Derek T. Puff, Ph.D.


Principal, Software Development

Juno Therapeutics, 2015-present

Architected and implemented a web-based infrastructure for capturing and analyzing data from Juno Therapeutics antibody discovery platform:

  • ASP.NET MVC 5, HTML5, and JavaScript web interface to allow entry, upload, and display of outcomes from molecular biology, protein production, and cell-based assays generated during the discovery workflow.
  • Web-based sequence analysis tools to parse DNA sequences and perform trimming, alignment, consensus, and validation, and render HTML5/SVG sequences and motifs.
  • Web-based task tracking dashboard to capture and coordinate ongoing activities in protein production and cell sciences teams, including delivery dates and mail/text alerts.
  • ASP.NET MVC Web API web services tier that provides RESTful exchange of JSON data from underlying data storage.

Designed and administered Oracle 12c instance to store workflow entities, DNA sequences, documents/reports, gel images, and assay metrics.

Interfaced with laboratory instruments and automation systems: label printer, liquid handler, flow cytometer, fluorescence plate reader.

Built a Next Generation Sequencing (NGS) pipeline to routinely process Illumina HiSeq/MiSeq FastQ files from antibody discovery campaigns:

  • Developed .NET/C# high-throughput parsing of DNA sequences to identify antibody binding domain frameworks and CDR’s.
  • Implemented ASP.NET MVC 5, HTML5, and JavaScript web interface to rank, compare, and search candidate sequences.

Built a catalog of nucleotide and amino acid sequences of antibody V,J genes from multiple species (culled from V-BASE and IMGT) and restriction enzyme recognition sites.

User Interface .NET 4.6, C#, WPF, ASP.NET MVC 5, HTML5, CSS, JavaScript, jQuery, SVG
Web Services RESTful ASP.NET MVC 5 WebAPI, JSON
Database Oracle 12c, ODP.NET
Development Tools Visual Studio 2015, TFS 2012, SQL Developer, Fiddler
Bioinformatics .NET Bio Toolkit, R, BLAST, IgBLAST, Clustal, Entrez, exonerate, V-BASE
Infrastructure VMware, ClickOnce, IIS 8

Principal Software Engineer

X-BODY Biosciences, 2012-2015

Architected and implemented a bioinformatics infrastructure for storage and analysis of antibody drug candidates from the X-BODY NGS (next-generation sequencing) discovery platform:

  • Developed DNA sequence processing pipeline to parse millions of DNA sequences into constituent antibody components and calculate aggregate statistics.
  • Sequence data was obtained from Illumina HiSeq (1x100) and MiSeq (2x250), Roche 454, and Sanger instrumentation.
  • Designed and administered Oracle 11g database running on Windows 2012 Server for storage of sequences, sequence metadata, and statistics.
  • Developed WCF and ASP.NET MVC 4 WebAPI web services that provided REST interface to sequence database.
  • Developed WPF application, deployed via ClickOnce, that provided internal scientists with data analysis and visualization capabilities that included tabular display of lead antibodies, charts of antibody binding performance, and colorized display of nucleotide and protein sequences.
  • Developed ASP.NET MVC 4 internal web site for browser-based functionality comparable to the Windows application described above.
  • Implemented advanced data analysis capabilities for BIND® Scanner in support of in-house drug discovery campaigns. Developed documentation and supporting materials for technology transfer of BIND® instrumentation platforms.
  • Worked closely with X-BODY scientists to provide timely support of ongoing customer collaborations, implementing as needed new features in the bioinformatics software, custom analysis tools, and database queries.
  • Designed and developed X-BODY public website, and posted events, press releases, and updated content.
User Interface .NET 4.5, C#, WPF, ASP.NET MVC 4, Telerik WPF/Kendo controls, JavaScript
Web Services WCF, ASP.NET MVC 4 WebAPI
Database PostgreSQL 8.4, Oracle 11g
Development Tools Visual Studio 2012, TFS 2012, SQL Developer
Infrastructure VMware, ClickOnce deployment, IIS 7

Director of Software Engineering

SRU Biosystems, 2001-2011

Architected and implemented BIND® View, a .NET 4.0 C# WinForms application for viewing images acquired from the SRU Biosystems BIND® Scanner:

  • Implemented interactive display, manipulation, and export of very large images.
  • Developed plug-in architecture for flexible and dynamic image processing and measurement.
  • Implemented image processing algorithms for detecting, measuring, and tracking motion of cells.
  • Designed binary file format and memory-mapping strategy for fast, low-memory access to acquired data.
  • Developed custom C# user controls for charting and microtiter plate visualization.
  • Implemented C/C++ libraries to control instrument hardware (motors and spectrophotometer).
  • Developed and implemented SQL Server database for persistence of experimental data and user preferences.

Architected and implemented EMS™, a C++/MFC user interface for acquiring, displaying, and analyzing data from the SRU Biosystems BIND® Reader:

  • Implemented 1-D signal processing algorithms for spectral peak estimation and function modeling.
  • Developed custom ActiveX controls for charting and data visualization.
  • Designed and implemented a C++/MFC user interface for hierarchical navigation of assay design and results.
  • Designed and implemented a client database for on-demand access to acquired and analyzed data.
Software Development C++, MFC, COM/ActiveX, .NET 4.0, C#, WinForms, WPF, MEF
Development Tools Visual Studio 2010, InstallShield, VisualBuild
Design Tools UML, Mindscape Lightspeed ORM
Source Code Control Visual Source Safe
Database MS Access, SQL Server 2008
Lifecycle Management Seapine TestTrack, Mercury Quality Center

Director of Product Development

MD Online, 2000-2001

Managed several teams of software engineers in the development of ImageMatch™, a medical image search engine:

  • Led successful company-wide preparation for product demonstration at industry trade show (Radiological Society of North America).
  • Designed and implemented medical image processing C++ class architecture.
  • Developed acquisition and processing pipeline for populating large-scale DICOM medical image database.
Software Development C++, Java, Swing, JSP, JDBC, JNI, MFC, Perl, ASP, Visual Basic
Development Tools Visual Studio, Visual Cafe, Forte, Rational Rose/Purify, UML
Source Code Control CVS, VSS
Database SQL, MS Access, Oracle 8i

Senior Software Engineer

Philips Healthcare (formerly Picker Medical Systems), Oncology Division 1996-1999
  • Developed software package for two- and three-dimensional interactive visualization of computed tomography (CT) data and radiation dose distributions for AcQSim™ and AcQPlan™ products.
  • Built reusable software components for function plotting and tabular display of data.
  • Wrote product design specifications and risk analyses for FDA review.