I am a Ph.D. student
in the MIT Machine Learning Group
the Broad Institute,
working on Bayesian methods for learning from
I am co-advised by
(MIT CSAIL) and
(Broad Institute of MIT & Harvard).
Before that, I was a Molecular Biology major at Pomona College,
a Fulbright scholar at the
Australian Centre for Ecogenomics,
intern at Fast Forward Labs,
and a microbiologist at Jasper Hill.
Bayesian tree models of cellular differentiation
[ MIT CSAIL, Broad Institute ]
Inferring probabilistic latent branching trajectories of
differentiation from single-cell gene expression (scRNA-seq).
Shiffman ME, W Stephenson,
G Schiebinger, T Campbell, J Huggins,
A Regev, T Broderick (2017)
Probabilistic reconstruction of cellular differentiation
trees from single-cell RNA-seq data. NIPS workshops in
Approximate Bayesian Inference and
Machine Learning in Computational Biology.
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)
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
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.
Shiffman ME, J Button, RJ Dutton (2014)
Cheese as a model microbial ecosystem. International Society
for Microbial Ecology (ISME) conference.
Shiffman ME, BM Charalambous (2012) The search
for archaeal pathogens. Reviews in Medical