💡 I like to build user-friendly tools to simplify complex analyses.
🎓 I work at Alberta Precision Labs doing emerging pathogen surveillence and research.
🌱 My current focus is writing modular and highly automated code.
✍️ In my free time, I'm usually doing yoga, climbing, cycling, hiking, camping, or otherwise getting dirty.
🎓 More about me!
Alberta Precision Labs - Lab Specialist (APL)
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Developed numerous tools for bioinformatic analysis (see downsampler, hnoss)
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Created modular bioinformatic pipelines (see quick-sequence-qc, basic-sequence-stats, basic-sequence-trimmer)
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Automated NGS workflows to improve turn around time
Universität Heidelberg - Masters of molecular bioscience, cancer biology (HU)
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Thesis project: scMethrix, a single cell methylation summarization tool and application in analysis of glioma-related
macrophages (see scMethrix and brainphageDNAme)
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Practical work performed at the German Cancer Research Center (DKFZ)
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Final grade: 1.8 GPA (German scale; approx 3.7 GPA in US scale)
University of British Columia - Honours Bachelor in microbiology (UBC)
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Thesis project: Observations of Transposable Element Richness and Diversity in Embryophytes (see EmbryophyteTEs)
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4th year abroad at Uppsala University taking courses for MSc in Mol.Bio. (UU)
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Final grade: 3.97 GPA
Center for Big Data Research in Health, UNSW
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Manuscript in progress for lifestyle risk factors contributing to glioma, as part of the Australian Genomics and Clinical
Outcomes of Glioma project
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Developed new analysis software for analyzing epidemiological data (see DAGnalysis and EpidExperiment)
Infection and Cancer Epidemiology group, DKFZ
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Developed novel large-scale epidemiological assay for syphilis-causing Treponema pallidum (>99% sensitivity and specificity)
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Build new analysis software in R and Shiny for handling multiplex serology data (see here)
Molecular Pathogenesis of Genetic Disorders group, HU
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Generated mutant neural cell lines with patient-specific mutations related to autism spectrum disorder and intellectual disabilities
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Quantified expression of autism-related genes in mutant neurons (i.e., SHANK2, GRIN2B, PSD95, Synaptophysin)
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Xue, Jinru, Erna Jia, Na Ren, Andrew Lindsay, and Haixin Yu. Circulating MicroRNAs as Promising Diagnostic Biomarkers for
Pancreatic Cancer: A Systematic Review. (2019). OncoTargets and Therapy
🚧 All my projects!
- scMethrix
- a single cell methylation summarization R package built-on the Bioconductor SummarizedExperiment.
- brainphageDNAme
- DAGnalysis
- EpidExperiment
- Multiplex Serology Dashboard
- scripts and validation of a novel serological assay for Treponema pallidum (syphilis).
- EmbryophyteTEs
- scripts for analyzing transposable elements in embryophytes.
- Downsampler
- tool to downsample NGS reads for validating minimum depth of coverage.
- quick-sequence-qc
- organism-agnostic QC module for NGS reads on Illumina and Nanopore sequencers
- basic-sequence-stats
- basic-sequence-trimmer
- lightsOutPy
- GameOfTheAmazons
- an AI-driven player for the chess variant Game of the Amazons.
- Tez
- a replication of the 90's game Lights Out, but allows for multiple other tesselation patterns. Available on the Google Play store.
- Mindusty Mods
- a collection of units, schematics, and scripts for logic processors in the factory game Mindustry.
- AudioToolkit
- a suite to tools to aid installing stereo system. Available on the Google Play store.
- OChemReaction
- UBCcards
- DNAart