I am a Ph.D. student in the MIT Machine Learning Group and at the Broad Institute, working on Bayesian methods for learning from single-cell studies.

I am co-advised by Tamara Broderick (MIT CSAIL) and Aviv Regev (Broad Institute of Harvard & MIT).

Before that, I was a Molecular Biology major at Pomona College, a Fulbright scholar at the Australian Centre for Ecogenomics, an intern at Fast Forward Labs, and a microbiologist at Jasper Hill.


Generative tree model

Bayesian tree models of cellular differentiation

[ MIT CSAIL, Broad Institute ]

Inferring probabilistic latent branching trajectories of differentiation from single-cell gene expression (scRNA-seq).

VAE latent spaceevolution

Variational autoencoders, in prose and code

[ Fast Forward Labs ]
    Whitepaper-style blog series for FFL:
  • Introducing variational autoencoders (blogpost)
  • Under the hood of the variational autoencoder (blogpost)
Bayley rind fungi

Microbial ecology and evolution

[ Australian Centre for Ecogenomics, Jasper Hill Farm, Harvard Systems Biology ]
    Computational and experimental approaches to microbial communities in marsupial guts, the human microbiome, and cheese.
  • Shiffman ME, RM Soo, PG Dennis, M Morrison, GW Tyson, P Hugenholtz (2017) Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ 5(e4075). (paper, blogpost)
  • Shiffman ME, Julie Button, Rachel Dutton (2014) Cheese as a model microbial ecosystem. International Society for Microbial Ecology (ISME) conference. (poster)
  • Shiffman ME, BM Charalambous (2012) The search for archaeal pathogens. Reviews in Medical Microbiology 23(3):45-51. (paper)