Benjamin Schiller Email & Phone Number

Tucson, Arizona, Us

Company summary: Lodestar is focused on advancing the diagnosis and treatment of rare disease patients. The company leverages AI/ML models to group patients by phenotype and uncover novel causes of disease. Lodestar also provides consulting services for other biotech companies.- Defined company strategy, drove fundraising activities, and refined pitch deck with co-founder- Migrated bioinformatics (germline variant calling) to cloud-optimized tooling (Sentieon, Snakemake)- Reduced pipeline runtime from 24 hours to under 1 hour for whole genomes- Partnered with LatchBio to improve Snakemake integration on their platform- Consultant for AI protein design startup: productionized their research pipeline using Nextflow and writing documentation for software development best practices

San Jose, California, Us

- Led team responsible for pipeline execution, development, and algorithmic improvements- Stabilized NGS pipeline output by creating a testing framework and script to compare pipeline output between executions, automating with Github actions, and enforcing sorting in the pipeline- Completed migration to Nextflow for workflow management- Reduced pipeline costs > 20% by migrating our AWS account to a different region

San Francisco, Ca, Us

- 2018-2021 Engineer Lead for a team focused on bioinformatics pipeline infrastructure; 2014-2018, Senior Bioinformatics EngineerEngineering Lead, March 2018 – Present- Hired and mentored a new team specialized in the support and development of our bioinformatics platform, including terrestrial and cloud computing- Establish and lead execution of a roadmap to enable running our existing bioinformatics pipelines in the cloud- Lead bioinformatics pipeline engineering for a year; team members dual reported to a product squad, where they worked on the automation for a product’s bioinformaticsSenior Software Engineer, July 2014 – March 2018- New bioinformatics pipelines: e.g., RP-PCR assay for tri-nucleotide repeat expansions, importing data generated on the Helix platform, and QC of Illumina sequencing runs- “QC Service”, a web service which consumes internal metrics (usually generated in the lab or during subsequent analysis) and produces internal quality reports that are used for automation and (as needed) manual review- RPC-style JSON web API for launching pipeline jobs on our compute cluster- Messaging service (RabbitMQ) for communication between software systems- Automated testing and deployment for several libraries and applications using Jenkins, Docker, and Fabric- Contributed automation for new lab processes (e.g. Sanger and array CGH confirmation methods; new instrument types) to in-house LIMS software- “ELT” service to normalize data from our LIMS database into Amazon Redshift db on a nightly basis

Palo Alto, California, Us

- Developed a clinically-validated, fully-automated production pipeline for high-throughput analysis of cell-free DNA sequencing data- Developed a custom Laboratory Information Management System (LIMS) using Django- Designed a pipeline module for analysis of copy-number variants from cell-free DNA sequencing data, including a high-level API, implemented as an R package, and integrated report generation- Designed and administered custom database in Postgresql for LIMS and storing bioinformatics results (genetic variants)- Established version control using git/github for the above resources- Led testing and validation of the above resources, and helped fix “bugs” that were found- Coordinated with consultants and service contractors for the maintenance and improvement of our IT resources, including data storage (100 TB scale), user accounts, networking and automated data backup- Coordinated frequently with lab personnel on analysis of R&D data and experiment design

Ph.D., Biochemistry And Molecular Biology

Bachelor Of Science With Distinction, Physics