23 papers · ranked by Valyu relevance
Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder + 4 more
'Nuno Nunes' 'Alexander R. Pico' 'Chris T. Evelo' 'Robert F. Murphy'] PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help…
Konstantinos Sidiropoulos, Guilherme Viteri, Cristoffer Sevilla, Steve Jupe + 16 more
Pathway databases like Reactome systematically associate proteins with their functions and link them into networks that describe the reaction space of an organism. The basic unit of a pathway database is a reaction in which molecules are transformed. Transformations include the chemical changes of intermediary…
Allison Pon, Timothy Jewison, Yilu Su, Yongjie Liang + 4 more
'Adam Maciejewski' 'Michael Wilson' 'David S. Wishart'] PathWhiz ([http://smpdb.ca/pathwhiz]()) is a web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from almost any place and…
Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola
Background Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments and layout algorithms often sacrifice low-level details to maintain high-level information, which…
Xiaoxi Dong, Kovidh Vegesna, Cory Brouwer, Weijun Luo
Pathway analysis is widely used in genomics and omics research, but the data visualization has been highly limited in function, pathway coverage and data format. Here we develop SBGNview a comprehensive solution to address these needs. By adopting the standard SBGN format, SBGNview greatly extend the coverage of…
Peter D. Karp, Suzanne Paley, Peter Midford, Markus Krummenacker + 6 more
'Richard Billington' 'Anamika Kothari' 'Wai Kit Ong' 'Pallavi Subhraveti' 'Ingrid M. Keseler' 'Ron Caspi'] 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…
Paul Murray, Fintan McGee, Angus G. Forbes
Background Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a…
Francesco Paduano, Angus Graeme Forbes
Background Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability…
Hsiang‐Yun Wu, Martin Nöllenburg, Ivan Viola
The concept of multilayer networks has become recently integrated into complex systems modeling since it encapsulates a very general concept of complex relationships. Biological pathways are an example of complex real-world networks, where vertices represent biological entities, and edges indicate the underlying…
Tibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva + 6 more
Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health. Pathway analysis offers structured insights into the biochemical processes within these communities. However, no existing tool…
Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen + 2 more
'Karl Kashofer' 'Dieter Schmalstieg'] Jointly analyzing biological pathway maps and experimental data is critical for understanding how biological processes work in different conditions and why different samples exhibit certain characteristics. This joint analysis, however, poses a significant challenge for…
Rafael Hernández-de-Diego, Sonia Tarazona, Carlos Martínez-Mira, Leandro Balzano-Nogueira + 3 more
The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental to understand interconnections across molecular layers and to fully leverage the biology discovery power offered by the multi-omics approach. We present here PaintOmics 3, a…
Mathurin Dorel, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of molecular…
Rashmi Rameshwari, Tannu Prasad
— The analysis and interpretation of relationships between biological molecules is done with the help of networks. Networks are used ubiquitously throughout biology to represent the relationships between genes and gene products. Network models have facilitated a shift from the study of evolutionary conservation between…
Authors not listed
Effective visualization of complex synthesis routes is critical for computeraided synthesis planning (CASP), yet current solutions are limited in scope, integration flexibility, and chemical intuition. We introduce RouteWise, a versatile, containerized web application designed to address these unmet needs. Its modular…
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…
Vinh T. Nguyen, Md Yasin Kabir, Tommy Dang
—Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains various biomolecules in different layers of the cell which is responsible for…
Soumita Ghosh, Abhik Datta, Hyungwon Choi
We present multiSLIDE, an open-source tool for query-driven visualization of quantitative single- or multiomics data. Using pathways and networks as the basis for data linkage, multiSLIDE provides an interactive platform for querying the multi-omics data by genes, pathways, and intermolecular relationships.…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
Ryan Miller, Sebastian Muraru, Ana Belén Malpartida, Josh Low + 7 more
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while…
J. L. Zhao, Morteza Karimzadeh, Hanye Xu, Abish Malik + 4 more
'Shehzad Afzal' 'Guizhen Wang' 'Niklas Elmqvist' 'David S. Ebert'] | Jieqiong Zhao | Morteza Karimzadeh | Hanye Xu | Abish Malik | | --- | --- | --- | --- | | Purdue University | University of Colorado Boulder | Purdue University | Davista Technologies | | zhao413@purdue.edu | karimzadeh@colorado.edu |…
Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot, Andrei Zinovyev
Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-throughput data are usually visualized on top of predefined network layouts which are not always adapted to a given data analysis task. We…
Samuel Genheden, Esben Bjerrum
We introduce a framework for benchmarking multi-step retrosynthesis methods, i.e. route predictions, called PaRoutes. The framework consists of two sets of 10,000 synthetic routes extracted from the patent literature, a list of stock compounds, and a curated set of reactions on which one-step retrosynthesis models can…