Charlie Murphy

Founder & Bioinformatics Software Engineer

Staff Bioinformatics Scientist (2023 - 2024)

• Led technical development of the single-cell minimal residual disease (scMRD) product for AML, owning requirements, software architecture, algorithm implementation, validation, and customer deployment.
• Built the core scMRD software stack: a Python analysis package, production Nextflow pipeline, and interactive per-patient reporting workflow that converted raw sequencing data into clinically interpretable results.
• Deployed and supported the scMRD platform for nine enterprise clients across cloud and on-premises environments, partnering with R&D, software engineering, and field bioinformatics to harden workflows for real customer data.

Poster: A Multiomic, Single-Cell Measurable Residual Disease (scMRD) Assay For Phasing DNA Mutations and Surface Immunophenotypes

Senior Bioinformatics Scientist (2021 - 2023)

• Designed and implemented patented scMRD algorithms for rare somatic variant detection in noisy single-cell sequencing data, combining a beta-binomial background error model with sparse matrix-based co-occurrence detection to improve sensitivity while reducing compute and memory overhead.
• Helped maintain and enhance the Mosaic Python SDK used by hundreds of clients, submitting dozens of pull requests to add Plotly visualizations, implement new analytical algorithms, resolve critical bugs, and enrich documentation.
• Built reusable Python and Nextflow analysis workflows with pandas, Plotly, and scikit-learn to support R&D studies, customer analyses, and internal product validation.

Senior Computational Biologist

• Extended and optimized a Python and CWL cfDNA pipeline that processed tens of gigabytes per sample.
• Migrated the pipeline from a local compute cluster to AWS by containerizing tools with Docker.
• Built a scalable Python and Plotly quality-control tool to identify sample swaps and contamination.
• Led a collaborative analysis of two cfDNA datasets to identify new clinical applications for the assay.
• Reviewed sample quality and mutations from MSK-ACCESS datasets before downstream analysis.

Senior Bioinformatics Scientist

• Led development of 13 Python analysis pipelines and reporting workflows deployed on AWS, while supervising an intern.
• Partnered with full-stack engineers to build React visualizations for pipeline results.
• Improved platform reliability with automated error detection, ticket creation, and pipeline runtime monitoring using Python, Django, and AWS.
• Led 14 client engagements, including enterprise projects for TCR/BCR repertoire analysis and CUT&RUN/CUT&Tag workflows.
• Supported customer growth and retention through webinars, workshops, technical writing, and direct support.

PhD Student in Computational Biology

• Developed Nextflow, Python, and R workflows to identify tumor-specific therapeutic targets.
• Collaborated with more than a dozen scientists on bioinformatics and statistical analyses that contributed to 12 peer-reviewed publications.

B.S. in Mathematics

Built a cross-platform React Native wrapper for uPlot that supports web, iOS, and Android.

github.com/murphycj/uplot-react-native

Created an open-source Python package and React web app for annotating and visualizing gene fusions.

Web app:

github.com/murphycj/agfusionweb-react

Python package:

github.com/murphycj/AGFusion