CV

Skills

  • Programming Languages: Python, Ruby, Perl, Java
  • Tools: Docker, Flask, Jupyter Notebooks, Pandas, Git
  • Databases: PostgresQL, MySQL, MongoDB
  • Bioinformatics: Cromwell, WDL, WES/TES, Best Practice Pipelines (BWA, GATK, Picard, etc.)
  • Other: Slurm, SGE, TeamCity, Ansible, Vagrant

Experience

I started out my career working in publically funded research institutes, focusing mostly on microbial, viral and metagenomics based research in various capacities. I then had the opportunity to work at Palantir (as a contractor) for a short period of time, working with large, interesting datasets. I then moved back into Genomics, into the diagnostics space where I've been for the past 6 years, helping develop genomics based assays for diagnosing cancer and rare genetic disease.

GeneDx, Associate Director, Software Development
March 2017 - August 2020

  • Led a team of Software/Data Engineers responsible for developing/maintaining automated data analysis pipelines for NGS and microarray data
  • Managed internal software release life cycles including development, testing/validation, CI/CD, and documentation.

Personal Genome Diagnostics (PGDx), Lead Software Engineer
August 2014 - March 2017

  • Managed development of genomic data analysis software for PGDx products, including an automated method for identifying false positive mutation calls in tumor genomics data
  • Provided support in deploying NGS analytical software into CLIA validated environment, including change management and infrastructure updates

HumanGeo / Palantir (Contractor), Senior Technologist
Jan 2013 - July 2014

  • Supported installation of Palantir data analysis platform across multiple Linux deployments
  • Data modeling and integration using Palantir internal DSL written in Groovy
  • Developed software to parse and transfer log data in real-time across multiple servers using Apache Flume

Institute for Genome Sciences (IGS), Senior Bioinformatics Engineer
August 2008 - Jan 2013

  • Development of parallel processing pipelines in PERL and web-based GUI development in HTML/CSS/Javascript/JSON
  • Development of Cloud based genomics analysis platform using Amazon AWS

The Institute for Genomic Research (TIGR), Bioinformatics Engineer
March 2006 - August 2008

  • Provided biologists and analysts with data management support for Prokaryotic and Eukaryotic genome annotation pipelines. Developed scripts to load data, launch compute pipelines, and verify data quality.

Education

Rochester Institute of Technology, Bachelors of Science, Masters of Science
Feb 2006 (GPA: 3.96)
Major: Bioinformatics; Minor: Spanish Language and Culture
Thesis: “Knowledge Based Structure Prediction of the Third Hypervariable Region of Antibodies" (Link)

Selected Publications

For a full list of publications, Google Scholar Results

Torene RI, Galens K, Liu S, Arvai K, Borroto C, Scuffins J, Zhang Z, Friedman B, Sroka H, Heeley J, Beaver E, Clarke L, Neil S, Walia J, Hull D, Juusola J, Retterer K. Mobile element insertion detection in 89,874 clinical exomes. Genet Med. 2020 Jan 22. Pubmed

Jones S, Anagnostou V, Lytle K, Parpart-Li S, Nesselbush M, Riley DR, Shukla M, Chesnick B, Kadan M, Papp E, Galens KG, Murphy D, Zhang T, Kann L, Sausen M, Angiuoli SV, Diaz LA Jr, Velculescu VE. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med. 2015 Apr 15;7(283):283ra53. Pubmed

Angiuoli, S. V., Matalka, M., Gussman, A., Galens, K., Vangala, M., Riley, D. R., Arze, C., White, J. R., White, O., & Fricke, W. F. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC bioinformatics. 2011 Aug 30;12:356. Pubmed

Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG. The IGS Standard Operating Procedure for Automated Prokaryotic Annotation. Stand Genomic Sci. 2011 Apr 29;4(2):244- 51. Pubmed

Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S, Riley D, Sundaram JP, Felix V, Whitty B, Mahurkar A, Wortman J, White O, Angiuoli SV. Ergatis: a web interface and scalable software system for bioinformatics workflows. Bioinformatics. 2010 Jun 15;26(12):1488-92. Epub 2010 Apr 22. Pubmed