Computational

Programming Languages: Python, R, Bash

Research computing: Unix, high-performance computing (HPC) clusters, job schedulers (Slurm, PBS), Git, Conda, containers (Docker, Singularity)

Workflows & Parallel Processing: Snakemake, OpenMPI, DeepHyper, Parsl

Documentation: HTML, CSS, GitHub Pages, Jekyll, Sphinx, Markdown, Adobe Illustrator, Jupyter notebooks

ML/AI libraries: PyTorch, TensorFlow, Keras, SciKit-Learn

Bioinformatics & Chemoinformatics libraries: DESeq2, edgeR, Bioconductor, RDKit

General libraries: Pandas, NumPy, Seaborn, Matplotlib, Tidyverse, ggplot2, R Shiny

Sequencing tools: Bowtie, TopHat, FastQC, Trimmomatic, Samtools, Bamtools, Bedtools, MACS, genome browsers (IGV, UCSC, MochiView), CRISPR screen analysis (MAGeCK, BAGEL, DrugZ)

Personal: Excellent communication, organization, efficiency, and troubleshooting skills. Inherent curiosity and the ability to rapidly learn new skills. Currently active public trust clearance.

Next-Generation Sequencing (NGS) analysis: custom sequencing methods, RNA-seq/transcriptomics, CRISPR screens, variant calling, and integration of published datasets (nucleosome positioning, transcription factor positioning, replication origins, replication timing, DepMap, ICGC, COSMIC, etc) into custom analyses

Wet-lab

Next-Generation Sequencing preparation:, WGS, RNA-seq, CRISPR/Cas9 knockout screens, custom sequencing methods (OF-seq, HydEN-seq, END-seq)

Primary and immortal cell culture: proliferation assays, transfection, transduction, CRISPR/Cas9

Standard molecular biology techniques: DNA/RNA extraction, PCR, cloning, qRT-PCR, Western & Southern blotting, immunoprecipitation, flow cytometry and analysis (including multi-color), immunofluorescence, comet assays, microscopy

Viral vector cloning and delivery: lentivirus, retrovirus, adeno-associated virus

Radioactive work: 32P, 35S, cesium source

Mouse work: breeding, xenograft transplantation, irradiation, drug delivery (oral gavage, IP, tail vein)

Yeast work: genetic engineering (standard methods, CRISPR-Cas9, crossing)