Machine learning meets microbiology to advance personalized phage therapy
Invited by Ulisse Ferrari, Andrea Di Gioacchino, PhD et Adèle James, PhD (PHAGOS, a start-up developing tailored made bacteriophage-based antibacterial solutions to combat antibiotic resistance) will speak on Friday February 7th. Meet at 2.00 PM - in the Institut de la Vision, R+3 metting room.
Abstract
According to the World Health Organization, the emergence of antibiotic-resistant bacteria is one of the top global public health and development threats of our time. A promising solution relies on using bacteriophages (or phages for short), viruses of bacteria that can kill their hosts in a very selective way. This extreme specificity is at the same time an asset and a challenge for phage therapy: it allows to design effective therapies with minimal side effects, but the phages used need to be selected in a time-efficient fashion based on the target pathogenic bacteria.
To achieve this personalized phage therapy concept, we designed a platform that puts together optimized microbiology experiments and advanced machine learning techniques. In this talk we will describe how the interplay between our wet and dry laboratories allows us to design a cure for bacterial infections from scratch in a few months. We will also explore how our research is deepening our understanding of phage-host interactions *in vitro* and *in vivo*, in particular by interpreting the parameters of Large Language Models trained on millions of phage proteins from public databases and fine-tuned on relatively small datasets of phage-bacteria interactions.
About Andrea Di Gioacchino
Andrea Di Gioacchino is a researcher specialized in the application of machine learning and statistical physics to biological data. He earned his Ph.D. in Statistical Physics of disorded systems from the University of Milan in Italy.
Following his doctoral studies, Andrea conducted postdoctoral research at institutions including the École Normale Supérieure (ENS) and the French National Centre for Scientific Research (CNRS). His research focused on utilizing machine learning methods, inspired by statistical physics, to uncover patterns in biological sequences such as proteins, RNA, and DNA. He concentrated on viral sequences, aiming to develop quantitative descriptions of host-pathogen interactions at the genomic level.
Currently, Andrea serves as a Head of Data at Phagos, a startup dedicated to combating antibiotic resistance and treating infectious diseases in animal farming through the use of bacteriophages. In this role, he leads a team to analyze experimental data and develop algorithms to enhance the understanding of phage-bacteria interactions, striving to identify more effective phages for therapeutic applications.
About Adèle James
Adèle James is specialised in ecology, evolution and virulence of bacteria and earned her Ph.D. in molecular microbiology from Sorbonne Université, where her research explored horizontal gene transfers and mechanisms of infection in marine pathogenic bacteria. Following her doctoral studies, Adèle transitioned into the biotechnology industry, and worked in droplet microfluidics and mass spectrometry applied to microbiology.
She co-founded phagos, an impact start-up developing tailored made bacteriophage-based antibacterial solutions to combat antibiotic resistance, with a focus on veterinary applications in 2021. As Chief Technology Officer, she leads the development and implementation of phagos scientific and technological strategies and vision by coordinating R&D efforts between the microbiology, bioinformatics and data teams.