John Urban Email & Phone Number

Proficient in genomics experimental design, execution, and data analysis.Experienced in: - Benchwork (e.g. DNA, RNA, Illumina, Nanopore/MinION, PacBio, PCR, cell culture) - Bioinformatics (e.g. assembly, gene annotation, Hi-C, differential expression, structural variation, long reads, DNA mods, single-cell, optical maps, peak calling, SNPs, etc..), and - Data analysis (e.g. statistical analysis and visualization in R and Python, hidden markov models, machine learning, deep learning). Particularly specialized in generating, analyzing, and developing bioinformatics pipelines to analyze data from multiple genomics technologies, including Illumina, PacBio, Oxford Nanopore, and BioNano Genomics.Primarily program in Python, R, and Bash. Also have experience with MatLab / Octave, SQL / PostgreSQL, and can debug programs written in other languages (e.g. cpp) when necessary. I now use ChatGPT/Bard/Gemini to help translate python and bash scripts into faster languages, such as cpp, to speed up my workflows. For machine/deep learning, I have experience with pertinent python libraries: NumPy, Pandas, MatPlotLib, Seaborn, SciKitLearn, TensorFlow, NLTK. I learn fast and can quickly adapt to any language. Operating in a Linux/Unix command-line environment is a matter of routine for most of my work as is working remotely on HPC clusters using SLURM. I also have experience working remotely with Amazon AWS EC2 instances.Code examples:- https://github.com/JohnUrban/fast5tools- https://github.com/JohnUrban/poreminion- https://github.com/JohnUrban/LexoNSseq2015- https://github.com/JohnUrban/sciara-project-toolsPublications:https://orcid.org/0000-0001-9270-6569