Ben Schiller
Staff Software Engineer at Heartflow
San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolBenjamin Schiller is an IT consultant and senior bioinformatics engineer with 15 years of experience helping early-stage and growth biotechs migrate, optimize, and operationalize NGS pipelines for cloud and on-prem environments. A former startup CTO and director-level leader at companies like Invitae, AccuraGen, and Guardant, he combines hands-on engineering with product and regulatory-aware SDLC practices (CLIA/CAP). He specializes in platform migrations (AWS/GCP/on-prem), workflow modernization (Nextflow, Snakemake), CI/CD and IaC, runtime cost optimization, and incident reduction—often cutting pipeline runtimes from days to hours. Benjamin contributes to widely used open-source genomics tools (notably pysam and MACS), improving cross-platform compatibility and paired-end parsing for real-world sequencing data. He works flexibly as a fractional advisor or short-sprint consultant across the SF Bay Area and remote US, and brings a PhD in Biochemistry & Molecular Biology plus physics training to bridge computational rigor with biological insight. Beyond typical ops wins, he’s known for embedding reproducible testing, runbooks, and CI-first practices that make regulated bioinformatics both scalable and auditable.
15 years of coding experience
5 years of employment as a software developer
Bachelor of Science Physics, Bachelor of Science Physics at Harvey Mudd CollegePh.D. Biochemistry and Molecular Biology, Ph.D. Biochemistry and Molecular Biology at University of California, San Francisco
Github Skills (8)
bioinformatics10
htslib10
python10
bam10
sam10
windows9
compatibility9
ng8
Programming languages (6)
Github contributions (5)
macs3-project/MACS
Jan 2012 - May 2013
MACS -- Model-based Analysis of ChIP-Seq
Role in this project:
Back-end Developer
Back-end DeveloperContributions:154 commits in 1 year 3 months
Contributions summary:Ben contributed to the `MACS` project, focusing on the underlying algorithms for ChIP-Seq analysis. Their commits primarily involved modifications and enhancements to the `cParser.pyx` file, focusing on improving the parsing of BAM and SAM file formats for paired-end sequencing data aligned with Bowtie. Furthermore, they implemented the `BAMPEParser` for paired-end data using fragment midpoints and optimized peak calling. They also made adjustments to peak calling and summary methods.
chip-seqatac-seqdnase-seqpeak-callerpython
pysam-developers/pysam
Feb 2011 - Mar 2011
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
Role in this project:Back-end Developer
Back-end DeveloperContributions:6 commits, 1 comment, 1 issue in 15 days
Contributions summary:Ben primarily focused on improving the `pysam` library, particularly concerning its compatibility and functionality. They added features such as mode auto-detection for reading SAM/BAM files, implemented Windows compatibility changes, and addressed various bug fixes to improve the library's stability. Their contributions also involved refactoring and consolidating code related to Windows compatibility and other minor bug fixes.
bcftoolshtslibpysampythonsamtools
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