People | fuscolab

Group Leader

Diana Fusco, PhD

Associate Professor, Dept. of Physics, University of Cambridge
Assistant Professor, Dept. of Physics, University of Cambridge (2018-2023)
Postdoctoral Researcher, University of California-Berkeley (2014-2018)
PhD in Computational Biology and Bioinformatics, Duke University (2014)
MSc in Theoretical Physics, Universita' degli Studi di Milano (2008)
BSc in Physics, Universita' degli Studi di Milano (2006)

Diana's interest in biology started as a physics undergrad studying topological properties of the transcriptional network in budding yeast. After that, she was hooked and moved to soft matter and protein self-assembly for her PhD, under the supervision of Dr. Charbonneau at Duke. Unsatisfied with addressing questions exclusively on the computational side, she embarked onto a hybrid postdoc in Dr. Hallatschek lab at UC Berkeley, where she studied the evolutionary consequences of spatial range expansion combining microbiology and mathematical modeling.

Postdocs

Temur Yunusov, PhD

Postdoctoral Associate, Department of Physics, University of Cambridge
Research Laboratory Coordinator, Sainsbury Laboratory, University of Cambridge (2013-2021)
PhD in Developmental Neuroscience, University of Cambridge (2013)
BSc in Ecology and Environmental Studies from the National University of Uzbekistan (2007)

After completing my BSc in Tashkent, I worked at the Institute of Regional Problems, Samarkand Academy of Sciences as part of a team analysing the soil and water quality of the Zerafshan river basin, in order to investigate the impact on flora in the region. My PhD research In Cambridge focused on the development of genetic tools to study the cholinergic interneurons in Drosophila melanogaster larvae. Upon completing my PhD I worked as a Research Laboratory Coordinator in the Sainsbury Laboratory at the University of Cambridge. My research there focused on studying the cellular interfaces between plants and both mutualistic (R. irregularis) and pathogenic (P. palmivora) microorganisms using a variety of techniques, including genetic manipulation, fluoresence imaging and microdissections.

My current work focuses on exploring the potential of the bacteriophage system as a model for studying strategies and mechanisms of evolution. Bacteriophages are uniquely adapted to take control over the bacterial metabolism and to replicate at maximum efficiency. The mechanisms and strategies they employ could shed light on metabolic processes in bacteria. To elucidate these, I plan to work on phage gene-editing to visualize phage-bacteria interactions at single-cell resolution and develop a system to use phages as probes to study the bacterial processes.

Abhirup Mookherjee

Postdoctoral Research Associate, Department of Physics, University of Cambridge
Postdoctoral Fellow, The Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem (2019-2022)
Ph.D. in Microbial Biotechnology, Department of Biotechnology, Indian Institute of Technology Kharagpur (2012-2019)
M.Sc. in Microbiology, West Bengal University of Technology (2011)
B.Sc. in Microbiology, University of Calcutta (2009)

I am a Microbiologist interested in understanding microbial antibiotic resistance and mitigating the same. During my Ph.D., I worked on microbial biotechnology where my primary goal was to bioprospecting endophytic fungi and yeasts for the synthesis of natural products (antimicrobial, antibiofilm, quorum sensing inhibitory, and antioxidant) compounds. In this work I sensed the urgency of discovering novel bioactive drugs valuable for the healthcare sector. In my previous postdoctoral research at the Hebrew University of Jerusalem, my research focused on identifying genetic elements involved in the host-independency, and self-biofilm-formation of the predator Bdellovibrio bacteriovorus. The greater goal of my study was to understand the cell biology of the predator for bioprospecting the same as a ‘living antibiotic’.

Currently, I am working on bacterial biofilm resilience using the model organism Bacillus subtilis with an interdisciplinary approach. We hypothesize that one of the reasons behind biofilm’s robustness is the ability of bacteria to respond to the environment in a coordinated fashion even if their decision occurs at the single-cell level (phenotypic plasticity).

