Related papers: gggenomes: effective and versatile visualizations …
Despite the fundamental importance of clustering, to this day, much of the relevant research is still based on ambiguous foundations, leading to an unclear understanding of whether or how the various clustering methods are connected with…
We are living in the big data age: An ever increasing amount of data is being produced through data acquisition and computer simulations. While large scale analysis and simulations have received significant attention for cloud and…
Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding…
Recent success in deep learning has generated immense interest among practitioners and students, inspiring many to learn about this new technology. While visual and interactive approaches have been successfully developed to help people more…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…
Continuous glucose monitoring (CGM) systems provide real-time, dynamic glucose information by tracking interstitial glucose values throughout the day (typically values are recorded every 5 minutes). CGMs are commonly used in diabetes…
Understanding the genetic basis of complex traits is a longstanding challenge in the field of genomics. Genome-wide association studies (GWAS) have identified thousands of variant-trait associations, but most of these variants are located…
Visualizations are an essential part of biomedical analysis result interpretation. Often, interactive networks are used to visualize the data. However, the high interconnectivity, and high dimensionality of the data often results in…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
We present Glyph - a Python package for genetic programming based symbolic regression. Glyph is designed for usage let by numerical simulations let by real world experiments. For experimentalists, glyph-remote provides a separation of…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
We present encube $-$ a qualitative, quantitative and comparative visualisation and analysis system, with application to high-resolution, immersive three-dimensional environments and desktop displays. encube extends previous comparative…
MPAgenomics, standing for multi-patients analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation, and (ii) genomic marker selection from multi-patient copy number and SNP data profiles. It provides wrappers…
A genome-scale reconstruction of human metabolism, Recon 2, is available but no interface exists to interactively visualise its content integrated with omics data and simulation results. We manually drew a comprehensive map, ReconMap 2.0,…
The purpose of this review is to introduce the reader to graph kernels and the corresponding literature, with an emphasis on those with direct application to chemoinformatics. Graph kernels are functions that allow for the inference of…
Graph Neural Networks (GNNs) extend the success of neural networks to graph-structured data by accounting for their intrinsic geometry. While extensive research has been done on developing GNN models with superior performance according to a…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Data visualization is essential for developing an understanding of a complex system. The power grid is one of the most complex systems in the world and effective power grid research visualization software must 1) be easy to use, 2) support…
Drug discovery aims at designing novel molecules with specific desired properties for clinical trials. Over past decades, drug discovery and development have been a costly and time consuming process. Driven by big chemical data and AI, deep…