences to appear
By determining which were the most common English words and phrases since the beginning of the 16th century, we obtain a unique large-scale view of the evolution of written text. We find that the most common words and phrases in any given…
We investigate a set of stochastic models of biodiversity, population genetics, language evolution and opinion dynamics on a network within a common framework. Each node has a state, 0 < x_i < 1, with interactions specified by strengths…
Analysing statistical properties of the normal forms of random braids, we observe that, except for an initial and a final region whose lengths are uniformly bounded (that is, the bound is independent of the length of the braid), the…
Understanding how words change their meanings over time is key to models of language and cultural evolution, but historical data on meaning is scarce, making theories hard to develop and test. Word embeddings show promise as a diachronic…
In this paper we consider the normalized lengths of the factors of some factorizations of random words. First, for the \emph{Lyndon factorization} of finite random words with $n$ independent letters drawn from a finite or infinite totally…
We developed a method for estimating the positional distribution of transcription fac-tor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs; OCT4, SOX2, NANOG, HNF1A,…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
Individuals differ in the time it takes to produce words when naming a picture. However, it is unknown whether this inter-individual variability emerges in earlier stages of word production (e.g., lexical selection) or later stages (e.g.,…
Let $W^{(n)}$ be the $n$-letter word obtained by repeating a fixed word $W$, and let $R_n$ be a random $n$-letter word over the same alphabet. We show several results about the length of the longest common subsequence (LCS) between…
Statistical studies of languages have focused on the rank-frequency distribution of words. Instead, we introduce here a measure of how word ranks change in time and call this distribution \emph{rank diversity}. We calculate this diversity…
The site frequency spectrum describes variation among a set of n DNA sequences. Its i'th entry (i=1,2,...,n-1) is the number of nucleotide sites at which the mutant allele is present in i copies. Under selective neutrality, random mating,…
Surprisal theory posits that the processing difficulty of a word is determined by its predictability in context, offering a potential link between human sentence processing and next-word predictions from language models. While language…
Gene expression in individual cells is highly variable and sporadic, often resulting in the synthesis of mRNAs and proteins in bursts. Bursting in gene expression is known to impact cell-fate in diverse systems ranging from latency in HIV-1…
Languages emerge and change over time at the population level though interactions between individual speakers. It is, however, hard to directly observe how a single speaker's linguistic innovation precipitates a population-wide change in…
Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise…
A fundamental concern in linguistics has been to understand how languages change, such as in relation to word order. Since the order of words in a sentence (i.e. the relative placement of Subject, Object, and Verb) is readily identifiable…
Gene transcription is a stochastic process that involves thousands of reactions. The first set of these reactions, which happen near a gene promoter, are considered to be the most important in the context of stochastic noise. The most…
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution…
The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the…