Benjamin L. Email and Phone Number

• Built modern, performant, high-quality applications for genetic counselors interacting with patients and for internal data miners at GeneDx. • Designed and deployed projects for processing, analyzing, storing, and reviewing large-scale clinical genomic sequence data. • Demonstrated experience in agile and incremental SDLC, covering planning, evaluation, design, development, testing, deployment, maintenance, and iteration. This encompasses backend server scripts, both new and… Show more • Built modern, performant, high-quality applications for genetic counselors interacting with patients and for internal data miners at GeneDx. • Designed and deployed projects for processing, analyzing, storing, and reviewing large-scale clinical genomic sequence data. • Demonstrated experience in agile and incremental SDLC, covering planning, evaluation, design, development, testing, deployment, maintenance, and iteration. This encompasses backend server scripts, both new and existing ETL pipelines, APIs, microservices, full-stack web applications, both relational and non-relational databases (RDBMS, NoSQL), and reusable software libraries leveraging MVC patterns, all while adhering to clean coding standards. • Rigorously and repeatedly tested software for functionality, performance, and security, employing automated CI/CD and local testing methodologies. • Actively participated in team peer programming, PR reviews, and code reviews; providing support and mentorship junior team members. • Collaborate closely with fellow engineers, product managers, and stakeholders. • Led developers, documenters, and testers throughout the software development life cycle (SDLC). Show less

Microbial Genomics Core; Dr. Mark Adams group; Dr. George Weinstock group. • Led and actively participated in the SDLC of custom software applications for the processing and analysis of large-scale clinical genomic data including WGS, mWGS, 16S, and RNASeq. • Managed genomic sequence data for research groups by writing and maintaining ETL analysis pipelines, triaging raw data from sequencers through QC checks, and directing it to appropriate pipelines. Also handled data archival… Show more Microbial Genomics Core; Dr. Mark Adams group; Dr. George Weinstock group. • Led and actively participated in the SDLC of custom software applications for the processing and analysis of large-scale clinical genomic data including WGS, mWGS, 16S, and RNASeq. • Managed genomic sequence data for research groups by writing and maintaining ETL analysis pipelines, triaging raw data from sequencers through QC checks, and directing it to appropriate pipelines. Also handled data archival and deposition to public repositories (e.g., NCBI SRA). • Designed and implemented web applications, one to track biological samples and corresponding sequencing libraries, and another for the modular display of sequencing runs and resulting FASTQ Q/C, as well as sample read counts. • Developed and standardized data analysis pipelines and scripts and migrated between pipeline frameworks (e.g. Nextflow and Civet). Designed and created databases for storage research data and metadata. • Managed sequence data for the NIH Integrated Human Microbiome Project (iHMP) research groups at Jackson Labs and Stanford. Aggregated, transformed, and consistently formatted (e.g., MIMARKS) a massive amount of sequence data and subject metadata. Collaborated with data managers from other nationwide research groups in the iHMP consortium to submit the data to the central repository. • Determined methods for tracking epidemiological and genomic data associated with SARS CoV-2 variants as they were detected and moved throughout the New England area by working with a team to create an analysis and data presentation workflow. Show less

• Facilitated setup of then state-of-the-art NGS sequencer (IonTorrent) for rapid sequencing of clinical microbial samples for research and diagnostic purposes. Installed software for data handling and analyses.• Worked as part of a team of scientists to rapidly sequence samples, assemble reads, and characterize the European E. coli O104:H4 strain responsible for a large outbreak in 2011.• Provided technology support to research groups by implementing, maintaining software for whole… Show more • Facilitated setup of then state-of-the-art NGS sequencer (IonTorrent) for rapid sequencing of clinical microbial samples for research and diagnostic purposes. Installed software for data handling and analyses.• Worked as part of a team of scientists to rapidly sequence samples, assemble reads, and characterize the European E. coli O104:H4 strain responsible for a large outbreak in 2011.• Provided technology support to research groups by implementing, maintaining software for whole genome shotgun (WGS) sequencing, phylogenetic analyses, primer design, and data storage and review. Show less

• Designed, programmed, and modified web applications and sites for charities and small businesses.• Developed flagship product for all operational business data accessible, searchable, and publishable via web interface. Designed accompanying wiki documentation site.

• Editorial, architectural, product advertising, portrait, and musical performance photography. • Retouched and processed images using Photoshop, Lightroom, Camera Raw, and Capture One. • Lighting setup crew and digital handler on commercial and location photo shoots. • Published in Billboard Radio Monitor, Boston Globe, St. Louis newspapers, websites, CD covers.

• Configured, implemented and supported a clinical data management system (Clintrial), safety data tracking system (Clintrace) and other applications used by pharmaceutical companies to record clinical study data; track adverse events; distribute data over a global network; catalog with coding dictionaries; and produce reports for government organizations e.g. FDA. Products were front-end GUIs on a backend Oracle database.• Organized and taught training classes for customers and consultants… Show more • Configured, implemented and supported a clinical data management system (Clintrial), safety data tracking system (Clintrace) and other applications used by pharmaceutical companies to record clinical study data; track adverse events; distribute data over a global network; catalog with coding dictionaries; and produce reports for government organizations e.g. FDA. Products were front-end GUIs on a backend Oracle database.• Organized and taught training classes for customers and consultants in use and configuration of applications. • Supervised customer support group; onboarded new hires on our product and database functionality. Show less