相关论文: Waiting for regulatory sequences to appear
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
In a simple pattern matching problem one has a pattern $w$ and a text $t$, which are words over a finite alphabet $\Sigma$. One may ask whether $w$ occurs in $t$, and if so, where? More generally, we may have a set $P$ of patterns and a set…
We surveyed 113 astronomers and 82 psychologists active in applying for federally funded research on their grant-writing history between January, 2009 and November, 2012. We collected demographic data, effort levels, success rates, and…
While there exist scores of natural languages, each with its unique features and idiosyncrasies, they all share a unifying theme: enabling human communication. We may thus reasonably predict that human cognition shapes how these languages…
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…
Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is…
In a language corpus, the probability that a word occurs $n$ times is often proportional to $1/n^2$. Assigning rank, $s$, to words according to their abundance, $\log s$ vs $\log n$ typically has a slope of minus one. That simple Zipf's law…
Over the past two decades, numerous studies have demonstrated how less predictable (i.e., higher surprisal) words take more time to read. In general, these studies have implicitly assumed the reading process is purely responsive: Readers…
Most languages use the relative order between words to encode meaning relations. Languages differ, however, in what orders they use and how these orders are mapped onto different meanings. We test the hypothesis that, despite these…
The prediction that (due to the limited amount of hydrogen available as fuel in the Sun) the future duration of our favourable terrestrial environment will be short (compared with the present age of the Earth) has been interpreted as…
Large Language Models (LLMs) have achieved unprecedented performance on many complex tasks, being able, for example, to answer questions on almost any topic. However, they struggle with other simple tasks, such as counting the occurrences…
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an…
Sequence organizations are viewed from two points: one is from informational redundancy or informational correlation (IC) and another is from k-mer frequency statistics. Two problems are investigated. The first is how the ICs exceed the…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…
Promotional language has been increasingly used to aid the communication of innovative ideas in science. Yet, less is known about its role in the context of technological innovation. Here, we use a validated and domain-diagnosed lexicon of…
Word matches are often used in sequence comparison methods, either as a measure of sequence similarity or in the first search steps of algorithms such as BLAST or BLAT. The D2 statistic is the number of matches of words of k letters between…
In this paper we review some recent results that shed light on a fundamental question in molecular systematics: how much phylogenetic `signal' can we expect from characters that have evolved under some Markov process? There are many sides…