Related papers: DNA Sequence Evolution with Neighbor-Dependent Mut…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network…
We study a general setting of neutral evolution in which the population is of finite, constant size and can have spatial structure. Mutation leads to different genetic types ("traits"), which can be discrete or continuous. Under minimal…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Evolution is simultaneously driven by a number of processes such as mutation, competition and random sampling. Understanding which of these processes is dominating the collective evolutionary dynamics in dependence on system properties is a…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
Domain Adaptation(DA) for dense prediction tasks is an important topic, which enhances the dense prediction model's performance when tested on its unseen domain. Recently, with the development of Diffusion-based Dense Prediction (DDP)…
In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
We consider detecting the evolutionary oscillatory pattern of a signal when it is contaminated by non-stationary noises with complexly time-varying data generating mechanism. A high-dimensional dense progressive periodogram test is proposed…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation…
Modelling the dynamics of dense granular media is a long standing challenge and essential to many natural phenomena and technological applications. Here, we trace back puzzling experimental observation of detailed-balanced steady states to…