Senior Scientific Software Engineer, Analytics and Workflows

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Advances in AI, data, and computational sciences are transforming drug discovery and development. Roche's Research and Early Development organisations at Genentech (gRED) and Pharma (pRED) have demonstrated how these technologies accelerate R&D, leveraging data and novel computational models to drive impact. Seamless data sharing and access to models across gRED and pRED are essential to maximising these opportunities. The new Computational Sciences Center of Excellence (CoE) is a strategic, unified group whose goal is to harness this transformative power of data and Artificial Intelligence (AI) to assist our scientists in both pRED and gRED to deliver more innovative and transformative medicines for patients worldwide.

The Analytics and Workflows group within the Center of Excellence (CoE) is dedicated to turning complex data into actionable insights that advance drug discovery and development. We leverage cutting-edge high-throughput technologies and foundational multimodal machine learning models to analyze large-scale biological data, enabling deeper understanding of disease mechanisms and the identification of novel therapeutic opportunities. Despite advances in these fields, however, transforming raw data and computational models into meaningful biological insights remains a key challenge. In this role, you'll work at the intersection of data science, biology, and engineering to build innovative analytical tools that bridge the gap between data generation and biological interpretation-helping unlock new avenues for scientific discovery and impact.

The Opportunity

Genentech seeks a talented and highly motivated Bioinformatics Software Engineer with expert knowledge of modern genomic data processing workflows and their application to cutting-edge biological sciences. The team you are joining supports scientists with highly scalable and reproducible workflows for the analysis of sequencing data from transcriptomic, genomic, perturbation and (epi)-genetic assays at the bulk and single-cell level.

The primary focus of this position is to establish a suite of workflows and tools for the characterization of cell lines for our growing cell therapies portfolio. You will evaluate, refine, and productionize genomic workflows and incorporate the results into our data platform. You will make use of and are an expert in state of the art variant calling workflows and can interpret the results in a variety of biological contexts. You will communicate your results in scientific discussions, create automated reports and sophisticated data bases and tools allowing for deep analysis of cell lines. To achieve this outcome you confidently evaluate and combine open-source, commercial and in-house developed solutions. A successful candidate will collaborate with interdisciplinary teams of Software Engineers, Computational Biology and Data Scientists to develop scientific workflows and tools that make this data available to machines and humans using a variety of interfaces.

Successful candidates will meet many of the following requirements

• You have a PhD in Software Engineering, Computer Science, Bioinformatics, or similar and 2 years of relevant experience in a clinical, academic or commercial setting. Alternatively, a Masters degree or equivalent and at least 5 years of relevant experience.

• You have expert knowledge of a modern bioinformatics workflow language (WDL, Nextflow, CWL or snakemake) and have deployed workflows in HPC or cloud environments

• You are an expert in variant calling and variant interpretation from short and long reads using traditional and novel deep learning methods..

• You have successfully analyzed large cohorts using an automated workflow system and were involved in all aspects of the process from data acquisition, over workflow development to data processing and interpretation.

• You have successfully delivered multiple software projects throughout the whole development cycle (planning, implementation, testing, release, maintenance) following modern software development practices.

• Experience in managing data according to FAIR principles as well as tracking data lineage, ensuring data quality and improving data discovery is a plus as well as experience with data standards used by large genomics consortia.

• You are able to break down large problems into smaller software components and can develop them independently or as part of a large team.

• You have strong experience in the use of a high-level, object oriented programming language such as Python, Go, R or Java and a strong understanding of Linux/Unix.

• You have knowledge of best practices for software engineering including but not limited to IaC, CI/CD, and software containerization and can develop, deploy and optimize solutions on several levels of the software stack.

• You are comfortable working both independently and collaboratively, and with handling several concurrent, fast-paced projects.

• You are able to execute technical projects at global scale, across multiple teams and time zones.

• You have a strategic, analytical mindset and ability to innovate using technology to advance business goals.

• You have strong communication skills and can untangle and discuss complex technical tasks.

• Prior experience in a life science or drug development environment is beneficial.

What to expect from us

• A highly collaborative and dynamic research environment where we aim to advance the rate of scientific discovery using purposefully built solutions.

• Access to large data sets, samples and compute resources.

• Access to state-of-the-art technologies and pioneering research.

• Participation in seminar series featuring academic and industry scientists.

• Campus-like lifestyle with a healthy work-life balance.

• Mentored opportunities to further develop professional skills.

The expected salary range for this position based on the primary location of California is $142,500 - $264,700. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance. This position also qualifies for the benefits detailed at the link provided below.

Benefits

This position requires working onsite 3 days per week.

Relocation benefits are available for this posting.

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Genentech is an equal opportunity employer. It is our policy and practice to employ, promote, and otherwise treat any and all employees and applicants on the basis of merit, qualifications, and competence. The company's policy prohibits unlawful discrimination, including but not limited to, discrimination on the basis of Protected Veteran status, individuals with disabilities status, and consistent with all federal, state, or local laws.

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