{"id":826072,"url":"https://alion.io/job/cellularintelligence-senior-bioinformatics-scientist","title":"Senior Bioinformatics Scientist","company":{"id":670515,"name":"Cellular Intelligence","domain":"cellularintelligence.com","url":"https://alion.io/company/cellularintelligence","size_band":"51-200","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Ashby","truth_index":null},"role":"Science & Research","role_family":"Science & Research","seniority":"senior","employment_type":"full_time","work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["Boston, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":160000,"max":190000,"currency":"USD","period":"year","gross":null,"usd_annual":190000},"salary_estimate":null,"experience_years_min":3,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Machine Learning","optional":false},{"name":"Python","optional":false}],"status":"live","first_seen_at":"2026-07-16T18:10:44Z","employer_posted_date":"2026-07-16","last_verified_at":"2026-09-30T05:03:33Z","board_verified":true,"closed_at":null,"days_open":76,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":76},"description":"About Cellular Intelligence\nCellular Intelligence is building a universal foundation model for cell signaling to understand, predict, and ultimately control how cells behave, transforming biology from trial and error into an engineering discipline. A clinical-stage AI company, Cellular Intelligence holds the global rights to STEM-PD, an investigational Phase 2-ready cell therapy for Parkinson's disease with FDA Fast Track designation, acquired from Novo Nordisk. The company's founding team includes repeat AI entrepreneur Micha Breakstone, Ph.D. (Chorus.ai, acquired for $575M), the Head of the Fundamental AI Group at MIT, and five professors from Harvard Medical School, the University of Pennsylvania, and the University of Washington, collectively holding five National Academy memberships. Based in Boston, Cellular Intelligence has raised over $70M from Khosla Ventures, the Chan Zuckerberg Initiative, Novo Nordisk, AMD Ventures, and others.\nCellular Intelligence’s Core Values\nWe show up - fully accountable, all-in, doing whatever it takes.\n\nWe act with urgency - swift, decisive, proactive.\n\nWe support one another - collaborative, helpful, empathetic.\n\nLocation: Boston, MA\nReports to: Director of Bioinformatics\n\nAbout the Role:\nWe seek a Senior Bioinformatics Scientist to own and develop the methods and pipelines that power our proprietary capsule platform and feed our Universal Virtual Cell-Signaling Model. Working across single-cell, spatial, and bulk RNA-seq, you'll build reproducible pipelines, develop new bioinformatics methods, and apply them to our data. You'll collaborate closely with wet lab scientists, software engineers, and machine learning researchers to advance novel sequencing protocols and our therapeutic programs. This is a hands-on role spanning single-cell and spatial omics, ideal for someone who thrives in a fast-paced, interdisciplinary environment and wants to help build our cell-replacement therapy platform from the ground up.\nResponsibilities:\nDevelop new bioinformatics methods for single-cell, spatial, and bulk transcriptomics data, and adapt and benchmark existing ones.\n\nBuild and maintain reproducible analysis pipelines for single-cell, spatial, and bulk RNA-seq, from QC and normalization through the downstream analysis appropriate to each modality (integration, clustering, annotation, differential expression).\n\nAnalyze large-scale single-cell and spatial transcriptomics data, from raw output through to biological interpretation, including visualization of spatial data.\n\nPartner with wet-lab scientists to bring novel multi-omic assays online, developing the analysis methods and pipelines that new experimental modalities require.\n\nCollaborate with wet-lab and computational scientists to design experiments and interpret results.\n\nProvide technical guidance and mentorship across the bioinformatics, ML, and engineering teams, including code and method reviews.\n\nQualifications:\nPhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field. Equivalent industry experience is also welcome.\n\n3+ years of experience developing, adapting, and benchmarking bioinformatics methods and building reproducible pipelines for large-scale single-cell and/or spatial transcriptomic data.\n\nHands-on experience with single-cell transcriptomics analysis.\n\nStrong Python and/or R programming skills.\n\nExperience building reproducible workflows with a pipeline manager (e.g. Nextflow or Snakemake), containers, and version control.\n\nExperience applying state-of-the-art large language models (LLMs) to bioinformatics projects.\n\nExcellent organizational and documentation habits.\n\nPrefered Qualifications:\nExperience with spatial transcriptomics data analysis and visualization.\n\nExperience applying and improving automated cell type annotation methods (e.g. marker-based and reference-based methods).\n\nExperience working at the interface of technology development and data analysis, particularly involving novel molecular biology or sequencing techniques.\n\nStrong domain knowledge in developmental biology or stem cell research.\n\nExperience mentoring scientists or reviewing scientific code.\n\nPrior experience in a startup or fast-paced, interdisciplinary environment.\n\nCellular Intelligence is committed to creating a diverse and inclusive workplace. We welcome and encourage applicants from all backgrounds, regardless of race, ethnicity, gender, sexual orientation, religion, disability, or age. We embrace differences and believe that a diverse workforce enhances our creativity, innovation, and overall success.","description_format":"text","description_chars":4602,"description_truncated":false,"requirements":{"experience_years_min":3,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"phd","optional":false},"security_clearance":false,"languages":[]},"benefits":[],"hiring_locations":[],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics"],"lifecycle":[{"event":"open","at":"2026-09-12T14:36:32Z"}],"liveness":{"score":19,"band":"cold","label":"Long shot","p_open":1,"p_active":0.524,"p_room":0.36,"age_days":75,"expected_fill_days":42,"reasons":["conf:0","win:tail","crowd:"],"computed_at":"2026-09-30T05:45:00Z"},"pay":{"stated_usd_annual":190000,"is_top_pay":true},"html_url":"https://alion.io/job/cellularintelligence-senior-bioinformatics-scientist","json_url":"https://alion.io/job/cellularintelligence-senior-bioinformatics-scientist.json","meta":{"generated_at":"2026-10-01T04:11:47Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","usage":{"tier":"crawler","counted_by":"address","units_charged":1,"used_today":3400,"day_limit":5000,"remaining_today":1600,"minute_limit":60,"resets_at":"2026-10-02T00:00:00Z"}}}