Senior Scientist, Computational Biology (Contractor) at Allogene Therapeutics in San Francisco, CA

Job description

About Allogene: Allogene Therapeutics, with headquarters in South San Francisco, is a clinical-stage biotechnology company pioneering the development of allogeneic chimeric antigen receptor T cell (AlloCAR T) products for cancer and autoimmune disease. Led by a management team with significant experience in cell therapy, Allogene is developing a pipeline of “off-the-shelf” CAR T cell product candidates with the goal of delivering readily available cell therapy on-demand, more reliably, and at greater scale to more patients. About the role: We are seeking a highly motivated Senior Scientist, Computational Biology to join our team. The Genomics & Bioinformatics function at Allogene is responsible for the full stack of computational biology and bioinformatics that underlies the company’s translational, clinical, and regulatory work — from multi-platform single-cell and flow cytometry analysis to clinical regulatory characterization to conference-ready data packages. This is an execution-focused, high-ownership role working directly under senior ED-level direction. The person in this seat will own hands-on analysis across active programs, build and maintain durable analytical pipelines, and contribute to the regulatory and scientific record in ways that have direct program impact. There is no handholding and no bureaucratic overhead — this is a place where a strong computational biologist can do consequential science quickly. Candidates interested in developing new analytical capabilities, advancing computational approaches, and helping strengthen our bioinformatics function are strongly encouraged to apply. This is not a support function. The analytical decisions made in this seat directly shape program strategy, regulatory packages, and external scientific communications. The person hired will work with cutting-edge allogeneic CAR-T data in an environment where computational biology is valued as a strategic scientific capability and an integral part of decision-making. This role can be based out of our headquarters in South San Francisco, CA hybrid onsite 3 days a week or remote with travel to Allogene’s South San Francisco headquarters. Responsibilities include, but are not limited to: Multi-platform omics analysis Perform hands-on single-cell RNA-seq, BCR/TCR repertoire, NanoString, and flow cytometry data analysis across CAR-T clinical and research programs Integrate data across platforms and timepoints to support translational and clinical decision-making Conduct cell kinetics, persistence, and MRD analyses for ongoing trials Lead response biomarker correlate analyses — identifying computational signatures associated with clinical outcomes Pipeline and data infrastructure Develop, document, and maintain reproducible analysis pipelines across platform data outputs Build and curate a regulatory- and inspection-ready repository of bioinformatics datasets, code, and metadata — structured for auditability and external review Contribute to GxP-adjacent tool validation documentation and data standards harmonization across programs Regulatory and CMC support Generate analysis outputs and supporting documentation for clinical regulatory characterization work Support IND amendments and regulatory information requests requiring computational re-analysis Contribute bioinformatics methods sections and supplemental data for regulatory submissions Support process characterization omics analyses for CMC packages Conference and publication support Provide analysis and figure generation for conference abstracts and posters (ASCO, ASH, ACR, ASCO-GU) Contribute to manuscript methods sections, supplementals, and reviewer response packages Interface with medical affairs to translate computational outputs into presentation-ready formats Cross-functional and cross-program engagement Work across active programs Support competitive landscape monitoring of publicly released omics/bioinformatics datasets from competitor programs Collaborate with and tr