Xiaoxu Yang
Assistant Professor at University of Utah
Salt Lake City, Utah, United States
Summary
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Senior🎓
Top SchoolXiaoxu Yang is an Assistant Professor and computational biologist with a decade of experience developing methods to detect and interpret genomic mosaicism across human tissues. Her lab combines experimental assays and machine learning—most notably DeepMosaic, a control-independent CNN classifier—to reveal somatic and germline mosaic variants that illuminate development, disease, and inheritance. Her work has traced human cortical development, uncovered sperm-borne mutation risks linked to miscarriages and congenital disorders, and identified pathogenic somatic mutations in cortical malformations, with findings published in Nature, Nature Genetics, Cell, and more. She brings a rare blend of hands-on wet-lab assay development (PASM/MPAS) and bioinformatics innovation, plus a track record of building the first noncancer mosaic knowledge base to aid clinical interpretation. Based in Salt Lake City and trained at Peking University, she translates deep genomic signals into actionable insights for genetics and clinical counseling.
10 years of coding experience
15 years of employment as a software developer
Bachelor of Science - BS, Biology/Biological Sciences, General, Bachelor of Science - BS, Biology/Biological Sciences, General at Beijing Normal UniversityDoctor of Philosophy (PhD), Bioinformatics, Doctor of Philosophy (PhD), Bioinformatics at Peking University
Chinese, English
Github Skills (25)
genetics10
bioinformatics10
prediction-model9
intermediate9
deep-learning9
calculation9
genomics9
sequencing8
mosaic8
anaconda6
perl6
snakemake6
annotations6
python5
parallel5
Programming languages (2)
Github contributions (5)
shishenyxx/PASM
Feb 2019 - Sep 2022
Here are scripts for Postzygotic Amplicon Sequencing for Mosaicism (PASM) and some codes for the method we now define as Massive Parallel Amplicon Sequencing (MPAS). We provided perl+R versions, python versions, and an extended snakemake version with all additional annotations. The scripts are useful for the calculation of variant allelic fraction based on deep sequencing data as well as additional annotations for mosaic variants.
Contributions:163 commits, 2 PRs, 175 pushes in 3 years 8 months
pythonfractionbioinformaticssequencing-datamethod
shishenyxx/MosaicBase
Mar 2022 - Dec 2022
MosaicBase is a comprehensive knowledgebase for postzygotic mosaic variants from noncancer disease-related and healthy human individuals
Contributions:14 commits, 4 PRs, 14 pushes in 9 months
knowledgebasehealthybioinformaticsmosaicdisease
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