Hello friends!

My name is Annabel Large (国晓瑛), and I’m a 6th year PhD candidate advised by Ian Holmes.

I develop mathematical models to describe how biological sequences evolve over time. Specifically, I parameterize stochastic processes using techniques from automata theory, mixture modeling, and deep learning. Statistical phylogenetics uses these models to predict what ancestral sequences looked like millions of years ago, or to forecast how a sequence might continue to change in the future.

I find myself at the intersection of probabilistic modeling, machine learning/artificial intelligence, and synthetic biology. To learn more, find my CV here.

Note: I am not the illustrator of children’s and young adult books. I have never been diagnosed with occipital neuralgia.

Preprints

• Annabel Large*, Ian Holmes. Nested birth-death processes are competitive with parameter-heavy neural networks as time-dependent models of protein evolution, bioRxiv 2026

Select Publications

• Svante Resjö, Jakob Willforss, Annabel Large*, Valentina Siino, Erik Alexandersson, Fredrik Levander, Erik Andreasson. Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days, Plant Physiology and Biochemistry 2024
• Anna Furches, David Kainer, Des Weighill, Annabel Large*, Piet Jones, Angelica M Walker, Jonathon Romero, Joao Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasyam, David Macaya-Sanz, Nan Zhao, Madhavi Z Martin, Xiaolan Rao, Richard A Dixon, Stephen DiFazio, Timothy J Tschaplinski, Jin-Gui Chen, Gerald A Tuskan, Daniel Jacobson. Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence, Frontiers in Plant Science 2019

You might know me from…

• my PhD program, the UC Berkeley - UCSF Graduate Program in Bioengineering
• my concurrent affiliation with UC Berkeley’s Center for Computational Biology
• my Fulbright Fellowship at the Swedish University of Agriculture, Alnarp
• my undergraduate years…
  • in the Chemical Engineering program at the University of Tennessee, Knoxville
  • with the Computation and Predictive Biology Group at Oak Ridge National Laboratory
  • with the Joint BioEnergy Institute at Lawrence Berkeley National Laboratory