Thon De Boer Email & Phone Number

San Francisco Bay Area

Developed the data ingestion pipeline and request management application for our application. Implemented Machine Learning and AI technologies to process medical and specimen data from a wide variety of sources and allow the data to be searches with natural language queries.

San Francisco Bay Area

In June 2020, following Illumina's acquisition of BlueBee Holding, NV, I joined Illumina as a Principal Software Engineer 1 in the Emerging Solutions group. In this role, I focused on developing a long-term data strategy for Illumina, with a particular focus on genetic analysis. One of my main responsibilities was to develop the Target Discovery pipeline using Python and to create various web applications for the Target Discovery team using Javascript and Dash components. These applications provided the team with valuable genetic analysis results obtained from the pipeline.Additionally, I developed a Proof-of-Concept application that utilized modern NLP technologies to extract knowledge from literature and clinical trials. The goal of this project was to enhance clinical trial enrollment and patient treatment options by integrating medical record data with genetic information obtained through DNA sequencing.

San Mateo, Ca, Usa

Prior to my role at Illumina, I served as the Director of Product Management at BlueBee Holding, NV. In this capacity, I was responsible for spearheading the development of the product vision, roadmap, and customer experience for the BlueBee Genomics Platform, with a strong focus on data science. Specifically, I defined technical requirements and user experiences for an interactive computing framework, APIs, and machine learning methodologies. I also developed Python libraries and Docker images for statistical genetics analysis in collaboration with engineering and bioinformatics teams, resulting in successful commercial launches of new products and product iterations.

Grass Valley

As a skilled Data Science Product Manager, I led the team responsible for migrating the legacy Pipeline Pilot software suite to the Dassault 3DExperience Platform cloud environment, serving as the Technical Product Manager. With the flagship product generating $20M in annual revenue and contributing 40% of the total revenue for the Biovia brand, I created a comprehensive three-year roadmap based on customer interviews. Leveraging my expertise in identifying new application areas, I successfully applied the Pipeline Pilot product to the Mining Industry, expanding its reach and driving business growth.

Santa Clara, Ca

As a seasoned professional in the Life Science industry, I have a track record of leveraging my genomic expertise to drive impactful projects. I designed, prototyped and developed a web application with server backend for a clinical diagnostic customer, which integrates knowledge extracted from the literature and clinical trial databases with medical records and genomic information. The application empowers genetic counselors with potential treatment options for their patients, resulting in more personalized and effective care.Additionally, I led the development of a cutting-edge RNA-SEQ analysis application for another customer in the Diagnostic industry, demonstrating my proficiency in advanced genomic techniques. As the key driver of Persistent Systems, Inc.'s Life Science business, I developed medium- and long-term strategies for the creation of software and services that cater to the Life Science industry, and successfully executed them.

Boulder, Co

We successfully launched the Archer Analysis software within 6 months and on budget from set of unrelated PERL scripts to a fully formed commercial quality software product with an easy to use UI. Lead a team of bioinformaticians and software engineer to support the Archer diagnostics business unit of Enzymatics.Enzymatics was acquired by QiaGen in Dec 2014 and spun off ArcherDX as an independent entity and I switched role to become the Sr. Product Manager for Software in the Marketing team, We successfully launched version 3.0 of the Archer Analysis software on time, providing fusion visualization and a wealth of other improvements as well as a custom assay designer tool for the support of the custom panel business.

Boulder, Colorado

I spearheaded the development and delivery of Archer Analysis and Design software for Enzymatics' Archer diagnostics business unit. Leveraging my expertise in software engineering, I led a team of bioinformaticians and software engineers to migrate a collection of disparate PERL scripts into a high-quality commercial software product. My technical proficiency in multi-platform implementation allowed the software to be easily hosted locally through VMware virtual machine technology, while also providing a cloud-based option for customers to trial our diagnostic kits and ensure accurate results. In addition, I brokered a strategic partnership with Dell to offer customers a complete air-gapped bare-metal solution designed for sensitive applications involving patient data. My genomic expertise and leadership resulted in successful delivery of the software on time and within budget, with exceptional customer satisfaction.

Redwood City, Ca

I led the successful transition of an array-based technology to a sequencing-based technology for the flagship OncotypeDX product. To achieve this, I developed and implemented a comprehensive bioinformatics pipeline using the Galaxy platform to analyze DNA- and RNAseq data. This implementation facilitated scalable sequence analysis pipelines with full automation, and a user-friendly web application.Additionally, I leveraged my genomic expertise to design and develop a companion diagnostic system for a drug-company partner. This system enabled efficient screening of candidates for their drug trials and played a pivotal role in the successful completion of the contract.

San Francisco Bay Area

I was instrumental in the successful launch of Avadis NGS (now known as Strand NGS), a cutting-edge software package for NGS analysis. Within a mere 8 months, I developed this comprehensive software from the ground up and rapidly grew its adoption. My contributions also extended to providing the R&D department with strategic guidance on the algorithms and analyses to be implemented, as well as conducting extensive research to support the development of the Next-Gen Sequencing software application. Leveraging my extensive expertise in NGS analysis, I played a pivotal role in driving the success of all the software business at Strand Scientific Intelligence (Strand Life Sciences).

