Cyndy Thooi

Biosciences Seminar Speaker: Maciek Wiatrak, Cambridge University

Place: 305, Bedford Way (26)

Date: 02/10/2025
Time: 11.00-12.00

Bacteria have evolved a vast diversity of functions and behaviours which are currently incompletely understood and poorly predicted from DNA sequence alone. To understand the syntax of bacterial evolution and discover genome-to-phenotype relationships, we curated over 1.3 million genomes spanning bacterial phylogenetic space, representing each as an ordered sequence of proteins which collectively were used to train a transformer-based, contextualised protein language model, Bacformer. By pretraining the model to learn genome-wide evolutionary patterns, Bacformer captures the compositional and positional relationships of proteins and can accurately: predict protein-protein interactions, operon structure (which we validated experimentally), and protein function; infer phenotypic traits and identify likely causal genes; and design template synthethic genomes with desired properties. Thus, Bacformer represents a new foundation model for bacterial genomics that provide biological insights and a framework for prediction, inference, and generative tasks.

Birkbeck’s annual Bernal lecture honours the pioneering spirit of JD Bernal, and this year shines a light on one of his most remarkable protégés.

The 2025 Bernal Lecture will be held under the title “The Harvest of an Eclectic Mind: Alan Mackay and the Rewriting of the Book of Crystallography.” The lecture celebrates the life and work of Alan Mackay, an independent thinker whose bold ideas helped reshape modern crystallography.

Mackay, who joined JD Bernal’s lab at Birkbeck more than 75 years ago, was known for questioning scientific conventions and pushing the boundaries of structural science. His  research on quasicrystals – structures that challenged accepted theories of symmetry and crystallography – later became the basis for a Nobel Prize-winning discovery.

The 2025 lecture will be delivered by Professor John Finney, a former Birkbeck student and close colleague of both Bernal and Mackay. Drawing on personal experience, Professor Finney will explore the unique intellectual environment of Bernal’s laboratory, a space where collaboration, curiosity and radical ideas thrived.

Established in 1968, the Bernal Lecture commemorates JD Bernal (1901–1971), former Professor of Physics and Chair of Crystallography at Birkbeck. A pioneer in X-ray crystallography, Bernal was also known for his interest in the social impact of science and his leadership during the Second World War. His legacy lives on through this annual event, which returned in 2024 after a pandemic-related pause.

Katherine Thompson, from Birkbeck’s Faculty of Science commented:

“Scientific research for the benefit of society is at the heart of Birkbeck, and the Bernal Lecture is always a highlight of our year. This time it is especially meaningful, as we commemorate the life, ideas, and legacy of two remarkable scientists: JD Bernal and Alan Mackay. The lecture will be delivered by John Finney, a former Birkbeck PhD student who knew and worked with both men. John went on to serve as Chief Scientist at the national neutron facility ISIS before becoming Quain Professor of Physics at UCL. We look forward to what promises to be a fascinating and thought-provoking evening.”

The lecture will be taking place on 23 September, 16:00 – 19:00, at Birkbeck Clore Management Centre. The event is open to the public, with all encouraged to attend.

Further Information

• Book your place on the Bernal Lecture

The Swiss government offers fellowships for British researchers to undertake a research project in Switzerland.

Switzerland has some of the world’s top universities and research institutes © Switzerland Tourism / Lorenz Richard The Swiss Government Excellence Scholarships give early-stage British researchers (Master’s degree or recent PhD) the opportunity to pursue a research project at postgraduate, doctoral or postdoctoral level at any of Switzerland’s universities or national research institutes. Applicants need to propose a research project that is supported by an academic supervisor at their institution of choice. Maximum duration is 12 months for research projects and 36 months for pursuing a PhD. The application deadline for Scholarships commencing in September 2026 is 5 December 2025.

Details and application guidelines.

For further information please contact Dr Lutz-Peter Berg (lutz-peter.berg@eda.admin.ch) at the Embassy of Switzerland in London.

A new project led by UCL seeks to develop the plants and food of the future, supported by UK government funding from the Advanced Research and Invention Agency (ARIA).

Professor Saul Purton (UCL Structural & Molecular Biology) and Dr Scott Lenaghan (University of Tennessee) are co-leading a project, supported by an £8.9 million grant, that aims to harness the power of organisms that capture energy from sunlight (photosynthesis) – both land plants and algae – for the sustainable, affordable, and accessible production of valuable compounds for healthcare and manufacturing.

Read the full article here.

TwinsUK is the UK’s largest study of adult twins who have contributed their health data over up to 30 years. Claire Steves, together with twins involved in the studies – Yvonne Haines and Sandra Coles, will talk about how this collaboration between scientists and participants has contributed to understanding of how we can stay healthy as we age.

Happy to announce that Prof. Franca Fraternali as a Keynote speaker this year at 3DSIG/ISMB in Liverpool! Prof. Fraternali will present cutting-edge AI and structure-based strategies for antibody design, from chain pairing prediction to beyond-CDR engineering.

You can still register to attend the conference and stay updated about the latest developments in Structural Bioinformatics and Computational Biophysics!

Find more information on the conference: https://www.iscb.org/ismbeccb2025/home

Congratulations to Professor Frances Brodsky on being elected a member of the American Academy of Arts and Sciences in the Cellular and Developmental Biology Section of Biological Sciences, in recognition of her outstanding scientific and leadership achievements.

We are proud to see Frances join the ranks of such distinguished individuals whose, in the words of Academy President L.L. Patton, “accomplishments speak volumes about the human capacity for discovery, creativity, leadership, and persistence. They are a stellar testament to the power of knowledge to broaden our horizons and deepen our understanding.”

Frances’s research focuses on membrane traffic in cells, and on the structure and function of clathrin and adaptor proteins that regulate these processes in health and disease.

Find out more about the Brodsky lab: https://www.ucl.ac.uk/biosciences/structural-and-molecular-biology/brodsky-lab/