Jordan Romeyer Dherbey

Graduate Students

Postdoctoral Research Associate in Microbial Physics, Department of Physics, University of Cambridge (2024 – Present)
Postdoctoral Wrap Up, Department of Microbial Population Biology, Research Group Microbial Molecular Evolution, Max Planck Institute for Evolutionary Biology (2023)
PhD in Microbial Evolutionary Biology, Department of Microbial Population Biology, Research Group Microbial Molecular Evolution, Max Planck Institute for Evolutionary Biology (2019 – 2023)
MSc 2 in Bio-Geosciences, Biological Anthropology, University of Bordeaux (2016 – 2017)
MSc 2 in Genetic Anthropology of Human Populations, University of Toulouse III (2015 – 2016)
MSc 1 in Cellular and Molecular Biology, Joseph Fourier University, Grenoble Alpes (2014 – 2015)
BSc in Biology, Joseph Fourier University, Grenoble Alpes (2013 – 2014)

I am a microbial evolutionary biologist with a particular interest in bacteriophage (phage) biology and evolution. My PhD work focused on the experimental evolution of phage resistance from modifications of the lipopolysaccharide (LPS, phage-host receptor) structure and how, in return, the phage evolves to overcome these resistances. I developed a bottom-up approach to study the natural LPS structure in ΦX174 – resistant E. coli C strains. I demonstrated that phage adaptation can be sped up by increasing phage and host diversities to overcome difficult-to-infect phage-resistant mutants. I also showed that the nature and location of mutations within the same LPS gene could cause very different phage-resistance phenotypes, indicating that LPS phenotypes leading to phage resistance are much more diverse than anticipated from the current LPS model.

Currently, I continue to explore phage-bacterium coevolution and, especially, investigate genotypes – phenotypes fitness maps in complex and more natural settings (i.e., colony biofilms). Biofilms are complex, non-clonal multicellular entities in a constant phenotypic flux. Thus, the main genetic and phenotypic mechanisms that drive the emergence (and re-emergence) of microbial resistances will certainly be different than the ones observed in well-mixed, liquid settings (i.e., almost exclusively mutations in genes linked to the host receptor). Similarly, the conditions required for phages to sustain their populations and overcome phage resistance will be different.

Nikhil Krishnan

PhD student in Physics and Gates Scholar, University of Cambridge
MD, Case Western Reserve University, Cleveland, Ohio (2020)
BSc. Biophysics, Case Western Reserve University, Cleveland, Ohio (2016)

As a medical student, I frequently helped take care of patients with antibiotic resistant infections. Through my clinical experiences, I encountered the daunting global crisis of antibiotic resistance first-hand. The apparent complexity of this problem compelled me to approach it as a physicist, striving to reduce the complexity of evolution into fundamental mechanisms. I am ecstatic to have the opportunity to work on a piece of this puzzle through my thesis project, which will examine how evolution acts on short- and long-range cell-to-cell interactions within bacterial biofilms through theory and simulations. As an aspiring physician-scientist, I am greatly motivated to carry forward this broad, interdisciplinary approach to further our understanding of microbial evolution and improve clinical strategies for prevention and treatment of antibiotic resistance.

Aaron Smith

PhD Student in Biological Physics, University of Cambridge
PGCE. Secondary Science with Physics, University of Cambridge (2021-22)
BA and MSc Natural Sciences, University of Cambridge (2017-21)

I completed my undergraduate degree during the height of the COVID-19 pandemic, which resulted in a slightly unusual career path, but a keen awareness of the value of good educators. Having now completed a teaching degree I am excited to put this to use during undergraduate supervisions alongside my research over the course of my PhD. I am interested particularly in how our (comparatively) simple models of bacteriophage behaviour work and where they break down, and I am excited to be working on models and technologies that may one day see life-saving medical application.

Hassan Alam

PhD student in Physics, University of Cambridge
MSc in Physics, University of Waterloo, Canada (2022)

I am interested in understanding the coevolution of phages and bacteria in complex microbial environments. For this purpose, I use mathematical models and develop algorithms to study possible evolutionary trajectories of phage-bacteria interactions. These interactions depend on many biological and physical factors like bacteria life, proximity, physical barriers, etc. Therefore, I explore how different biophysical parameters control viral fitness in microbial systems. These theoretical studies also guide my experiments to test my hypotheses on phage-bacteria ecosystems.

Anna Tarodi

PhD student in Physics and Gates Scholar, University of Cambridge
MASt in Physics, University of Cambridge (2023)
BSc in Physics with Theoretical Physics, King’s College London (2022)

I am working on elucidating how collective emergent phenomena arise in bacterial communities when individual cells aggregate to form biofilms. I am employing experimental and computational techniques to discover how environmental cues and interactions influence the dynamics of single bacterial cells within a biofilm. My investigation involves the matrix-motility lifestyle switch of Bacillus Subtilis in microfluidic experiments in varied conditions. I am interested in how the collective dynamics of cells influences the health of ecosystems and the health of individuals, in case of human pathologies for example, where biofilms are linked to increased antimicrobial resistance.

