Prof Alice Cleynen

As a kid I was always a very good student, and, not to brag, an excellent one in mathematics. But not a very interested one, not caring too much. Until in 8th grade we learnt about the dogma of molecular biology. I can still visualize the pages of the textbook, and how I was beyond amazed. From that day I wanted to become a geneticist, not really knowing what that entailed as a career.

And yet, as an impressionable kid, I let people convince me that I should pursue the mathematics path. I went to this very French "prépa" school, met this wonderful maths teacher who made me want to become one. I remember how much she enjoyed proving theorems, how she herself was fascinated by the beauty of maths, and I fell in love with that too.

I'll skip the next few years of my math training (because suddenly I was no longer the best student in class?) until I met Stéphane Robin in my very last module of Master's and he agreed to take me on as a PhD student, in a co-supervision with Sandrine Dudoit at UC Berkeley, and we designed a project around UTR usage in yeast. Five years after high school I was finally re-acquainted with genetics. And being a math teacher suddenly became not such an exciting idea. A few years later I applied to a postdoctoral position at Harvard with Giovanni Parmigiani... just a few hours after it had been awarded to someone else! This turned out to be just perfect, as Giovanni, unable to support a second postdoctoral salary, onboarded one of the world's most renowned myeloma experts, Hervé Avet-Loiseau, and here began my journey with cancer-related questions, samples, specifics, and desire to make an impact. Just as the central dogma had fascinated me by the encoding of life in four letters, cancer started fascinating me with its "emperor of all maladies," the self-optimisation of a cell against the community optimisation of the organism, the self-exploitation of the code against the sharing of the roles of the tissues.

In 2015 I joined CNRS as a Chargée de Recherche in Montpellier, bringing my cancer interests to the lab, but still in search of a more methodological angle to my research. Almost immediately (and on a scientific misunderstanding!) I started a very strong collaboration with Benoîte de Saporta on Piecewise Deterministic Markov Processes. I immediately saw their huge potential as a model for patient follow-up, and how they could finally be used to make a difference for patients now, rather than for patients in the future.

I also almost immediately joined the CNRS committee for interdisciplinary research, where I realized how little biology I actually knew, and how I would never make a significant impact if I did not learn more. In 2018 I decided that I would either join a biology lab for a year, or take a sabbatical to go back to university and take a biology course. In 2019 I was awarded a European Marie-Curie grant to go spend a year at the John Curtin School of Medical Research at the ANU in Canberra. Covid and personal challenges postponed the visit to 2022. This is where I met Nikolay Shirokikh, with whom a collaboration started around estimating the degradation of mRNA through Direct RNA Sequencing.

It quickly became obvious that I would learn more, and in a much more fascinating way, via my collaboration with Nikolay than I would have sitting on a bench at university. Nikolay quickly convinced me of the wide opportunities provided by sequencing full-length native RNA molecules, while teaching me all about translation, ribosomes, modifications, etc. I hope I convinced him that cancer patient samples were an avenue that could benefit most from the technology if we developed the appropriate tools: by definition the materials are very limited, preventing multiple independent experiments, and at the same time so much is still to be learned and understood there!

Nikolay returned the visit to my lab in 2025, I visited ANU again in 2025-2026 (but Nikolay had run away to Perth by then), and we strengthened the collaboration by creating biocodecs, our joint lab where expertise from many disciplines is welcome.

For me the driving question remains, "what can we do for cancer patients now?" Nikolay convinced me that RNA is the key aspect, and that Direct RNA Sequencing is currently the best technology to unravel all of RNA's features and secrets. Remains to bring everything together: patient diagnosis, follow-up, treatment allocation, to improve the quality of life of cancer patients.

One thing that keeps amazing me on my path is the number of people who have trusted me and given me a chance without really knowing me. It starts with Stéphane (of all the Master's modules, my grade in his was my worst, just above a pass, and yet he trusted I could still become a good researcher), Giovanni, Benoîte, and Nikolay, but there are many more, who have not had such a determining role in my career, but whose support has definitely made me want to deserve it, and helped me become more confident. They have taken a chance, and I am most grateful to them. I am still learning to reproduce that, and there have been instances when it has been most rewarding.