Menlo Park, Ca

I played a critical role in the success of Complete Genomics. I led the development of innovative products and services that supported the sequencing of thousands of human genomes. I was responsible for managing the development of analyses, data formats, and delivery mechanisms for the massive volumes of data produced during the sequencing process. My expertise in genomic data analysis allowed me to develop efficient methods for data processing, storage, and retrieval. I ensured that Complete Genomics delivered high-quality, accurate, and reliable genomic data to customers. Through my contributions, Complete Genomics was able to advance the field of genomics and provide valuable insights into the genetic basis of human diseases.

Santa Clara, Ca

I have led the development and growth of GeneSpring, the renowned flagship product of Silicon Genetics, by driving adoption rates up by over 150%. I have overseen the development of GeneSpring, a powerful gene expression analysis software that has been consistently referenced in hundreds of journal articles, demonstrating its status as the gold standard in the field. In 2008 alone, over 1600 articles cited GeneSpring as the go-to tool for gene expression studies.In addition to my leadership role in driving adoption and development, I have produced and presented comprehensive marketing plans to the executive team and have played an integral role in high-level decision-making about the future of the company. As a demonstration of my technical expertise, I developed the R integration plugin and multiple R scripts to extend the functionality of GeneSpring, contributing to its growing reputation as a versatile and cutting-edge software tool for genomic analysis.Overall, my expertise in genomics, combined with my ability to lead development, create marketing strategies, and make high-level decisions, has enabled me to make significant contributions to the success of Silicon Genetics and GeneSpring.

Redwood City, Ca

I have led the development and growth of GeneSpring, the renowned flagship product of Silicon Genetics, by driving adoption rates up by over 150%. I have overseen the development of GeneSpring, a powerful gene expression analysis software that has been consistently referenced in hundreds of journal articles, demonstrating its status as the gold standard in the field. In 2008 alone, over 1600 articles cited GeneSpring as the go-to tool for gene expression studies.In addition to my leadership role in driving adoption and development, I have produced and presented comprehensive marketing plans to the executive team and have played an integral role in high-level decision-making about the future of the company. As a demonstration of my technical expertise, I developed the R integration plugin and multiple R scripts to extend the functionality of GeneSpring, contributing to its growing reputation as a versatile and cutting-edge software tool for genomic analysis.Overall, my expertise in genomics, combined with my ability to lead development, create marketing strategies, and make high-level decisions, has enabled me to make significant contributions to the success of Silicon Genetics and GeneSpring.

Siena Area, Italy

I successfully established the bioinformatics department for an innovative biotechnology startup company based in Italy. In this role, I conducted cutting-edge research on Alzheimer's disease and Ion Channels, utilizing my extensive knowledge of genomics to identify novel drug targets. Using innovative homology and other advanced bioinformatics tools, I was able to discover new members of the Ion channel family, which were utilized as targets for drug discovery efforts. I made significant contributions to the development of novel drug therapies, demonstrating my ability to drive impactful results in the field of genomics.

Washington D.C. Metro Area

I have successfully managed teams and products focused on molecular biology data analysis. In my previous role as GenoMax Product Manager, I led a team of six application scientists to design and implement an Enterprise Bioinformatics platform that utilized an Oracle database, C++ middle layer, and a JAVA GUI. My responsibilities included gathering feedback and requirements for the system, authoring functional requirements documents, and chairing product meetings to make key decisions.In addition to managing the development of GenoMax, I also served as a QA Manager, where I significantly reduced the bug count in the VectorNTI release. In this role, I managed a team responsible for testing and validating the software applications, and introduced professional testing procedures that helped grow the department from one to a team of seven. My expertise in genomic analysis, combined with my experience in project management and software development, has enabled me to drive innovation and deliver results in the field of molecular biology.

Cambridge, United Kingdom

I developed and launched a web-based visual BLAST-results viewer focused on the discovery of transcript structure of EST-sequences. In just six months, I successfully delivered a cutting-edge solution that helped unlock new insights into gene expression analysis. In addition, I was responsible for the maintenance of critical molecular biology databases such as EMBL, SWISSPROT, and TREMBL, as well as programs like GCG, BLAST, and SRS. My expertise in PERL, Java(script), C++, and csh enabled me to develop powerful scripts that supported over seven thousand users of the HGMP Bioinformatics services.Furthermore, I played an instrumental role in the development of the EMBOSS Molecular Biology suite of programs as a contributor alongside Peter Rice and Alan Bleasby at the Sanger Centre. My contributions led to the development of several packages in EMBOSS, expanding the range of available tools for genomics research. I was also a lecturer and coach for graduate and undergraduate biology students on Bioinformatics courses at the HGMP-RC. My dedication to sharing knowledge and supporting the next generation of genomics experts underscores my passion for the field.

Doctor Of Philosophy (Ph.D.), Biochemistry And Molecular Biology

Phd, Molecular Biology

Activities and Societies: Gyrinus NatansConducted independent research for seven years on the genetic background of the microbial process.