Laboratory of Systems and Synthetic Microbiology
Laboratory of Systems and Synthetic Microbiology
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We are an interdisciplinary team of scientists and engineers interested in understanding and engineering microbial systems to learn about nature and to apply this knowledge in health, agriculture, and industry. We collaborate with several other labs across the world to work on these problems together. Links to their websites and information about joining us are provided in the resource page.
PI
Somenath Bakshi (Google Scholar)
Associate Professor (January 2023 - )
Assistant Professor (January 2019 - January 2023)
Postdoctoral research, Harvard University (September 2014 - Nov 2018)
PhD, University of Wisconsin Madison (December 2013)
Email: somenath.bakshi@eng.cam.ac.uk Phone: +44 1223 3 32753
Tech Support
James Macleod
James is a Principal Technician of the Bio-Engineering Laboratories.
Email: rjm239@eng.cam.ac.uk Phone: +44 1223 7 64097
Narges Khadem Hosseini
Narges is a Principal Technician in Biological laboratories. She provides technical support for the students.
Email: nk616@cam.ac.uk Phone: +44 1223748509
Postdocs/ Research Associates
Alma Wu
Alma is a postdoc in synthetic biology. She completed her PhD at the University of Sydney in 2023, focusing on antibiotic resistance plasmids, and now works on engineering stable genetic circuits on both plasmids and chromosomes for therapeutic applications.
Email: ayw32@cam.ac.uk
ResearchGate: https://www.researchgate.net/profile/Alma-Wu
PhD Students
Georgeos Hardo
Georgeos is 5th year PhD student in Biological Sciences (Systems & Synthetic Biology) from the BBSRC DTP programme. His current research is about developing image analysis tools for high-throughput single-cell microscopy, and using these tools to study bacterial dormancy and antibiotic persistence.
Charlie Wedd
Charlie is the 4th year PhD student from the EPSRC Sensor CDT programme. His research focusses on characterising the timing and noise of bacteriophage infection cycle within individual cells using high-throughput time lapse microscopy.
Email: cdw42@cam.ac.uk
Jack Bradley
Jack is first-year PhD student from the AgriForwards CDT. His research centers on creating a bioreactor array tailored for the automated maintenance and monitoring of microbial cultures. His primary objective is to use this setup for analyzing the performance and lifespan of genetically modified microbes.
Email: jb2524@cam.ac.uk
Erez Li
Erez is currently a 1st year PhD student. His focus lies in comprehending how physiological heterogeneity among bacterial cells influences their reaction to treatments involving antimicrobials and bacteriophages, and subsequently, how this phenomenon shapes the overall response at the population level.
Email: rl627@cam.ac.uk
Aparna Kaaraal Mohan
Aparna is a 1st year PhD student from the EPSRC Sensor CDT programme. She is working on developing microfluidic-microscopic approaches to understand the effects of cellular dormancy towards phage therapy.
Aaron Smith
Aaron Smith
Aaron is a 2nd year PhD student. He is captivated by the fascinating intersection of biological physics, where complex systems can be elegantly described by a few characteristic equations and variables. His passion lies in expanding these models, particularly in understanding how a bacteriophage's traits interdepend on each other, the host, and the environment. Aaron is privileged to work within two supportive groups spanning Physics and Engineering departments, leveraging cutting-edge microfluidic facilities to advance his research.
Email: atss2@cam.ac.uk
Massimo Zambernardi
Massimo is an MEng project student, currently undertaking a UROP. He is working on video-object segmentation and lineage reconstruction of bacteria growing in microfluidic devices, with the aim of facilitating the analysis of physiological heterogeneity at the single-cell level.
Email: mz453@cam.ac.uk
Kieran Abbott
Kieran Abbott
Kieran is a 1st year PhD student, jointly affiliated with the Zarkan Group in the Department of Genetics. His research involves developing a genetically-encoded fluorescent sensor for bacterial membrane potential and utilising timelapse microfluidics-microscopy to study bacterial antibiotic persistence at the single-cell level.
Email: ka537@cam.ac.uk
Alumni
James Morgan-James was a research assistant, who was developing a modular, open-source bioreactor. He aimed it at conducting long-term evolution experiments involving microbes (2023)
Robbie Hodgeon - MEng project student, Limits of spatial resolution in high-througput single-cell imaging of bacteria (2022)
Ruizhe Li - MEng project student, Limits of temporal resolution in high-througput single-cell imaging of bacteria (2022)
James Morgan - MEng project student, Engineering a fossil-collection system for automated record-keeping of evolving mcirobial cultures (2022)
Yu an Han - MEng project student, Adaptive image segmentation using pseudolabelling (2022)
Nandini Praveenkumar - Mini project from Photonics CDT, designing Inline optical sensors for monitoring cell density
Eva Chatry - MPhil Biotechnology student, Modelling effects of protein maturation on reporter signal dynamcis (2021)
Ben Wilson - MEng project student, Adapting widefield microscopy for imaging microbial biofilms (2021)
Dustin Baek - MEng project student, Computer vision approaches for image based barcode recognition (2021)
Ishaan Vadgama - MEng project student, Quantifying morphological dynamics of bacteria in microfluidic devices (2021)
Ali Ahmed - MEng project student, Single-cell analysis of fitness costs of antibitoic resistance (2021)
Jake Gozdziewski - MPhil Biotechnology student, Microscopic inspection of microbial ageing (2020)
Rui Li - MEng project student, Deep-learning approaches for image processing (2020)
Roman Streslov - MEng project student, Computational fluid dynamics for microfluidics design optimisation (2020)
Francis Treherne Pollock - MEng project student, Analysing impacts of point-spread function on microscope images (2020)
Jorge Garcia Condado - MEng project student, Deep-learning for morphological analysis of bacterial cells (2019)
Soham Garg - MEng project student, Engineering a miniature microbial bioreactor (2019)
Maximilian Noka - MEng project student, A virtual microscopy platform to generate syntehtic images to train machine-learning image segmentation models (2019)
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