CV
General Information
| Name | Kian Kelly |
| Title | Bioinformatics Scientist (NGS / Variant Calling) |
| Focus | Somatic & germline variant detection, low allele frequency modeling, NGS algorithm development |
Experience
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Jun 2025 – Now Bioinformatics Scientist
Watchmaker Genomics - Designed and developed NGS secondary analysis algorithms for variant and biomarker detection in oncology applications
- Developing a somatic variant caller in Rust using trinucleotide error modeling and binomial hypothesis testing
- Improved low allele frequency variant detection performance through statistical modeling approaches
- Optimized indel calling in germline TAPS Variant Caller (TVC)
- Built and maintained production Nextflow pipelines with CI and cloud deployment
- Evaluated clinical relevance of variant calls using cBioPortal and annotation tools
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2022 – 2025 Graduate Researcher (PhD)
University of California, Riverside - Performed large-scale genomic and metagenomic analysis using Python and R
- Developed sequencing pipelines (Nanopore + Illumina)
- Studied microbial ecology and environmental adaptation
- First author and co-author publications in New Phytologist, ISME Journal, bioRxiv
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2021 Undergraduate Research Fellow
Cornell University - Generated cryo-EM data for plant membrane protein NPF3
- Performed 2D class reconstruction using cryo-EM pipelines
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2020 – 2021 Research Assistant
Fort Lewis College - Supported molecular biology workflows including cloning and recombineering
- Assisted CRISPR plasmid construction and microbial studies
Publications
- First-author and co-author publications in ISME Journal, New Phytologist, and bioRxiv focusing on fungal genomics and microbial ecology
Selected Tools
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TAPS+ Variant Caller (TVC)
- Germline variant caller designed for TAPS+ sequencing data
- CpG-aware, read-oriented model that reduces methylation-induced false positives
- Uses binomial genotype inference over allele counts with explicit error modeling
- Incorporates CpG context from both reference genome and read-level signals
- Developed within Watchmaker Genomics
- Optimized indel calling performance in Rust implementation without compromising runtime
- Github -> https://github.com/watchmaker-genomics/TVC
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Somatic Variant Caller (in development, not released)
- Ultra-low allele frequency somatic variant caller implemented in Rust
- Based on trinucleotide-context error modeling and binomial hypothesis testing
- Designed for sensitive detection of rare somatic mutations in noisy sequencing data
- Currently in active development (not publicly released)
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DspikeIn
- Collaborative contribution to a framework for absolute abundance microbiome profiling
- Enables correction of compositional bias in microbial community analysis
- Applied to host-associated microbiomes across vertebrate systems
- Co-authored resulting publication on absolute abundance and microbial network structure
- Github -> https://github.com/mghotbi/DspikeIn
Teaching
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2022 – 2023 Microbiology Teaching Assistant
University of California, Riverside - Led discussion sections for 100+ students
- Supported instruction and exam preparation
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2019 – 2022 Lead Peer Educator
Fort Lewis College - Tutored scientific writing and communication
- Delivered academic workshops
Skills
- Python, R, Rust, Bash
- Variant calling (germline & somatic)
- NGS analysis (Illumina, Nanopore)
- Genome assembly and annotation
- Metagenomics and phylogenetics
- Trinucleotide error modeling
- Binomial hypothesis testing
- F1 / precision-recall benchmarking
- GATK, Mutect2, Nextflow, GitHub Actions, HPC
Honors & Activities
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Fellowships
- NSF ExFAB Biofoundry Fellow
- Chancellor’s Distinguished Fellow (UC Riverside)
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Field Work
- Volunteer Firefighter & First Responder (Indian Peaks Fire & Rescue)