I’m Ken Youens-Clark. My day job is writing bioinformatics code at the University of Arizona. I also like to write, cook, play music, and ride bicycles.

Resume

Education

  • MS in Biosystems Engineering, Univ. of Arizona, Tucson, AZ, 2015-19
  • BA in English Literature, minor in music, Univ. of North Texas, Denton, TX, 1990-95
  • Northwest Rankin High School (valedictorian), Brandon, MS, 1990

Professional Experience

Author

Tiny Python Projects (Manning, 2020)

https://www.manning.com/books/tiny-python-projects

This text grew from the materials I developed teaching basic programming skills to undergraduate and graduate students at the University of Arizona. The crux of the text is teaching how to write tested, documented, and reproducible programs. We use Python to explore the principles of test-driven development (TDD).

University of Arizona, Tucson, AZ

Senior Scientific Programmer, August 2014-Present

Developer on iMicrobe.us (Youens-Clark 2019), a website for searching and analyzing metagenomic data. During coursework for MS, studied statistics, machine learning, various programming languages, and taught programming with novel course materials. Also developed various HPC pipelines and analysis tools (shell, Rust, Python, R). Duties range from bioinformatics hacking, research, mentoring students and junior developers, and classroom teaching.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

Scientific Informatics Manager II, July 2001-August 2014

Work on Gramene.org (Youens-Clark 2010), a comparative genomics resource for plants. Duties included development of databases and search interfaces for markers/sequences, genetic diversity, QTL, ontologies, comprehensive search tool, managing servers, light sysadmin tasks, writing documentation, presenting at meetings, tracking bugs, project management, etc. Created “CMap” software for the visualization of comparative maps (Youens-Clark 2009). Started and lead development of SQL::Translator Perl module for conversion of SQL DDLs.

Boston.com / New York Times Digital, Boston, MA

Software Engineer, June 1999-February 2001

Boston.com is the Internet site for The Boston Globe. Developed several applications using the LAMP (Linux/Apache/MySQL/Perl) stack including “mp3.boston.com” for local bands to share music, “ae.boston.com” for the arts and entertainment calendar, and an application for anonymous, collective generation of haiku.

Cadence Network, LLC, Cincinnati, OH

Internet and Client/Server Developer, August 1998-May 1999

Developed web-based tools using Microsoft tools (MS-SQL Server/IIS/ASP/Visual InterDev, VB) for reporting energy management and usage.

Rapidigm, Inc., Cincinnati, OH

Software Consultant, November 1997-August 1998

Created software in Delphi/Interbase for long-term care facilities (nursing homes). Programming responsibilities included software security and accounting packages.

Thorsoft, Inc., Cincinnati, OH

Account Executive, July 1996-October 1997

Supported clients on third-party, Windows-based customer-relation management software. Responsibilities included installation, customization, data conversion, training, sales, and technical support. Wrote extensions in Visual Basic, Access, and Delphi.

Bio-Synthesis, Inc., Lewisville, TX

Webmaster/Advertising Manager, May 1995-June 1996

Learned Microsoft Access and began managing the marketing databases. Learned HTML, FTP, and assumed the role of company webmaster.

Selected Publications

Youens-Clark, Ken, Matt Bomhoff, Alise J. Ponsero, Elisha M. Wood-Charlson, Joshua Lynch, Illyoung Choi, John H. Hartman, and Bonnie L. Hurwitz. iMicrobe: Tools and data-driven discovery platform for the microbiome sciences. GigaScience 8, no. 7 (July 2019).

Youens-Clark, K., B. Faga, I. V. Yap, L. Stein, and D. Ware. CMap 1.01: A Comparative Mapping Application for the Internet. Bioinformatics 25, no. 22 (July 2009): 3040–3042.

Youens-Clark, K., E. Buckler, T. Casstevens, C. Chen, G. DeClerck, P. Derwent, P. Dharmawardhana, et al. Gramene Database in 2010: Updates and Extensions. Nucleic Acids Research 39, no. Database (November 2010): D1085–D1094.

Hurwitz, Bonnie L., Jana M. U’Ren, and Ken Youens-Clark. Computational Prospecting the Great Viral Unknown. Edited by Andrew Millard. FEMS Microbiology Letters 363, no. 10 (March 2016): fnw077.

Watts, G. S., K. Youens-Clark, M. J. Slepian, D. M. Wolk, M. M. Oshiro, G. S. Metzger, D. Dhingra, L. D. Cranmer, and B. L. Hurwitz. 16S RRNA Gene Sequencing on a Benchtop Sequencer: Accuracy for Identification of Clinically Important Bacteria. Journal of Applied Microbiology 123, no. 6 (November 2017): 1584–1596.