Resume

Zachary L. Skidmore

Professional Summary:

Senior bioinformatics and quantitative scientist with 12+ years spanning Tier 1 academic research and industry. Proven expertise in study design, cancer genomics analysis, and pipeline/software development. Author of high-impact publications and patent co-inventor. Experienced mentor and instructor, developed and taught multiple bioinformatics courses. Seeking a senior or lead bioinformatics scientist position to apply deep technical expertise and expand leadership scope.

Education:

University of Illinois
Master Of Engineering in Bioinformatics

Chicago, IL
May 2013

Work Experience:

Delfi Diagnostics
Position: Senior Quantitative Scientist, Translational Science, Data Science - Research

Remote
Aug 2022 - Present

2023 - 2025 Highlights

Co-developed and submitted intellectual property for differentiating histological subtypes of lung cancer using cfDNA features WO2024173277A2
Lead author and bioinformatic scientist for development and application of ctDNA monitoring on a prospective phase III clinical trial (CAIRO5) using fragmentomics PMID: 39433569
Trained and maintained a random forest model to predict ctDNA fraction from plasma
Engaged with drug development companies in the application and analysis of ctDNA monitoring across multiple cancer types
Contributed to more than 15+ translational science projects from inception through publication, resulting in numerous domestic and international conference presentations/abstracts and manuscripts (under review)
Contributed to the analysis and presentation of scientific data in support of multi-million dollar partnerships with pharmaceutical companies and academic collaborators

McDonnell Genome Institute, Washington University Department of Medicine
Position: Staff Scientist

St. Louis, MO
Nov 2013 - Aug 2022

2020 - 2022 Highlights

Lead author and analyst for a study of non-cirrotic hepatocellular carcinoma (WGS/WES/Custom Capture) PMID: 35568002
Lead author and analyst for a treatment naive/relapse study of small cell lung cancer (WGS/WES/RNAseq) (Pending Publication)
Lead author and analyst of a protocol for scTCRseq and scRNAseq for canine samples PMID: 38649520
Implemented modifications to existing H. sapiens workflows to be compatible with multiple species PMID: 33556121
Built a custom workflow to detect viral integration sites from dual indexed viral reads PMID: 34019588
Implemented machine learning algorithm to classify and refine somatic variant calls using extreme gradient boosting models
Optimized analysis scripts for the RegTools software package to be faster and less memory intensive.

2018 - 2019 Highlights

Created and instituted Common Workflow Language (CWL) bioinformatic pipelines: bioinformatic-workflows; analysis-workflows
Created and maintained docker images for bioinformatic analysis
Trained staff scientists in various bioinformatic and programming skill sets.
Created static websites and subsequent material for genomic visualization, precision medicine, and RNAseq.
Advised and/or performed analysis on TCR clonotype repertoire, HLA prediction, neoantigen prediction, ctDNA, WGS, WES, RNAseq PMIDs: 31390566, 31618044, 31467059, 31685621, 31902496, 32665297, 34036230, 33556121, 33547198
Prototyped shiny application for interrogation of saturation mutagenesis assays saturation-mutagenesis-viz

2013 - 2017 Highlights

Led development and publication of Genomic Visualization in R (GenVisR) library on bioconductor DOI: 10.18129/B9.bioc.GenVisR PMIDs: 27288499, 34506690
Consulted on design and implementation of Clinical Interpretations of Variants in Cancer (CIViC) database; Co-organized first Biohackathon for CIViC at the Netherlands Cancer Institute; Submitted and curated database entries PMID: 28138153
Mentored and assisted graduate and undergraduate students in analyzing projects and writing manuscripts.
Assisted in the maintenance and improvement of institute project management and analysis software (perl) PMID: 26645048
Conducted statistical and bioinformatic analysis for next generation sequencing data (Benchmarking Alignment, Clonotype Expansion, Cancer Genomic Alterations, etc.) PMID: 26531824, 26563128, 27058228, 27029710, 27181063, 27681435
Performed next generation sequencing analysis and presented results for cancer genomic tumor board n-of-1 cases

Workshops, Instruction & Community Leadership:

Teaching assistant/content author for Cancer Research Institute bioinformatics workshop

2024, 2025

Instructor/content author for genomic visualizations workshop
- Physalia-courses, Freie Universität Berlin, Germany
- Evomics, Workshop on Genomics, Český Krumlov, Czech Republic

2017, 2019
2019, 2020

Teaching assistant/contributing author for Precision Medicine workshop
- PR Informatics, Glasgow, Scotland

2018

Contributing author for RNAseq workshop

Selection of Scientific Expertise

cfDNA Fragmentomics & Liquid Biopsy Data Analysis

shallow-WGS Fragmentomic Profiling
shallow-WGS Aneuploidy Detection
Nucleosome Footprinting
Early Cancer Detection and Modeling

Next-Generation Sequencing Analysis

Pre/Post Alignment QC (e.g. FastQC, Picard, samtools)
Read Alignment (Burrows-Wheeler & K-mer Based)
Somatic/Germline Variant Calling
Variant Annotation and Filtering (e.g. VEP)
CNA/SV Detection
LOH Detection
Illumina-based WES/WGS/RNA-seq workflows
UMI-Aware Processing (e.g. fgbio)

Cancer Genomics & Tumor Biology Bioinformatics

Liquid and Solid Tumors
Tumor Heterogeneity and Clonal Evolution
Pathway Analysis
Genomic Visualization and Interpretation
Tumor Purity Estimation
Data Mining and Large Cohort Processing

RNAseq Analysis

Differential Expression
GSEA
Transcript Quantification
Alternative Splicing
scRNA-seq

Statistical Analysis

Hypothesis Testing (Parametric/Non-Parametric)
Survival Analysis (Kaplan-Meier)
Batch Effect Detection/Correction
Power Analysis
Distribution-based Modeling (e.g., binomial, negative binomial, poisson)

Cancer Immunotherapy Data Analysis

Checkpoint Inhibitor Biomarker Profiling
TCR Sequencing and Clonotype Repertoire Diversity
HLA-Typing (e.g. OptiType)
Neoantigen prediction (e.g. pVACtools)
Immune Cell Deconvolution (e.g. CIBERSORT)
TIL quantification from RNAseq

Machine Learning and Modeling in Genomics

Random Forest
Extreme Gradient Boosting
Generalized Linear Models
Cross-Validation
Model Evaluation (ROC, AUC, Precision-Recall)

Experimental Design

Cohort Stratification
Univariate and Multivariate Analysis
Longitudinal Study Frameworks
Prospective/Retrospective Study Design

Selection of Technical Skills

Advanced

R (inc. ggplot2, data.table, S4)
UNIX
GNU Utils (incl. awk, sed, vim)
Docker (incl. Image building)
Git/GitHub
High Performance Computing (e.g. LSF, Slurm)
Amazon Web Services (incl. EC2, S3)
Confluence/JIRA

Proficient

Common Workflow Language and Pipeline Implementation
Perl
Jekyll/Static Site Building
HTML/Web Development

Familiar

SQL
Python
CSS/SASS
D3.js