Related papers: Pan-genome Analysis of Angiosperm Plastomes using …
Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory…
Chloroplast sequences from the Lamiales order were analyzed using the Pangenome Research Toolkit (PGR-TK). Overall, most genera and families exhibited a high degree of sequence uniformity. However, at the genus level, Utricularia,…
Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is:…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
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…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Pseudoprogression (PsP) occurs in 20-30% of patients with glioblastoma multiforme (GBM) after receiving the standard treatment. In the course of post-treatment magnetic resonance imaging (MRI), PsP exhibits similarities in shape and…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
BACKGROUND: Breast cancer has emerged as one of the most prevalent cancers among women leading to a high mortality rate. Due to the heterogeneous nature of breast cancer, there is a need to identify differentially expressed genes associated…
PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome…
We define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
The leaves of angiosperms contain highly complex venation networks consisting of recursively nested, hierarchically organized loops. We describe a new phenotypic trait of reticulate vascular networks based on the topology of the nested…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
The number of complete chloroplastic genomes increases day after day, making it possible to rethink plants phylogeny at the biomolecular era. Given a set of close plants sharing in the order of one hundred of core chloroplastic genes, this…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
Biological processes underlying the basic functions of a cell involve complex interactions between genes. From a technical point of view, these interactions can be represented through a graph where genes and their connections are,…
Background: In recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes. However, the wealth of genomic and proteomic data available today necessitates efficient…
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors, of which 15-25% develop metastatic disease with 5-year survival rates reported as low as 34%. PPGL may indicate hereditary syndromes requiring stricter,…
Annotating 3D medical images demands substantial time and expertise, driving the adoption of semi-supervised learning (SSL) for segmentation tasks. However, the complex anatomical structures of organs often lead to significant class…
Genome-resolved metagenomics has contributed largely to discovering prokaryotic genomes. When applied to microscopic eukaryotes, challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the…