Jeb Rosen

Code (2004-present)

Software has been my interest, hobby, and/or day job for going on two decades. These are some of the technologies I currently use, or would consider using again:

Web: HTML, CSS, JavaScript, TypeScript
Frameworks/libraries: VanillaJS/DOM, d3, three.js
Databases: Postgres, MySQL, sqlite
Operating Systems: Arch Linux, OpenBSD
.NET: C#, WinForms, WPF
Other: OCaml, Doodad, Python, Rust, Java, C, C++, LaTeX
Tools: git, graphviz, syncthing, KDE Plasma

OneRail (2022-present)

I currently work at OneRail, which provides final-mile delivery solutions with an emphasis on automation, optimization, real-time visibility, and issue resolution.

ISB (2018-2022)

I previously worked in Arian Smit's group within the Hood-Price Lab at the Institute for Systems Biology. We researched methods of discovery and identification of both known and unknown repetitive features in genomic DNA, especially Transposable Elements (TEs), and published and maintained several specialized programs and databases for TE research including Dfam, RepeatMasker, and RepeatModeler.

Storer, J. M., Hubley, R., Rosen, J., and Smit, A. F. A. (2022). “Methodologies for the De novo Discovery of Transposable Element Families” Genes, 13(4), 709. https://doi.org/10.3390/genes13040709
Storer, J. M., Hubley, R., Rosen, J., and Smit, A. F. A. (2021). “Curation Guidelines for de novo generated transposable element families.” Current Protocols, 1, e154. https://doi.org/10.1002/cpz1.154
Storer, J., Hubley, R., Rosen, J., et al. (2021). “The Dfam community resource of transposable element families, sequence models, and genome annotations.” Mobile DNA, 12, 2. https://doi.org/10.1186/s13100-020-00230-y
Flynn, J. M., Hubley, R., et al. (2020). “RepeatModeler2 for automated genomic discovery of transposable element families.” Proceedings of the National Academy of Sciences, 117(17), 9451-9457. https://doi.org/10.1073/pnas.1921046117
All publications: https://orcid.org/0000-0002-8832-1276

UM (2016-2018)

At the University of Montana I was part of a research team dedicated to the visualization and analysis of mass spectrometry data:

Handy, K., Rosen, J., Gillan, A., Smith, R. (2017). “Fast, axis-agnostic, dynamically summarized storage and retrieval for mass spectrometry data.” PLoS ONE 12(11): e0188059. https://doi.org/10.1371/journal.pone.0188059
Rosen, J., Handy, K., Gillan, A., et al. (2017). “JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals.” BMC Bioinformatics 18, 469. https://doi.org/10.1186/s12859-017-1883-6