Our group has several ongoing projects.

  • Bayesian phylogenomic inference using Monte Carlo methods, including Sequential Monte Carlo, MCMC, and approximate Bayesian computation. See the STS software and beagle library for examples of recent work in this area.
  • Understanding the development of the infant gut microbiome, the relationship with maternal microbiota, and the development of atopy. In collaboration with a large team led by Prof. Shyamali Dharmage and with support of the National Health and Medical Research Council, we are studying the microbiota found in the breast milk of families that are at risk for atopy.
  • Forensic analysis of microbial samples using phylogenetic analysis of metagenome data. In collaboration with the labs of Jonathan Eisen at UC Davis and Erick Matsen at FHCRC we develop the PhyloSift software, which provides an integrated set of tools for Bayesian phylogenetic & ecological analysis of metagenomic data.
  • Development of advanced techniques for studying microbial genomes and metagenomes by tightly coupled development of computational inference methods and next-generation sequencing techniques. Two examples of recent work in this area are the development of metagenomic Hi-C and the development of full length 16S ribosomal gene sequencing on the Illumina MiSeq.
  • Comparative genomics and genome assembly. We are developing and applying wet-lab protocols and software pipelines to sequence the genomes of microbial isolates en masse using the Oxford Nanopore, Pacific Biosciences, and Illumina platforms. Recent work in this area includes the A5-miseq assembly pipeline.