Related papers: Pan-genome Analysis of Angiosperm Plastomes using …
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon, and Neolycopersicon groups. We present a…
A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…
We present an applied study in cancer genomics for integrating data and inferences from laboratory experiments on cancer cell lines with observational data obtained from human breast cancer studies. The biological focus is on improving…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
Accurate detection and segmentation of brain tumors is critical for medical diagnosis. However, current supervised learning methods require extensively annotated images and the state-of-the-art generative models used in unsupervised methods…
When delineating lesions from medical images, a human expert can always keep in mind the anatomical structure behind the voxels. However, although high-quality (though not perfect) anatomical information can be retrieved from computed…
Pattern analysis of tandem repeats in gene is an indispensable computational approach to the understanding of the gene expression and pathogenesis of diseases. This research applied a computational motif model and database techniques to…
Optical emission-line diagnostic diagrams, such as the classical BPT, are widely used to identify ionisation mechanisms in galaxies but often suffer from degeneracies, especially when multiple sources coexist. We critically evaluate the…
PURPOSE: The medical literature relevant to germline genetics is growing exponentially. Clinicians need tools monitoring and prioritizing the literature to understand the clinical implications of the pathogenic genetic variants. We…
Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and…
Context. The classification of active galactic nuclei (AGNs) is a challenge in astrophysics. Variability features extracted from light curves offer a promising avenue for distinguishing AGNs and their subclasses. This approach would be very…
Global climate change has reduced crop resilience and pesticide efficacy, making reliance on synthetic pesticides inevitable, even though their widespread use poses significant health and environmental risks. While these pesticides remain a…
Lately the non-linear optical third harmonic generation (THG) microscopy is starting to emerge as a laboratory standard for label-free studies in biological samples. In this study, the THG signals produced from corn starch granules are…
Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…
Principal component analysis (PCA) is routinely used in population genetics to assess genetic structure. With chromosomal reference genomes and population-scale whole genome-sequencing becoming increasingly accessible, contemporary studies…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method…
The task of data integration for multi-omics data has emerged as a powerful strategy to unravel the complex biological underpinnings of cancer. Recent advancements in graph neural networks (GNNs) offer an effective framework to model…