Stefan Amshey

I currently work as part of the NetAffx team (formerly Affymetrix), part of the Genetic Sciences Division of Thermo Fisher Scientific. In this role I have designed and implemented several new internally-facing web-based tools. These tools support our microarray design and marketing teams by allowing them to quickly identify content related to the research interests of our customers. In addition, I have also helped modernize and automate our microarray annotation pipeline which collates public annotation data (ClinVar, OMIM, etc.) associated with the array content for our customers. I have supported nearly 100 new microarray designs so far.

I was the engineering manager of a team of 5 dev/ops engineers working on a suite of legacy products: Digital Commons/DC Network, Selected Works, and ExpressO. While in this role I was responsible for managing parallel development initiatives. I represented the engineering goup in product planning and prioritization of initiatives. As a manager I supported and encouraged employee development by hosting code reviews and learning sessions on topics like relational vs NoSQL databases, the Django framework, Javascript, and many others. I also supported operations including resolving customer service escalations and performing pager duty. I managed the team while we introduced the Agile process and introduced a new architecture using an AWS cloud-hosted micro-services model, and also modernized the internal process.

I developed a sequence data management pipeline for analyzing, archiving, and reporting on output from HiSeq and Pacific Biosciences gene sequencers. This was a very high-throughput environment (around 50 sequencers) that performed parallel processing on a compute cluster hosted and managed by Lawrence Berkeley Labs (our partner organization).

I joined a small start-up development team developing an automated system for exploring consumer media consumption trends. The process used media samples from TV, internet, and wireless devices and matched them against rolling databases of known content using Shazam, and delivered anonymized reports of user media consumption trends.

I was part of the Systems Engineering team responsible for maintenance and development of the Premium Download Manager (PDM) – the back-end content management and delivery service for purchasable content (ringtones, apps, etc.) on T-Mobile Sidekick devices. We were using Perl, Oracle, and I handled service escalations for a service supporting over 1 million concurrent users.

I developed an internal web product called SACRED used in drug target validation by identifying meaningful variations in gene expression level among genes with low baseline expression levels or large fold variation.

I was part of the Data Integration services team. I was responsible for development and support on our gene microarray expression analysis software suite.

Development on Incyte's flagship bioinformatics data pipeline: Lifeseq Gold.