{"id":2211282,"url":"https://alion.io/job/origin-computational-biologist-spatial-transcriptomics","title":"Computational Biologist, Spatial Transcriptomics","company":{"id":3779673,"name":"Origin Bio","domain":"origin.bio","url":"https://alion.io/company/origin-9","size_band":"11-50","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Work at a Startup","truth_index":null},"role":"Biotech","role_family":"Biotech","seniority":null,"employment_type":"full_time","work_mode":"remote","remote_scope":"stated_countries","remote_scope_basis":"inferred_company_offices","remote_working_hours":null,"hiring_geo_confidence":"inferred","locations":["San Francisco, United States"],"countries":["US"],"hiring_countries":["US"],"hiring_countries_total":1,"salary":{"min":140000,"max":170000,"currency":"USD","period":"year","gross":null,"usd_annual":170000},"salary_estimate":null,"experience_years_min":null,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Immunohistochemistry","optional":false},{"name":"Python","optional":false},{"name":"Single-Cell Sequencing","optional":false}],"status":"live","first_seen_at":"2026-09-29T00:42:34Z","employer_posted_date":null,"last_verified_at":"2026-09-29T00:42:34Z","board_verified":false,"closed_at":null,"days_open":45,"trust":{"level":"not_scored","repost_count":null,"flags":[],"days_open":45},"description":"Origin Bio is producing matched spatial transcriptomics, histopathology images and clinical datasets from real patient tumours. We’re looking for a computational biologist to own post-run QC and secondary analysis of our Xenium data, from transcript-level and cell-feature outputs through to datasets aligned with post-run H&E images.\nWhat you’ll work on\nDevelop reproducible QC workflows for transcript detection, background signal, cell segmentation, transcript assignment, tissue and imaging artefacts, and variation across samples and runs.\nAlign post-run H&E whole-slide images to Xenium DAPI images and assess registration accuracy across each tissue section.\nWork with pathologists to bring tumour regions and other histological annotations into the spatial data.\nAnalyse the data beyond cell typing: investigate cell states, spatial neighbourhoods, tumour-immune interactions, differential expression and other patterns that emerge from the tissue. Use relevant single-cell reference datasets where helpful.\nIdentify meaningful questions that require analysis of the data to answer. For selected questions, derive well-supported reference results and turn the work into reproducible tasks that evaluate whether AI models can reach those results from the underlying data.\nHelpful past experience\nPhD or postdoctoral research in spatial biology or equivalent hands-on industry experience. Xenium or CosMx experience is especially valuable; experience with other spatial platforms is welcome.\nAnalysis of oncology tissue, H&E whole-slide images, or multiple imaging modalities such as IHC and immunofluorescence.\nStrong Python or R skills and experience building reproducible analysis workflows.\nExperience with scRNA-seq or bulk RNA-seq analysis, including the use of reference data to interpret spatial measurements.\nSound statistical judgement: recognising noise, batch effects, experimental artefacts and confounding variables, and knowing when an apparent biological finding needs further validation.\nThis is a full-time role. We prefer someone who can work with us in person in San Francisco, but we’re open to the right person working remotely.","description_format":"text","description_chars":2156,"description_truncated":false,"requirements":{"experience_years_min":null,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"phd","optional":false},"security_clearance":false,"languages":[]},"benefits":[],"hiring_locations":[{"name":"United States","iso":"US","kind":"country"}],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics","Oncology Therapeutics"],"lifecycle":[{"event":"open","at":"2026-10-10T03:05:21Z"}],"visa":[],"liveness":{"score":12,"band":"cold","label":"Long shot","p_open":0.6,"p_active":0.463,"p_room":0.45,"age_days":44,"expected_fill_days":23,"reasons":["seen:44","win:tail"],"computed_at":"2026-11-12T10:38:37Z"},"pay":{"stated_usd_annual":170000,"is_top_pay":false},"html_url":"https://alion.io/job/origin-computational-biologist-spatial-transcriptomics","json_url":"https://alion.io/job/origin-computational-biologist-spatial-transcriptomics.json","meta":{"generated_at":"2026-11-13T12:27:56Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","about":"Alion is a live layer of people, companies and AI agents: who they are, whether they are real and active right now, what they do and how to work with them, readable by people and by agents and paid per call.","catalog":"https://alion.io/catalog.json","usage":{"tier":"crawler_verified","counted_by":"address","units_charged":1,"used_today":25067,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-11-14T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.1,"usd":0.01,"plus_per_slice":{"credits":0.05,"usd":0.005}},"unit":"per company, plus each slice with data","note":"the employer in depth","call":{"mcp_tool":"get_company","arguments":{"id":3779673},"rest":"https://alion.io/mcp/rest/get_company?id=3779673"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Forigin-computational-biologist-spatial-transcriptomics"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"free","price":{"credits":0,"usd":0},"unit":"per slice","note":"pay, demand and time to fill for this role and place","call":{"mcp_tool":"market_stats"},"human":"https://alion.io/catalog?offer=market.stats&for=job%2Forigin-computational-biologist-spatial-transcriptomics"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.1,"usd":0.01},"unit":"per posting in a list","note":"similar open postings","call":{"mcp_tool":"search_jobs"},"human":"https://alion.io/catalog?offer=job.search&for=job%2Forigin-computational-biologist-spatial-transcriptomics"},{"id":"company.verify","title":"Is this company real and active right now","status":"pilot","price":null,"unit":"per company","request":{"url":"https://alion.io/catalog/request","method":"POST","body":"{\"offer\": \"company.verify\", \"for\": \"job/origin-computational-biologist-spatial-transcriptomics\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Forigin-computational-biologist-spatial-transcriptomics"}],"agent":{"mcp":"https://alion.io/mcp/jobs","mcp_open":"https://alion.io/mcp/open","next":[{"tool":"get_job","arguments":{"id":2211282}},{"tool":"search_jobs","arguments":{"company":"origin.bio","detail":"compact"}},{"tool":"match_people","arguments":{"job_id":2211282},"note":"people open to offers who fit this vacancy"}],"note":"The same data through MCP tools: https://alion.io/mcp/open needs no sign-in (compact searches, postings, people); https://alion.io/mcp with an Alion account has everything. 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