John Urban
Postdoctoral Research Associate
Baltimore, Maryland, United States
Summary
👤
Senior🎓
Top SchoolJohn Urban is a postdoctoral research associate with 11 years of experience designing and executing genomics experiments and building end-to-end bioinformatics pipelines for Illumina, PacBio, Oxford Nanopore, and BioNano data. He combines hands-on bench skills—ultra-long read prep, DNA/RNA work, and cell culture—with strong computational expertise in Python, R, Bash, HMMs, and modern ML/deep learning libraries to extract biological insight at scale. His work spans genome assembly, DNA modification analysis, replication-origin mapping, and routine HPC/SLURM and AWS-driven workflows, reflecting a rare full-stack genomics skillset. He is a fast learner who debugs across languages (including C++) and publishes open-source tools such as fast5tools and poreminion that support long-read community workflows. Based in Baltimore, he brings academic rigor from Brown and Carnegie Institution labs to practical, reproducible computational biology.
11 years of coding experience
1 year of employment as a software developer
Bachelor of Science, Biology, Bachelor of Science, Biology at William Paterson University of New JerseyPh.D. Candidate in Dept of Molecular Biology, Cellular Biology and Biochemistry, Functional and Computational Genomics Track, Ph.D. Candidate in Dept of Molecular Biology, Cellular Biology and Biochemistry, Functional and Computational Genomics Track at Brown UniversityCertificates of Completion, Data analysis, computer science, bioinformatics, machine learning, Certificates of Completion, Data analysis, computer science, bioinformatics, machine learning at Massive Open Online Courses (MOOCs)
Github Skills (59)
bedtools10
structural-variation10
genome-analysis10
genome-assembly10
sequencing10
blast9
genomes9
assembler9
bioinformatics9
pathogen9
comparative-genomics9
genomics9
rna-seq8
hdp8
git-workflow8
Programming languages (13)
Github contributions (5)
JohnUrban/sciaratools2
May 2021 - Mar 2026
Contributions:38 pushes, 1 branch in 4 years 10 months
JohnUrban/AMPure
Nov 2017 - May 2025
Contributions:5 pushes, 1 branch in 7 years 6 months
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