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 cheese microbiologist at Jasper Hill.
Bayesian tree models of cellular differentiation
[ MIT CSAIL, Broad Institute ]Inferring latent cell state dynamics (along a probabilistic branching continuum) from static snapshots (single-cell profiles of gene expression).
Shiffman M, WT Stephenson,
G Schiebinger, J Huggins, T Campbell,
A Regev, T Broderick (2018) Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data. arXiv:1811.11790
(paper, poster '18, poster '17, talk)
Creative probabilistic programming
for biology (abstract, poster)
[ Fast Forward Labs ]Whitepaper-style blog series for FFL.
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, J Button, RJ 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)