Paul Mcmurdie - Head Of AI, Data, And Technology

Paul Mcmurdie

Head Of AI, Data, And Technology

San Francisco, California, United States

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Summary

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Senior

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Top School

Paul Mcmurdie is Head of AI, Data, and Technology with 14 years of experience applying statistics, bioinformatics, and engineering to translational health problems spanning inflammatory bowel disease, Type 2 diabetes, and oncology. He combines hands-on AI/ML method development with technical leadership—building analysis infrastructure, leading teams, and steering biomarker discovery efforts that supported a Phase 2 success and multiple patent filings. An active open-source contributor, Paul has helped maintain widely used R packages such as phyloseq and dada2, and his analytics libraries have been downloaded over 500,000 times. He holds deep academic training from Stanford (PhD and postdoc) and has co-authored 30+ peer-reviewed papers with more than 30,000 citations, reflecting a rare blend of methodological rigor and applied impact. Known for turning complex, high-dimensional sequencing and metabolomics datasets into robust, reproducible inference, he also brings practical experience optimizing pipelines for scale and error correction in sequencing. Based in San Francisco, he thrives at the intersection of research, product, and production-grade data science.

14 years of coding experience

9 years of employment as a software developer

The University of Arizona

Postdoctoral Fellow Statistics, Postdoctoral Fellow Statistics at Stanford University

Stackoverflow

Stats

7,345reputation

2.3mreached

28answers

8questions

Badges

generics

top-5%

statistics

top-5%

Github Skills (16)

bioinformatics10

r10

microbiome9

metagenomics9

data-analysis9

data-structure9

generics9

statistics9

data-structures9

sequence-alignment8

ggplot8

slot6

geometric-mean6

github6

roxygen6

Programming languages (4)

RCHTMLPython

Github contributions (5)

joey711/phyloseq

Aug 2011 - Nov 2022

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

Role in this project:

Back-end Developer

Contributions:828 commits, 27 PRs, 98 pushes in 11 years 4 months

Contributions summary:Paul's commits primarily focused on fixing bugs within the accessor methods. The code changes involved modifications to the taxonomy class with addition of new methods to handle specific types of datasets. Further, the code fixes addressed issues regarding the reordering of the tree and the handling of a number of data conditions during the import functions.

sequencing-datasequencinggenomicsphyloseqbioinformatics

benjjneb/dada2

Dec 2014 - Jul 2017

Accurate sample inference from amplicon data with single nucleotide resolution

Role in this project:

Back-end Developer

Contributions:23 commits, 8 PRs, 9 pushes in 2 years 7 months

Contributions summary:Paul's primary contribution involved modifying and maintaining the `dada2` package, focusing on code related to sequence input/output, plotting methods, and filtering. Their work included fixing namespace issues, correcting build warnings, and updating vignettes to ensure they appear in the package documentation. They also implemented a function to plot substitution pairs from DADA results, and improved the `fastqPairedFilter` function.

metabarcodingmetagenomicsampliconinferenceresolution

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