Moe Vali

PhD student in Physics, University of Cambridge
Part III Physics, University of Cambridge (2023)
BSc Physics (Natural Sciences), University of Cambridge (2022)

My interests lie in applying innovative machine learning and spectroscopic methods to better understand complex living systems, aiming to generate new (and potentially out-of-distribution) microbial communities. Such communities are driven by local and non-local interactions that govern their assembly and thus output. I hope to utilise neural networks to better understand these ubiquitous, n-body, dynamic systems whereby a deeper understanding of their mechanisms and ultimately manipulation are pressing challenges.

Yulin Du

PhD Student in Physics, University of Cambridge
MSc in Physics, École Polytechnique Fédérale de Lausanne, Switzerland (2023)
BSc in Physics, Huazhong University of Science and Technology, China (2020)

Captivated by the essence of the universe and nature, my physics journey started from high energy theory during my undergrad. Not content with only observing and calculating particles, I moved to a more interesting and complex area: the study of life at its most elementary level. After some basic exploration of bacteria and worms during my Master, as a doctoral student, I am now exploring biofilms, seeking to understand their characteristics and functions from a physicist’s perspective. My work aims to construct models to describe the complex interaction between bacteria and environment, and within bacterial communities, and to conduct some experiments to test them. By bridging physical theories with biological phenomena, I wish to illuminate the evolution dynamics of biofilms, with the hope of contributing to their application and management in human daily life.

Oliver Kurilov

MPhil Student, Physics, University of Cambridge
BSc., Computational Biology with Mathematics, University of California - Los Angeles (2023)

Throughout my undergraduate degree, I specialized in developing and analyzing computational models of soft matter, biomaterials and molecular systems. I am most captivated by the physical and mechanical processes governing the genesis of complex molecular architecture and biofilm morphology. In my work, I hope to contribute to the ongoing modelling efforts to understand mechanical instability in biophysical context. My primary goal is to explore macroscopic mechanical properties of biofilms that emerge from the microscopic cell-cell and cell-substrate interactions through computing, combining agent-based and diffusion fields modelling

Undergraduate Students

Joseph Steane: Part III Physics Student (2023-24)
Xingjian Hou: Part III Physics Student (2023-24)
James Bridson: Part III Systems Biology Student (2023-24)

Former Members

Dr. Racha Majed: Postdoctoral Research Associate (2019-2021) - currently working for a start-up in Oxford
Armin Eghdami: Physics Master Student (2020) - currently graduate student at UC Berkeley
Dr. Michael Hunter: Physics PhD student (2018-2022) - currently postdoc in the Tropini Lab, UBC
Hannah Horton: Summer Undergraduate Research Student (2020)
Siqi Fang: Summer Undergraduate Research Student (2020)
Tongfei Liu: Summer Undergraduate Research Student (2019)
Sherry Jiatong Jiang: Summer Undergraduate Research Student (2019)
Chris Dickinson: Part III Physics Student (2019-20)
Callum Holmes: Part III Physics Student (2019-20)
Amy Bowen: Part III Physics Student and Summer Undergraduate Research Student (2020-21) - currently PhD student at the Francis Crick Institute
Brendan Beh: Part III Physics Student (2020-21)
Caredig ap Tomos: Summer Undergraduate Research Student (2021)
Peter Hampshire: Part III Physics Student (2021-22) - currently PhD student at MPI for Complex Systems
Shashvat Verma: Part III Physics Student (2021-22) - currently Research Assistant in the Bohndiek Lab
Joseph Knight: Part III Physics student (2022-23) - currently PhD student at the University of Edinburgh
Kirke Joamets: Part III Physics student (2022-23)
Zhisong Liu: Part III Physics student (2022-23) - currently PhD student at UT Austin
Gil Krikler: Part III Systems Biology student (2022-23)
Pannaree Boonyuen: Part III Systems Biology student (2022-23)
Ed Wheeler: Summer Undergraduate Research Student (2023)
Crispin Turner: Summer Undergraduate Research Student (2023)
James Longstaff: Summer Undergraduate Research Student (2023)