Related papers: gggenomes: effective and versatile visualizations …
Networks or graphs are widely used across the sciences to represent relationships of many kinds. igraph (https://igraph.org) is a general-purpose software library for graph construction, analysis, and visualisation, combining fast and…
Phylogenetics is a fundamental component of evolutionary analysis frameworks in biology and linguistics. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has highlighted the necessity for phylogenetic software to…
This work presents some characteristics of MoNet, a digital platform for the modeling and visualization of complex systems. Emphasis is on the ideas that allowed the successful progressive development of this modeling platform, which goes…
Knowledge Graphs (KG) constitute a flexible representation of complex relationships between entities particularly useful for biomedical data. These KG, however, are very sparse with many missing edges (facts) and the visualisation of the…
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
Representing source code in a generic input format is crucial to automate software engineering tasks, e.g., applying machine learning algorithms to extract information. Visualizing code representations can further enable human experts to…
We provide a view on high-dimensional statistical inference for genome-wide association studies (GWAS). It is in part a review but covers also new developments for meta analysis with multiple studies and novel software in terms of an…
We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
A variety of genome-wide profiling techniques are available to probe complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher-level interactions that cannot be detected…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
Quantum computing is a rapidly evolving field that enables exponential speed-up over classical algorithms. At the heart of this revolutionary technology are quantum circuits, which serve as vital tools for implementing, analyzing, and…
GCsnap2 Cluster is a scalable, high performance tool for genomic context analysis, developed to overcome the limitations of its predecessor, GCsnap1 Desktop. Leveraging distributed computing with mpi4py[.]futures, GCsnap2 Cluster achieved a…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
Evaluating visualization systems in niche domains such as genomics is challenging due to scarcity of domain experts and difficulty recruiting a representative user base. While LLM-based synthetic personas are increasingly used to ease…
We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…