Bioinformatics Analyst

Who We Are We are a life sciences platform technology company developing tools to better understand tissue biology. We are a team of scientists and engineers with a passion for biology and technology development. Our flagship product is a platform kit that allows researchers to add spatial metadata to their single-cell genomics assays on solid tissues. We are based in the San Francisco Bay Area and backed by venture capital and non-dilutive grant funding from the NIH. We have a shared vision of transforming research and drug discovery, advancing medicine and improving human health. About the Role We are seeking an experienced Bioinformatics Contractor specializing in single-cell transcriptomics. In this role, you will take ownership of our dry-lab data workflows—from raw sequencing data to biological interpretation—allowing our internal team to focus on expanding wet-lab operations. The ideal contractor is an expert in the Python single-cell ecosystem, comfortable navigating cloud environments, and skilled at translating complex computational outputs into clear insights for collaborators. Key Responsibilities Core Data Analysis & Delivery (Critical Path) • End-to-End scRNA-seq Analysis: Process and analyze raw sequencing data (FASTQs) from diverse tissue types, driving the workflow through to downstream biological interpretation. • Quality Control & Primary Processing: Perform rigorous QC, execute standard primary alignment and quantification pipelines via the command line, and synthesize processing metrics. • Custom Downstream Analysis: Utilize Python-based environments to perform cell clustering, cell-type annotation, differential expression analysis, and generate custom endpoints tailored to specific collaborator needs. • Cloud & Remote Execution: Efficiently manage high-throughput data and execute heavy compute jobs using cloud infrastructure and remote terminal environments. Pipeline Automation & Tool Development (Non-Critical Path) • Pipeline Engineering: Design and implement automated workflows to streamline raw data QC, primary processing, and post-run data management. • Metrics & Reporting Dashboards: Develop internal tools or interactive dashboards to aggregate QC and mapping metrics across multiple experiments for easy stakeholder review. • Wet-Lab Data Support: Collaborate with the wet-lab team to create scripts, utilities, or data-handling solutions that simplify experimental tracking and metadata handoffs. Qualifications Required Technical Expertise • Advanced Python Proficiency: Deep experience using Python as your primary language for data science and bioinformatics, with expert command of standard single-cell analysis and data manipulation libraries. • Single-Cell Expertise: A proven track record of analyzing scRNA-seq datasets across multiple, diverse tissue types. • Command Line & CLI Tools: High comfort level with Linux/Unix environments for executing command-line bioinformatics tools and managing remote file systems. • Modern Development Environments: Proficiency using interactive notebooks for exploratory analysis alongside structured IDEs for robust code development. • Cloud Infrastructure: Hands-on experience managing data and compute instances within cloud platforms (e.g., AWS, GCP) using secure remote access tools. Preferred Experience (Nice-to-Have) • Workflow Automation: Experience writing or maintaining workflow management systems (e.g., Nextflow, Snakemake, or custom pipeline wrappers). • Data Visualization: Experience building interactive data applications or integrating data scripts with cloud APIs/shared spreadsheets. • Wet-Lab Translation: Ability to translate wet-lab experimental designs into structured computational metadata and vice-versa. Professional Attributes • Strong Communication: Ability to present complex data endpoints clearly to both internal wet-lab scientists and external customers. • Autonomy: Proven ability to manage time effectively as a contractor, estimating task completion accurately, ensuring deliverables are clear and unambiguous, delivering high-quality code and insights with minimal oversight. Additional Details We are a fast-paced, deep-tech biotools start-up. In innovation, biological experiments don’t always go exactly according to plan. We look for team members who are flexible, resilient, and willing to occasionally work past 5 PM to ensure an experiment is successfully completed and data is captured and analyzed in a timely fashion. This is a fully remote, computational contract role, but our main laboratory is located in Berkeley, CA. We do not require a strict 9 AM – 5 PM schedule, but we do require daily overlap (at least 6 hours) with Pacific Standard Time (PST) working hours for team syncs, Slack communication, and collaborator check-ins. You have the autonomy to set your own schedule, provided that project milestones are met on time, communication remains prompt, and customer deliverables are achieved on schedule. The compensation for this role will be $50 – $80/hour, depending on experience, for up to 10 hours per week. The term of this contract is 2 months and may be extended.