Abstract:
Across oceans, soils, plant roots, the human gut, and extreme habitats, microbiomes and viruses encode a vast “functional dark matter” of proteins with no clear roles. This talk introduces a unifying view of environment-spanning protein-family catalogs built directly from metagenomes and metatranscriptomes. These catalogs transform raw sequence deluges into interpretable, comparable units of function. It will be shown how reference-free family discovery exposes previously unseen diversity across ecosystems and reveals conserved motifs and domain architectures that traditional genome-centric approaches miss. Emphasis will be given on the scalable bioinformatics that makes this possible: linear-time sequence clustering for billions of proteins, profile-based annotation layered onto rich environmental metadata, and structure-informed inference that leverages modern protein-folding breakthroughs. Finally, the talk will outline practical, cross-biome workflows for hypothesis generation such as linking families to enzymes, pathways, and ecological traits.

Bio:
Georgios A. Pavlopoulos earned a BSc/Diploma in Computer Science from the National and Kapodistrian University of Athens (NKUA) in Greece; an MRes in Bioinformatics from the University of Leeds (Department of Biochemistry) in the UK; and a PhD in Bioinformatics from EMBL-Heidelberg in Germany. He also holds a joint MBA from the Athens University of Economics and Business (AUEB) and the National Technical University of Athens (NTUA).
His research career includes postdoctoral work at KU Leuven’s Department of Electrical Engineering (ESAT) in Belgium, and roles as a bioinformatics instructor and postdoctoral researcher at the University of Crete’s Faculty of Medicine in Greece, and at the DOE Joint Genome Institute at Lawrence Berkeley National Laboratory in California.
Since 2018, he has consulted in bioinformatics for several U.S. companies and led the bioinformatics program at the Biomedical Sciences Research Center “Alexander Fleming” (BSRC) in Greece, serving as Director of Bioinformatics (Research Associate Professor) and as an elected member of the Scientific Board at the Institute of Fundamental Biomedical Research (IFBR). In parallel, he served as Head of Bioinformatics at NKUA’s Center of New Biotechnologies and Precision Medicine for five years.
In 2024, he was appointed Director of Research (Research Full Professor) at BSRC “Alexander Fleming.” He is also one of the founders and a BoD member of BioInnovation Greece and the founder and CEO of GC2 Data Science. His work has been recognized among the top 2% of scientists in his field, and he has secured competitive grants, organized international conferences, and published extensively in high-impact journals, including Nature, Science, Cell, Nucleic Acids Research, and Nature Biotechnology.
Pavlopoulos’s lab focuses on genomics and metagenomics, biological networks, text mining, data visualization, big data analysis, high-performance computing, data integration, machine learning, knowledge management and representation, and personalized medicine.