Fellow

Tom Ellis

Sponsored by Philipp Holliger

Tom Ellis

My research seeks to push synthetic biology beyond the design and construction of small sets of interacting genes and regulators and instead scale this work to the engineering of whole chromosomes and genomes. In my group at Imperial College London, we predominantly focus on using baker’s yeast as a testbed for developing new tools, methods and design principles for whole-chromosome construction. We were part of the international Synthetic Yeast Genome (Sc2.0) project to create a synthetic yeast genome and are now extending this work, developing AI-designed chromosomes for application-specific yeast.

At the LMB, we collaborate with Julian Sale’s group to develop and optimise methods to design, construct, edit and rearrange DNA up to a million bases in length and move this DNA from microbial cells into mammalian cells to test its function. This technology opens up entirely new approaches to test DNA functions at new scales in medically relevant organisms.

Selected Publications

Randomizing the human genome by engineering recombination between repeat elements.Koeppel J, Ferreira R, Vanderstichele T, Riedmayr LM, Peets EM, Girling G, Weller J, Murat P, Liberante FG, Ellis T, Church GM, Parts LScience 387(6733): eado3979 (2025)
Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.Blount BA, Lu X, Driessen MRM, Jovicevic D, Sanchez MI, Ciurkot K, Zhao Y, Lauer S, McKiernan RM, Gowers GF, Sweeney F, Fanfani V, Lobzaev E, Palacios-Flores K, Walker RSK, Hesketh A, Cai J, Oliver SG, Cai Y, Stracquadanio G, Mitchell LA, Bader JS, Boeke JD, Ellis TCell Genom 3(11): 100418
Technological challenges and milestones for writing genomes.Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan SC, Schloss JA, Stracquadanio G, Trefzer A, Bader JS, Church GM, Coelho CM, Efcavitch JW, Güell M, Mitchell LA, Nielsen AAK, Peck B, Smith AC, Stewart CN, Tekotte HScience 366(6463): 310-312 (2020)
Engineering a Model Cell for Rational Tuning of GPCR Signaling.Shaw WM, Yamauchi H, Mead J, Gowers GF, Bell DJ, Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis TCell 177(3): 782-796.e27 (2020)