About me
Omnigenics. Molecular diagnostics. Excellence in DEI.
I harness sequencing technologies to understand gene regulation and molecular function. My research borrows principles from statistics, biophysics, graph theory, text as data, and evolutionary biology to answer questions in neurodegeneration, human genetics, RNA biology, and social science. I previously led the Queer Science Society and the Diversity and Science Lecture series.
My work has been featured in The Atlantic, Quanta magazine, the American Statistical Association’s podcast Practical Significance, and the Stanford Alumni podcast The Champions.
Education
Stanford University
| Stanford, CA
Ph.D. in Genetics | September 2014 - July 2019
Greenleaf & Pritchard labs
M.S. in Medicine | September 2014 - July 2019
Advised by Ben Barres, Medical Genetics experience w/Akash Kumar
University of Washington | Seattle, WA
B.S. in Microbiology and in Biochemistry | September 2009 - June 2013
Gelb & Shendure labs
Ph.D. in Genetics | September 2014 - July 2019
Greenleaf & Pritchard labs
M.S. in Medicine | September 2014 - July 2019
Advised by Ben Barres, Medical Genetics experience w/Akash Kumar
University of Washington | Seattle, WA
B.S. in Microbiology and in Biochemistry | September 2009 - June 2013
Gelb & Shendure labs
Experience
Octave Bioscience |
Data Science
Data Scientist | June 2024 - Present
Exai Bio | Computational Biology & Algorithms
Staff Scientist, Bioinformatics | June 2023 - June 2024
University of California, San Diego | Yeo lab
Helen Hay Whitney Foundation Postdoctoral Fellow | September 2019 - June 2023
University of Washington | Shendure lab
Research Scientist Assistant | June 2013 - July 2014
Undergrad researcher | November 2011 - June 2013
Data Scientist | June 2024 - Present
Exai Bio | Computational Biology & Algorithms
Staff Scientist, Bioinformatics | June 2023 - June 2024
University of California, San Diego | Yeo lab
Helen Hay Whitney Foundation Postdoctoral Fellow | September 2019 - June 2023
University of Washington | Shendure lab
Research Scientist Assistant | June 2013 - July 2014
Undergrad researcher | November 2011 - June 2013
What I do
Programming languages I
know:
R, AWK, Bash, Python, C++, Java, Perl
Software I use:
R: dplyr, ggplot2, VGAM, Shiny, ComplexHeatmap, igraph
Python: Pandas, requests, Snakemake, scikit-learn
Apps: Illustrator, Sublime Text, CellProfiler, Overleaf
Command line: samtools, bcftools, bedtools, STAR, HOMER, PLINK
Omics modalities I analyze:
Olink, RNA-seq, ATAC, eCLIP, GWAS, MIPs, CRISPR screens
Databases I consult:
PPMI, gnomAD, COSMIC, Cancer DepMap, CCLE, GENCODE, Rfam
Resources I contributed:
Cas9 off-target calculator
Co-essential gene network browser
Skipper RNA-protein interactions
DASL diverse speaker database
R, AWK, Bash, Python, C++, Java, Perl
Software I use:
R: dplyr, ggplot2, VGAM, Shiny, ComplexHeatmap, igraph
Python: Pandas, requests, Snakemake, scikit-learn
Apps: Illustrator, Sublime Text, CellProfiler, Overleaf
Command line: samtools, bcftools, bedtools, STAR, HOMER, PLINK
Omics modalities I analyze:
Olink, RNA-seq, ATAC, eCLIP, GWAS, MIPs, CRISPR screens
Databases I consult:
PPMI, gnomAD, COSMIC, Cancer DepMap, CCLE, GENCODE, Rfam
Resources I contributed:
Cas9 off-target calculator
Co-essential gene network browser
Skipper RNA-protein interactions
DASL diverse speaker database
Selected publications
Boyle EA,
Her HL, Mueller JR, Naritomi JT, Nguyen GG, Yeo GW. Skipper
analysis of eCLIP datasets enables sensitive detection of
constrained translation factor binding sites (2023) Cell
Genomics.
Boyle EA, Li YI, Pritchard JK. An expanded view of complex traits: from polygenic to omnigenic (2017) Cell.
Boyle EA, Goldberg G, Schmok JC, Burgado J, Izidro Layng F, Grunwald HA, Balotin KM, Cuoco MS, Chang KC, Ecklu-Mensah G, Jagannatha P, Pekar J, Iyer M, DASL Alliance, Yeo GW. Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM (2023) PLOS ONE.
Boyle EA†, Becker WR†, Bai HB†, Chen JS, Doudna JA, Greenleaf WJ. Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement (2021) Science Advances.
Boyle EA, Pritchard JK, Greenleaf WJ. High‐resolution mapping of cancer cell networks using co‐functional interactions (2018) Molecular Systems Biology.
Findlay GM†, Boyle EA†, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair (2014) Nature.
Boyle EA, O’Roak BJ, Martin BK, Kumar A, Shendure J. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing (2014) Bioinformatics.
Boyle EA, Li YI, Pritchard JK. An expanded view of complex traits: from polygenic to omnigenic (2017) Cell.
Boyle EA, Goldberg G, Schmok JC, Burgado J, Izidro Layng F, Grunwald HA, Balotin KM, Cuoco MS, Chang KC, Ecklu-Mensah G, Jagannatha P, Pekar J, Iyer M, DASL Alliance, Yeo GW. Junior scientists spotlight social bonds in seminars for diversity, equity, and inclusion in STEM (2023) PLOS ONE.
Boyle EA†, Becker WR†, Bai HB†, Chen JS, Doudna JA, Greenleaf WJ. Quantification of Cas9 binding and cleavage across diverse guide sequences maps landscapes of target engagement (2021) Science Advances.
Boyle EA, Pritchard JK, Greenleaf WJ. High‐resolution mapping of cancer cell networks using co‐functional interactions (2018) Molecular Systems Biology.
Findlay GM†, Boyle EA†, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair (2014) Nature.
Boyle EA, O’Roak BJ, Martin BK, Kumar A, Shendure J. MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing (2014) Bioinformatics.