Georgios A. Pavlopoulos

NORMA 3.0: aesthetic and group-aware visualization and analysis of annotated biological networks

NORMA 3.0 provides enhanced visualization and analysis of annotated biological networks with improved group representation and layout algorithms.

Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D

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

ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes

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

ResLit: A Large-Scale Automated Literature Mining Database for Antimicrobial Resistance

ResLit couples BioMistral-7B screening with two-pass Qwen3-30B extraction to build an antimicrobial-resistance database of 3,120 genes and 13,593 mutations, evidence-tiered against CARD, ResFinder, and NCBI RGC.

Accelerating Inference in Genomic Foundation Models via Speculative Decoding

This paper introduces speculative decoding to accelerate genomic and proteomic sequence generation using foundation models without compromising prediction quality.

Agroforestry transition increases insect diversity and reorganizes soil function in a Mediterranean orchard

The paper examines how transitioning to agroforestry in a Mediterranean orchard affects insect diversity and soil function over a 10-year period.

WasteFams: A database of protein families from global wastewater microbiomes

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

nf-core/proteinfamilies: A scalable pipeline for the generation of protein families

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

lncAPNet enables the deciphering of lncRNA and mRNA connections in patient transcriptomic data

lncAPNet identifies lncRNA-mRNA interactions in cancer transcriptomic data using a graph-based deep learning framework, revealing lncRNA drivers in CLL and PRAD.

Quadrupling the protein family space with global metagenomics

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

A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions

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

metagRoot: A comprehensive database of protein families associated with plant root microbiomes

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: A Massively Parallel Reporter Assay Database

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.

invertiaDB: A Database of Inverted Repeats Across Organismal Genomes

invertiaDB is a database of inverted repeats across 118,070 organisms, providing a centralized resource for searching, visualizing, and downloading inverted repeat data.

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19

APNet identifies differentially active drivers of severe COVID-19 using a sparse deep learning model combined with co-expression networks, outperforming existing methods in patient classification.

Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life

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

kmerDB: A Database Encompassing the Set of Genomic and Proteomic Sequence Information for Each Species

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): advanced integration and interpretation of functional enrichment results from multiple sources

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

SCALA: A web application for multimodal analysis of single cell next generation sequencing data

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: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

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

The network makeup artist (NORMA-2.0): Distinguishing annotated groups in a network using innovative layout strategies

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

OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

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

FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists

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.

NORMA-The network makeup artist: a web tool for network annotation visualization

NORMA is a web tool that visualizes and analyzes networks with annotations, allowing users to interactively explore and compare multiple networks.

VICTOR: A visual analytics web application for comparing cluster sets

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

The Network Analysis Profiler (NAP v2.0): A web tool for visual topological comparison between multiple networks

The paper introduces NAP v2.0, a web tool for comparing topological features of multiple networks, offering 2D/3D visualization and interactive analysis.

Arena3Dweb: Interactive 3D visualization of multilayered networks.

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

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

Proximity-dependent biotinylation (BioID) of 28 SARS-CoV-2 proteins in human cells maps 5,415 proximal interactions with 2,128 host targets across basal and poly(I:C) conditions.