A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context

V Robin, A Bodein, MP Scott-Boyer… - Frontiers in Molecular …, 2022 - frontiersin.org
At the heart of the cellular machinery through the regulation of cellular functions, protein–
protein interactions (PPIs) have a significant role. PPIs can be analyzed with network …

Tulip—a huge graph visualization framework

D Auber - Graph drawing software, 2004 - Springer
The research by the information visualization community (" Info Viz") shows clearly that using
a visual representation of data-sets enables faster analysis by the end users. Several …

Evaluating effects of background stories on graph perception

Y Zhao, J Shi, J Liu, J Zhao, F Zhou… - … on Visualization and …, 2021 - ieeexplore.ieee.org
A graph is an abstract model that represents relations among entities, for example, the
interactions between characters in a novel. A background story endows entities and …

Topicnets: Visual analysis of large text corpora with topic modeling

B Gretarsson, J O'donovan, S Bostandjiev… - ACM Transactions on …, 2012 - dl.acm.org
We present TopicNets, a Web-based system for visual and interactive analysis of large sets
of documents using statistical topic models. A range of visualization types and control …

Multiscale visualization of small world networks

D Auber, Y Chiricota, F Jourdan… - IEEE symposium on …, 2003 - ieeexplore.ieee.org
Many networks under study in information visualization are" small world" networks. These
networks first appeared in the study of social networks and were shown to be relevant …

Contact area–dependent cell communication and the morphological invariance of ascidian embryogenesis

L Guignard, UM Fiúza, B Leggio, J Laussu, E Faure… - Science, 2020 - science.org
INTRODUCTION Within each animal species, embryonic development is highly
reproducible, ensuring the faithful production of a complex organism with precisely arranged …

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data

TC Freeman, S Horsewell, A Patir… - PLoS computational …, 2022 - journals.plos.org
Graphia is an open-source platform created for the graph-based analysis of the huge
amounts of quantitative and qualitative data currently being generated from the study of …

MorphoSeq: full single-cell transcriptome dynamics up to gastrulation in a chordate

HL Sladitschek, UM Fiuza, D Pavlinic, V Benes… - Cell, 2020 - cell.com
Single-cell RNA sequencing (scRNA-seq) provides a leap forward in resolving cellular
diversity and developmental trajectories but fails to comprehensively delineate the spatial …

Traffic engineering using segment routing and considering requirements of a carrier IP network

T Schüller, N Aschenbruck, M Chimani… - IEEE/ACM …, 2018 - ieeexplore.ieee.org
Internet Service Providers are challenged by increasing traffic demands. Advanced Traffic
Engineering (TE) is one way to overcome this challenge. Segment Routing (SR) is a …