相关论文: Waiting for regulatory sequences to appear

An astrophysical model is proposed to answer Fermi's question. Gamma-ray bursts have the correct rates of occurrence and plausibly the correct energetics to have consequences for the evolution of life on a galactic scale. If one assumes…

Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly thereafter, it was proven that the languages…

Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…

Motivated by applications in bioinformatics, we consider the word collector problem, i.e. the expected number of calls to a random weighted generator of words of length $n$ before the full collection is obtained. The originality of this…

Finding optimal evolutionary trees from sequence data is typically an intractable problem, and there is usually no way of knowing how close to optimal the best tree from some search truly is. The problem would seem to be particularly acute…

Clinicians and scientists have traditionally focussed on whether their findings will be replicated and are very familiar with the concept. The probability that a replication study yields an effect with the same sign, or the same statistical…

What factors impact the comprehensibility of code? Previous research suggests that expectation-congruent programs should take less time to understand and be less prone to errors. We present an experiment in which participants with…

The most common gene regulation mechanism is when a transcription factor protein binds to a regulatory sequence to increase or decrease RNA transcription. However, transcription factors face two main challenges when searching for these…

Genome replication, a key process for a cell, relies on stochastic initiation by replication origins, causing a variability of replication timing from cell to cell. While stochastic models of eukaryotic replication are widely available, the…

In the domain of face recognition, there exists a puzzling timing discrepancy between results from macaque neurophysiology on the one hand and human electrophysiology on the other. Single unit recordings in macaques have demonstrated face…

Brain-computer interfaces (BCI) are an important mode of alternative and augmentative communication for many people. Unlike keyboards, many BCI systems do not display even the 26 letters of English at one time, let alone all the symbols in…

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…

The rate of occurrence of words is not uniform but varies from document to document. Despite this observation, parameters for conventional n-gram language models are usually derived using the assumption of a constant word rate. In this…

Recursive processing is considered a hallmark of human linguistic abilities. A recent study evaluated recursive processing in recurrent neural language models (RNN-LMs) and showed that such models perform below chance level on embedded…

We consider the number of occurrences of subwords (non-consecutive sub-sequences) in a given word. We first define the notion of subword entropy of a given word that measures the maximal number of occurrences among all possible subwords. We…

The early start to life naively suggests that abiogenesis is a rapid process on Earth-like planets. However, if evolution typically takes ~4Gyr to produce intelligent life-forms like us, then the limited lifespan of Earth's biosphere…

Achieving super-human performance in recognizing human speech has been a goal for several decades, as researchers have worked on increasingly challenging tasks. In the 1990's it was discovered, that conversational speech between two humans…

Certain periodical cicadas exhibit life cycles with durations of 13 or 17 years, and it is now generally accepted that such large prime numbers arise evolutionarily to avoid synchrony with predators. Less well explored is the question of…

There are two methods for counting the number of occurrences of a string in another large string. One is to count the number of places where the string is found. The other is to determine how many pieces of string can be extracted without…

Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…