25 papers · ranked by Valyu relevance
Walters, Skylar Sargent, Valderrama, Arthea + 12 more
The rapid growth of genomic data has created unprecedented opportunities for discovery [[2]][[1]][[19]]. However, extracting meaningful insights from these data often requires navigating specialized interfaces, mastering domain-specific visualization tools, and understanding complex data formats. Furthermore, many…
Sehi L’Yi, John Conroy, Priya Misner, David Kouřil + 4 more
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and reliable biological insights. Consequently, the genomics community has…
Aditeya Pandey, Sehi L’Yi, Qianwen Wang, Michelle A. Borkin + 1 more
1## Introduction The almost ubiquitous availability of genomic data has revolutionized research in biology and medicine. By interpreting genomic and epigenomic data, researchers can improve our understanding of the genetic causes and mechanisms that underlie common and rare diseases. Visualization, as an efficient…
Sehi L’Yi, Nils Gehlenborg
A series of recent studies has focused on designing cross-resolution and cross-device visualizations, i.e., responsive visualization, a concept adopted from responsive web design. However, these studies mainly focused on visualizations with a single view to a small number of views, and there are still unresolved…
Noah Spies, Justin Zook, Arend Sidow, Marc Salit
Visual inspection and analysis is integral to quality control, hypothesis generation, methods development and validation of genomic data. The richness and complexity of genomic data necessitates customized visualizations highlighting specific features of interest while hiding the often vast tide of irrelevant…
Mary Goldman, Brian Craft, Akhil Kamath, Angela Brooks + 2 more
UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. The investigator-driven platform consists of a web-based Xena Browser and turn-key Xena Hubs. Xena showcases seminal cancer genomics datasets from TCGA, Pan-Cancer Atlas, PCAWG, ICGC…
Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng + 1 more
Growing popularity and diversity of genomic data demands portable and versatile genome browsers. Here, we present an open source programming library, called GIVE that facilitates creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage…
Gregg A Helt, John W Nicol, Ed Erwin, Eric Blossom + 4 more
'Steven G Blanchard Jr' 'Stephen A Chervitz' 'Cyrus Harmon' 'Ann E Loraine'] Background Visualization software can expose previously undiscovered patterns in genomic data and advance biological science. Results The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid…
Etienne Sollier, Jessica Heilmann, Clarissa Gerhäuser, Michael Scherer + 2 more
The vast amount of publicly available genomic data requires analysis and visualization tools. Here, we present figeno, an application for generating publication-quality FIgures for GENOmics. Figeno particularly focuses on multi-region views across genomic breakpoints and on long reads with base modifications.…
Thomas Hackl, Markus J. Ankenbrand, Bart van Adrichem, David E. Wilkins + 1 more
genomics Authors: ['Thomas Hackl' 'Markus J. Ankenbrand' 'Bart van Adrichem' 'David E. Wilkins' 'Kristina Haslinger'] - 1. Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands - 2. Julius-Maximilians-Universität Würzburg, Fakultät für Biologie…
Etienne Sollier, Jessica Heilmann, Clarissa Gerhauser, Michael Scherer + 3 more
Recent advances in sequencing have led to the generation of many different types of genomic and epigenomic data, which require visualization tools for facilitating analysis and interpretation. An important requirement for such tools is the support of various data types, for large datasets, and for generating…
Nowlan H. Freese, David C. Norris, Ann E. Loraine
Genome browsers that support fast navigation through vast data sets and provide interactive visual analytics functions can accelerate research and help scientists achieve deeper insight into data. Previously, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop…
Sabrina Nusrat, Theresa Harbig, Nils Gehlenborg
The following literature surveys focusing on genomic data visualization are all aimed at audiences in the bioinformatics and biology research communities. Therefore, their review of visualization tools is often more focused on features available to the users than on formalizing the description of common tasks and…
Malte Mader, Ronald Simon, Stefan Kurtz
Background A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative…
Sol Shenker, Eric Lai
The recent beyond-exponential growth in diverse collections of deep sequencing datasets creates enormous opportunities for discovery, concomitant with new challenges for displaying and interpreting these data. Notably, the availability of scores of whole genome sequences in multiple species clades enables comparative…
John L. Portwood, Ethalinda K. Cannon, Olivia C. Haley, Laura E. Tibbs-Cortes + 2 more
Genome visualization has existed for as long as assembled genomes, with an array of tools and approaches to meet researchers’ needs. The genome browser is one of these tools, and it has become a critical analytical resource for geneticists, genome biologists, and breeders. The evolution of genome browser capabilities…
S. Nusrat, T. Harbig, N. Gehlenborg
Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research…
Yuncan Ai, Hannan Ai, Fanmei Meng, Lei Zhao
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromosome, plasmid, and phage) with farther divergences (much…
Kevin Mildau, Christoph Büschl, Jürgen Zanghellini, Justin J.J. van der Hooft
Computational metabolomics workflows have revolutionized the untargeted metabolomics field. However, the organization and prioritization of metabolite features remains a laborious process. Organizing metabolomics data is often done through mass fragmentation-based spectral similarity grouping, resulting in feature sets…
Denise Slenter, M. Kutmon, Chris T. Evelo, Egon L. Willighagen
Metabolomics data analysis for phenotype identification commonly reveals only a small set of biochemical markers, often containing overlapping metabolites for individual phenotypes. Differentiation between distinctive sample groups requires understanding the underlying causes of metabolic changes. However, combining…
Murat Cihan Sorkun, Dajt Mullaj, J. M. Vianney A. Koelman, Süleyman Er
Visualizing chemical spaces streamlines the analysis of molecular datasets by reducing the information to human perception level, hence it forms an integral piece of molecular engineering, including chemical library design, high-throughput screening, diversity analysis, and outlier detection. We present here ChemPlot…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Authors not listed
In chemoinformatics, chemical databases have great importance since their main objective is to store and organize the chemical structures of molecules and their properties, from basic information such as chemical structure to more complex like molecular fingerprints or other types of calculated or experimental…
Authors not listed
Large-scale de novo nucleic acid synthesis is a powerful tool enabling researchers to better understand and engineer biological systems. Fields ranging from genomics to nucleic acid therapeutics to synthetic biology make use of high-throughput experimental approaches requiring access to large pools or libraries of DNA…
Fernanda I. Saldívar-González, José L. Medina-Franco
Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the…