23 papers · ranked by Valyu relevance
Rolando Garcia-Milian
Pathway and functional enrichment analysis is a cornerstone of omics data interpretation, enabling researchers to map differentially expressed proteins or genes onto curated biological processes, signaling cascades, and molecular functions. While tools such as Ingenuity Pathway Analysis (IPA), g:Profiler, and Enrichr…
Lingran Xiao, Yanfei Wang, Shiying Li, Lingxi Chen + 1 more
The pathway is a biological term that refers to a series of interactions between molecules in a cell that cause a certain product or a change in the cell [NIH20]. Pathway analysis is a powerful method for gene expression analysis [Cir17]. Through pathway maps, the lists of genes that are differently expressed across…
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…
Giovanni Micale, Salvatore Alaimo, Alfredo Pulvirenti, Toma Tebaldi
After uploading input data, by clicking on “Compare,” a multilayer network of pathways is shown, where each layer is a pathway associated with a specific phenotype ([vbaf212-F1]). Visualization makes use of visNetwork R package ([https://datastorm-open.github.io/visNetwork/]()) and the Sugiyama layout. Intra-layer…
Julian Müller, Florian P. Bayer, Mathias Wilhelm, Maximilian G. Schuh + 2 more
'Maximilian G. Schuh' 'Bernhard Kuster' 'Matthew The'] Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a…
Manjunatha Beduru Krishnamurthy, Harish P S, Abhishek Subramanian
Genome-scale metabolic network (GSMN) models are rigorously curated, cellular-level representations of metabolism that enable flux-based metabolite fate discovery, metabolic engineering, drug target identification and context-specific multi-omics integration. However, the inherent complexity of model architectures…
Jeff Baumes, Thomas M. O’Connell
A primary objective of metabolomics studies is identifying the critical metabolic pathways that are altered under specific conditions. There are a number of tools such as enrichment or over-representation algorithms which can identify pathways, but tools for visualizing these pathways beyond static diagrams are…
Philipp Eberhard, Martin Kern, Michael Aichem, Hanna Borlinghaus + 8 more
Advancements in technology for high-throughput screenings lead to ever-increasing datasets in biochemical research, as exemplified by . Investigating this wealth of information requires effective approaches, and one such strategy involves defining pathways of biochemical reactions and associating the data with their…
Manjunatha Beduru Krishnamurthy, Pasupula Sridhar Harish, Abhishek Subramanian, Daisuke Kihara
Several GSMN-specific tools assist metabolic network visualization, analyses and refinement, albeit, with significant limitations in scope and flexibility of use. Comparison of NAViFluX features with other tools is provided in [btag191-F2]. Analysis-oriented tools like FLUXestimator are purely focused on single-cell…
Tibo Vande Moortele, Pieter Verschaffelt, Qingyao Huang, Nadezhda T. Doncheva + 6 more
'Nadezhda T. Doncheva' 'Tanja Holstein' 'Caroline Jachmann' 'Peter Dawyndt' 'Lennart Martens' 'Bart Mesuere' 'Tim Van Den Bossche'] Metaproteomics, the study of collective proteomes in environmental communities, plays a crucial role in understanding microbial functionalities affecting ecosystems and human health.…
Yifei Ge, Feifan Zhang, Yijiang Liu, Chao Jiang + 8 more
Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approaches often suffer from extensive functional redundancy caused by…
Shuzhao Li
Emerging biochemical data require effective pathway visualization. However, traditional metabolic maps were based on manual layouts, falling behind new scientific discoveries. Automated visualization of metabolic pathways has been investigated heavily, but resulted in few consensuses. We report here a new approach…
William G. Ryan V., Smita Sahay, John Vergis, Corey Weistuch + 3 more
'Jarek Meller' 'Robert E. McCullumsmith' 'Gerald Lushington'] In bioinformatics, pathway analyses are used to interpret biological data by mapping measured molecules with known pathways to discover their functional processes and relationships. Pathway analysis has become an essential tool for interpreting large-scale…
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…
Travis M. Blimkie, Andy An, Robert E. W. Hancock, Stacey D. Finley
R package pathlinkR is designed to aid transcriptomic analyses by streamlining and simplifying the process of analyzing and interpreting differentially expressed genes derived from human RNA-Seq data. It provides an integrated approach to performing pathway enrichment and network-based analyses, while also producing…
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…
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…
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.…
Thibault Rolland, Fabrizio De Vico Fallani
To facilitate the identification of significant connectivity patterns, many methods have been developed based on the rearrangement of the nodes so as to avoid link criss-cross. However, real networks are often embedded in a geometrical space and the nodes code for an intrinsic physical feature of the system that one…
Mark Eastwood, J. G. A. Pocock, Mostafa Jahanifar, Adam Shephard + 7 more
Models Authors: ['Mark Eastwood' 'J. G. A. Pocock' 'Mostafa Jahanifar' 'Adam Shephard' 'Skiros Habib' 'Ethar Alzaid' 'Abdullah Alsalemi' 'Jan Lukas Robertus' 'Nasir Rajpoot' 'Shan E Ahmed Raza' 'Fayyaz Minhas'] Summary Digital pathology has gained significant traction in modern healthcare systems. This shift from…
Jianping Zhou, Junhao Li, Guangjie Zheng, Yunqiang Zhu + 2 more
Knowledge Graph Authors: ['Jianping Zhou' 'Junhao Li' 'Guangjie Zheng' 'Yunqiang Zhu' 'Xinbing Wang' 'Chenghu Zhou'] Abstract. In this paper, we propose a multi-view visualization technology for spatio-temporal knowledge graph(STKG), which utilizes three distinct perspectives: knowledge tree , knowledge net, and…
James Scott-Brown, Benjamin Bach
—This paper introduces NetPanorama, a domain-specific language and declarative grammar for interactive network visualizations. Exploring complex networks with multivariate, geographical, or temporal information often require bespoke visualization designs, such as adjacency matrices, arc-diagrams, small multiples…
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…