CV/Resume

PDF copy here (due to limited space some material is not included in the PDF copy)

Education

PhD. in Biomedical Science, Northwestern University (2023)
BSc. in Molecular Biology, Loyola University Chicago (2014)

• Certificates: Management for Scientists and Engineers from Northwestern University Kellogg School of Management
• Select Coursework: Bioinformatics, Quantitative Biology, Biostatistics I/II (Statistical Survey/Regression Analysis), Mathematical Statistics I/II (Probability Theory/Statistical Inference), Machine Learning, Information Management for Data Science (SQL/database management)
• Bootcamps: Programming Concepts & Fundamentals, R Programming, R Tidyverse, Python Programming, Data Wrangling and Visualization in Python

Skills

• Python: NumPy, Pandas, Scikit-learn, PyTorch, SciPy, Statsmodels, Matplotlib, Biopython, RPy2 (R API for Python programing language), Dash/Plotly, and more
• Other Languages: R (Tidyverse suite of pakcages, ggplot2, DESeq2 and other specific bioinformatics libraries), SQL (SQLite), Unix/Linux shell scripting (bash)
• Tools/Miscellaneous: Git, GitHub actions, AWS (S3 cloud storage), Slurm, NextFlow/NF-Core, Tableau, Excel

Experience

Northwestern University, Department of Microbiology-Immunology (Chicago, IL)
Graduate Research Assistant (January 2017 – Present)

• Studied the role of KSHV in HIV-associated cancers using both sequence and non-sequence based high-throughput technologies, such as genome-wide CRISPR screening, bulk and single-cell RNA (scRNA) sequencing, and automated drug screening
• Served as the primary data scientist in support of 3 grants, including on the largest single-cell genomics study conducted at Northwestern University to-date

Loyola University Chicago, Department of Bioinformatics (Chicago, IL)
Research Assistant (May 2010 – Aug 2015)

• Studied the microbial diversity of the Chicago’s Lake Michigan using targeted (bacterial 16S rRNA) and (viral genome) shotgun sequencing approaches
• Developed a ChIP-based assay for assessing histone modifications of aberrantly expressed tandem repeat sequences in human cancers

Projects

Dissertation: The Role of FLICE-Inhibitory Proteins in Primary Effusion Lymphoma (Access)

• Identified novel regulators of ligand-independent, TRAIL-R1-mediated cell death and cFLIP dependence in KSHV-associated lymphoma using genome-wide synthetic CRISPR rescue screens
• Published in the prestigious Cell Death & Differentiation & selected as a monthly reader’s choice paper

Transcriptomic Analysis of KSHV Infection (Private Repo)

• Deployed multiple supervised (KNN, linear regression) and unsupervised (deep count autoencoder, PCA, UMAP, and Leiden clustering) machine learning techniques alongside traditional statistical inference methods (Chi-square, NB-GLM, and Kolmogorov-Smirnov) on single cell data for QA, cleaning, and hypothesis formation & testing
• Estimated sample sizes necessary for stable algorithm performance via bootstrapping of single-cell pilot experiment samples, leading to a 33% reduction in research expenditures
• Developed a fast Cython-based tool for analysis of miRNA/k-mer enrichment in bulk RNA samples (rolling hash algorithm + hypergeometric testing)

Natural Language Processing on RPG Content (Repo)

• Scraped and cleaned 3K+ pieces of fan-generated RPG content scraped from Reddit
• Predicted multiclass labels using both TF-IFD bag of words (one-vs-rest SVM/SVC) and sequence based (RoBERTA- based transformer), achieving a macro- F1 score of .88 and AUC of .99

Predicting Used Car Value (Repo)

• Imputed values for extensively incomplete dataset using single-variable, iterative methods
• Performed ordinal (random forest) regression on the dataset to predict vehicle value on a heavily obfuscated and incomplete dataset, achieved an R2 of 0.91 and concordance index of 0.95

PiPy-AWC (Repo)

• Automated water level controller for home aquaria using a Raspberry Pi
• I developed this in part to practice software design patterns like factories, observer/callback, etc.

Publications

Assessment of a metaviromic dataset generated from nearshore Lake Michigan.

Watkins S, Kuehnle N, ..., Putonti C. (2015). "Assessment of a metaviromic dataset generated from nearshore Lake Michigan." Marine and Freshwater Research. 67(11).


Druggable host gene dependencies in primary effusion lymphoma.

Kuehnle N, Gottwein E. (2022). "Druggable host gene dependencies in primary effusion lymphoma." Curr Opin Virol. 56:101270.


CRISPR screens identify novel regulators of cFLIP dependency and ligand-independent, TRAIL-R1-mediated cell death

Kuehnle N, Osbourn S, Liang Z, Manzano M, and Gottwein E. (2023). "CRISPR screens identify novel regulators of cFLIP dependency and ligand-independent, TRAIL-R1-mediated cell death." Cell Death and Differentation. 30, 1221–1234.