A PhD project developed at i3S and FCUP is exploring how artificial intelligence can transform the microorganisms that inhabit the human body into forensic evidence.
The collection of microorganisms that inhabit the human body, known as the microbiome, could become a valuable source of evidence in criminal investigations. This is the challenge at the heart of the PhD project being developed by Ahmad Hassan at the Institute for Research and Innovation in Health (i3S) and the Faculty of Sciences of the University of Porto (FCUP).
Even Jessica Fletcher, the protagonist of the television series Murder, She Wrote, never imagined anything quite like this.
Funded by the European Union through the Marie Skłodowska-Curie Actions – Doctoral Networks, as part of the NATURAL TRACES European network, the research combines deep learning, generative artificial intelligence (AI), and bioinformatics to address challenges with a range of practical applications, including the geolocation of biological traces, individual identification, and estimation of the post-mortem interval.
“The goal of this PhD project is to develop algorithms capable of transforming complex microbiome data into robust, legally defensible forensic evidence,” explains Nádia Pinto, researcher at i3S and FCUP alumna, whose background is in Mathematics and Applied Mathematics.
From forensic genetics to AI and bioinformatics
At i3S, PhD student Ahmad Hassan will work in an interdisciplinary environment bringing together experts in forensic genetics, population genetics, mathematical modelling, and data science. At the Department of Computer Science of FCUP (DCC-FCUP), he will join a research ecosystem focused on artificial intelligence, bioinformatics, and computational biology.
“This environment enables the development, testing, and validation of advanced computational methods and algorithms that can help translate the complexity of biological data into innovative and robust technological solutions,” says Pedro Gabriel Ferreira, professor at DCC-FCUP.
For Ahmad Hassan, joining this PhD programme represents a unique opportunity for advanced training and international scientific collaboration.
“This PhD project allows me to grow as an independent researcher, collaborate with international partners, and contribute to advancing forensic science so that, in the future, these tools can be used by professionals in the field and by the justice system,” he says.
Enrolled in FCUP’s Doctoral Programme in Computer Science, Ahmad Hassan is supervised by Pedro Gabriel Ferreira (FCUP), Nádia Pinto (i3S), and Daniel Ramos (Autonomous University of Madrid).
The NATURAL TRACES network is coordinated by the University of Frankfurt and brings together ten doctoral researchers, along with beneficiaries and partners from fourteen countries. Its main objective is to develop new approaches for using environmental DNA (eDNA), microbiomes, and other non-human biological traces as forensic evidence.
The network covers a wide range of research areas, including forensic entomology, pollen analysis, fungal analysis, environmental DNA, as well as bioinformatics and AI methods for interpreting complex datasets. Within the consortium, i3S and FCUP lead the development of bioinformatics and AI methods for microbiome analysis, strengthening Portugal’s contribution to a new generation of tools supporting forensic investigations.
According to Nádia Pinto, the project reinforces i3S’s strategic commitment to genomic medicine and computational biology:
“This PhD project contributes to strengthening the institute’s capacity to develop machine learning tools and probabilistic models for interpreting complex omics data — large-scale biological datasets generated by high-throughput technologies — demonstrating how these technologies can have an impact beyond healthcare, particularly in forensic science.”