Professional Preparation

 

Staff Scientist, Biostatistics, Whole Biome, San Francisco. 2016-present.

 

 Biostatistician, Second Genome Inc., San Francisco. 2014-2016

 

 Research Associate, Statistics Department, Stanford University, 2014.

 

 Postdoctoral fellow, Statistics Department, Stanford University, 2010-2013.

 

 PhD in in Environmental Engineering, Genomics, Stanford University. 2005-2010.

 

Ms, Stanford University. 2004-2005.

 

BSc, University of Arizona. 2000-2004.

 

 
Selected Publications

 

Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson, Susan P Holmes (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods.

 

Ben J Callahan, Kris Sankaran, Julia A Fukuyama, Paul J McMurdie, Susan P Holmes (2016) Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000Research. 

 

Daniel B DiGiulio, Benjamin J Callahan, Paul J McMurdie et al. (2015) Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences.

 

Paul J McMurdie, Susan Holmes (2015) Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. Bionformatics

 

Paul J McMurdie, Susan Holmes (2014) Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol.

 

Paul J McMurdie, Susan Holmes (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.

 

 

 

 Google Scholar profile: https://scholar.google.com/citations?user=nNQ1LtMAAAAJ