Nathan Schaefer
Postdoctoral Scholar at University of California, San Francisco
Aarhus, Central Denmark Region, Denmark
Summary
👤
Senior🎓
Top SchoolNathan Schaefer is a postdoctoral bioinformatician with nine years of experience applying population genomics, statistical methods, and single-cell multi-omic analysis to probe human-specific brain development and disease vulnerability. He develops practical tools—most notably CellBouncer—for demultiplexing, QC, and ambient RNA correction in pooled single-cell experiments, and has implemented fast heuristic algorithms for ancestral recombination graph inference to enable novel population-genomic scans. At UCSF he combines tetraploid inter-species cell lines, Perturb-seq analyses, and evolutionary history to tie regulatory mutations to cellular phenotypes across development. Nathan blends deep computational rigor with an experimental sensibility, prioritizing QC and scalable pipelines that reduce batch effects and make complex pooled designs tractable. He is interested in leveraging neural-network predictors of variant impact and integrating allele-frequency history with single-cell functional genomics to reveal human-specific biology.
10 years of coding experience
11 years of employment as a software developer
Bachelor’s Degree, Biology, Botany, Computer Science certificate, Honors in the Liberal Arts, Bachelor’s Degree, Biology, Botany, Computer Science certificate, Honors in the Liberal Arts at University of Wisconsin-MadisonUniversity of California Santa Cruz
Github Skills (19)
sequencing8
rna-seq6
bioinformatics6
ancestry6
coverage5
chip-seq4
covariance4
lift4
python4
genome-analysis3
3d3
venn-diagram3
inference3
structural-variation2
single-cell-genomics2
Programming languages (5)
Github contributions (5)
nkschaefer/cellbouncer
Oct 2024 - Apr 2026
Tools for pooled single cell sequencing experiments: demultiplex cells, infer doublet rate, assign treatments/sgRNAs, infer ambient RNA from allele matching
Contributions:1 release, 1 PR, 68 pushes in 1 year 7 months
sequencing
nkschaefer/numty-dumpty
Feb 2024 - Nov 2025
Contributions:1 release, 22 pushes, 1 branch in 1 year 8 months
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