Daniel Bottomly
Senior Computational Biologist, McWeeney Research Group
Portland, Oregon, United States
Summary
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Senior🎓
Top SchoolDaniel Bottomly is a Senior Computational Biologist with 12+ years of experience designing scalable workflows and statistical models for high-throughput sequencing and functional genomics. Based in Portland and rooted at OHSU, he led seminal projects—his early 'bottomly' RNA-seq dataset remains a benchmark—and scaled sequencing and data systems for the BeatAML consortium to create one of the largest mutation/expression and drug-screen collections in AML. He builds pragmatic, problem-driven machine learning and network-based prioritization tools (notably HitWalker/HitWalker2) that bridge inhibitor/siRNA assays, interaction networks, and clinical genomics. Comfortable supervising small teams and coordinating software engineers, he combines hands-on development (R, Python, Django, Neo4j) with data management, visualization, and reproducible workflow design. An underappreciated strength is his knack for turning exploratory research tools into broadly cited infrastructure—HitWalker2 became influential for its early graph-database usage as much as for its biology.
12 years of coding experience
13 years of employment as a software developer
M.S., Bioinformatics/Computational Biology, M.S., Bioinformatics/Computational Biology at Health and Science jobsB.S., Genetics and Cell Biology, B.S., Genetics and Cell Biology at Washington State University
Github Skills (5)
querying8
database4
databases3
sql3
sqlite3
Github contributions (5)
dbottomly/plethy
Aug 2013 - Dec 2016
Contributions:44 commits, 6 pushes, 3 branches in 3 years 4 months
biodev/beataml2.0_data
Jul 2022 - Mar 2025
Contributions:1 release, 4 pushes, 2 tags in 2 years 9 months
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