Interpretation of differential gene expression results of RNA-seq data: review and integration

A McDermaid, B Monier, J Zhao, B Liu… - Briefings in …, 2019 - academic.oup.com
Differential gene expression (DGE) analysis is one of the most common applications of RNA-
sequencing (RNA-seq) data. This process allows for the elucidation of differentially …

Ontology visualization methods—a survey

A Katifori, C Halatsis, G Lepouras, C Vassilakis… - ACM Computing …, 2007 - dl.acm.org
Ontologies, as sets of concepts and their interrelations in a specific domain, have proven to
be a useful tool in the areas of digital libraries, the semantic web, and personalized …

WebGestalt: an integrated system for exploring gene sets in various biological contexts

B Zhang, S Kirov, J Snoddy - Nucleic acids research, 2005 - academic.oup.com
High-throughput technologies have led to the rapid generation of large-scale datasets about
genes and gene products. These technologies have also shifted our research focus from …

TreeDyn: towards dynamic graphics and annotations for analyses of trees

F Chevenet, C Brun, AL Bañuls, B Jacq, R Christen - BMC bioinformatics, 2006 - Springer
Background Analyses of biomolecules for biodiversity, phylogeny or structure/function
studies often use graphical tree representations. Many powerful tree editors are now …

Virtual reality for the observation of oncology models (VROOM): immersive analytics for oncology patient cohorts

CW Lau, Z Qu, D Draper, R Quan, A Braytee, A Bluff… - Scientific reports, 2022 - nature.com
The significant advancement of inexpensive and portable virtual reality (VR) and augmented
reality devices has re-energised the research in the immersive analytics field. The immersive …

A hybrid space-filling and force-directed layout method for visualizing multiple-category graphs

T Itoh, C Muelder, KL Ma, J Sese - 2009 IEEE Pacific …, 2009 - ieeexplore.ieee.org
Many graphs used in real-world applications consist of nodes belonging to more than one
category. We call such graph ldquomultiple-category graphsrdquo. Social networks are …

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API

N Kono, K Arakawa, R Ogawa, N Kido, K Oshita… - PloS one, 2009 - journals.plos.org
Background Biochemical pathways provide an essential context for understanding
comprehensive experimental data and the systematic workings of a cell. Therefore, the …

High-performance integrated virtual environment (HIVE) tools and applications for big data analysis

V Simonyan, R Mazumder - Genes, 2014 - mdpi.com
The High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-
based infrastructure developed for the storage and analysis of genomic and associated …

Systems biology of autophagy in leishmanial infection and its diverse role in precision medicine

V Guhe, P Ingale, A Tambekar, S Singh - Frontiers in Molecular …, 2023 - frontiersin.org
Autophagy is a contentious issue in leishmaniasis and is emerging as a promising
therapeutic regimen. Published research on the impact of autophagic regulation on …

Intelligent mining of large-scale bio-data: Bioinformatics applications

FS Golestan Hashemi, M Razi Ismail… - Biotechnology & …, 2018 - Taylor & Francis
Today, there is a collection of a tremendous amount of bio-data because of the
computerized applications worldwide. Therefore, scholars have been encouraged to …