Fotis A. Baltoumas

Arena3D 3.0 is a web server for exploring, analyzing, and sharing multilayered biological networks in 3D with various layouts and visualization tools.

ArthroVerse compiles and annotates protein families from arthropod-associated microbiomes to explore functional diversity and host-microbe interactions.

WasteFams catalogs 3,887 non-redundant protein families from wastewater metagenomes and metatranscriptomes, providing structural, taxonomic, and functional annotations for microbial function discovery.

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

metagRoot provides a database of 71,091 enriched protein families from plant root microbiomes, annotated with structural and functional information to aid in microbiome research.

MPRAbase is a curated database of MPRA experiments that provides access to 17.7 million regulatory elements tested across 35 cell types and 4 organisms.

Quadrupia identifies and characterizes G-quadruplex sequences across 108,449 genomes, revealing taxonomic patterns and experimentally validating key structures.

kmerDB provides a database of genomic and proteomic sequence information, including kmers, quasi-primes, and primes, for 45,785 genomes and 22,386 proteomes.

Flame (v2.0) integrates and visualizes functional enrichment results from multiple tools, supporting more organisms and offering interactive analysis features.

SCALA is a web-based tool for analyzing scRNA-seq and scATAC-seq data, offering integrated analysis and visualization of cell populations, trajectories, and regulatory networks.

Arena3Dweb provides an interactive 3D visualization tool for multi-layered networks with clustering, directional connections, and integration capabilities.

NORMA-2.0 is a web tool that uses layout strategies to group annotated network elements, improving visualization of network heterogeneity.

OnTheFly2.0 automates biomedical entity recognition and analysis from documents, revealing inflammatory and senescence pathways in severe COVID-19.

FLAME is a web tool that enables the analysis of multiple gene lists through functional and literature enrichment, offering interactive visualizations and support for 197 organisms.

VICTOR is a web application that compares clustering results using visual analytics tools and multiple metrics.

Arena3Dweb provides an interactive 3D web tool for visualizing multilayered networks, supporting drug repurposing and GPCR signaling pathway analysis.