Related papers: Evolutionary genomics of transposable elements in …
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…
Based on recent studies regarding high-temperature (high-$T_c$) La-Y ternary hydrides (e.g., $P{\bar{1}}$-La$_2$YH$_{12}$, $Pm{\bar{3}}m$-LaYH$_{12}$, and $Pm{\bar{3}}m$-(La,Y)H$_{10}$ with a maximum $T_c \sim 253$ K), we examined the phase…
The aim of this study is to investigate the relation that can be found between the phylogeny of a large set of complete chloroplast genomes, and the evolution of gene content inside these sequences. Core and pan genomes have been computed…
Background: Single-stranded whole-genome bisulfite sequencing (ssWGBS) enables DNA methylation profiling in low-input and highly fragmented material, including cell-free DNA. In widely used post-bisulfite protocols, Adaptase-mediated…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created…
Context. An important ingredient in binary evolution is the common-envelope (CE) phase. Although this phase is believed to be responsible for the formation of many close binaries, the process is not well understood. Aims. We investigate the…
On a stack of stable maps, the psi classes are modified by subtracting certain boundary divisors. These modified psi classes are compatible with forgetful morphisms, and are well-suited to enumerative geometry: tangency conditions allow…
The recent discovery of a new population of stars exhibiting unusual elemental abundance patterns characterized by enhanced Ti to Ga elements and low alpha and n-capture elements suggests the contribution of a new class of supernovae,…
We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…
Topological features of gene regulatory networks can be successfully reproduced by a model population evolving under selection for short dynamical attractors. The evolved population of networks exhibit motif statistics, summarized by…
On a space of stable maps, the psi classes are modified by subtracting certain boundary divisors. The top products of modified psi classes, usual psi classes, and classes pulled back along the evaluation maps are called twisted descendants;…
Flexible models for probability distributions are an essential ingredient in many machine learning tasks. We develop and investigate a new class of probability distributions, which we call a Squared Neural Family (SNEFY), formed by squaring…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
Background: Transposed elements (TEs) have a substantial impact on mammalian evolution and are involved in numerous genetic diseases. We compared the impact of TEs on the human transcriptome and the mouse transcriptome. Results: We compiled…
In our paper selected linguistic features of genomes to study the statistics of the gene codes are considered. We present the information theory from which it follows that if the system is described by distributions of hyperbolic type it…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
We present the Dartmouth Stellar Evolution Emulator (DSEE), a flow-based stellar evolution model emulator trained on a comprehensive database comprising over eight million evolutionary tracks that vary across twenty input-physics dimensions…
Transgenerational inheritance of a trait is presumably affected by both genetic and environmental factors but remains poorly understood. We studied the effect of genetic polymorphisms on transgenerational inheritance of yeast segregants…