{"id":1330033,"url":"https://alion.io/job/singular-genomics-systems-sr-bioinformatics-scientist","title":"Sr. Bioinformatics Scientist","company":{"id":3782968,"name":"Singular Genomics Systems","domain":"singulargenomics.com","url":"https://alion.io/company/singular-genomics-systems","size_band":"11-50","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Greenhouse","truth_index":null},"role":"Science & Research","role_family":"Science & Research","seniority":"senior","employment_type":null,"work_mode":"hybrid","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"explicit","locations":["San Diego, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":131600,"max":154800,"currency":"USD","period":"year","gross":null,"usd_annual":154800},"salary_estimate":null,"experience_years_min":null,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Linux","optional":false},{"name":"Python","optional":false},{"name":"Single-Cell Sequencing","optional":false},{"name":"AWS","optional":true},{"name":"CI/CD","optional":true},{"name":"Docker","optional":true}],"status":"live","first_seen_at":"2026-08-19T15:22:58Z","employer_posted_date":"2026-08-19","last_verified_at":"2026-10-23T18:28:35Z","board_verified":true,"closed_at":null,"days_open":65,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":65},"description":"jobs-description--reformatted\njob-details-module\">\n\">\n\">\ntDkzEJDIRFQsxPLGUrnliPvxjwidpxCOYBGZ\nt-14 t-normal\njobs-description-content__text--stretch\" data-artdeco-is-focused=\"true\">\nABOUT SINGULAR GENOMICS\nSingular Genomics is inventing at the forefront of genomics, one of the world’s fastest-growing industries. The commercially available G4® Sequencing Platform is a powerful, highly versatile benchtop genomic sequencer designed to produce fast and accurate results. In addition, the company is currently developing the G4X™ Spatial Sequencer, an upgrade to the G4, which will leverage Singular’s proprietary sequencing technology, applying it as an in situ readout for transcriptomics, proteomics and fluorescent H&E in tissue, with spatial context. Singular Genomics’ mission is to empower researchers and clinicians to advance science and medicine.\nWe foster a culture of creativity and technical excellence, both catalysts for innovation. We celebrate diversity, emphasize collaboration and, as we rapidly mature, we are constantly looking at ways we can do better for our people.\nOur Headquarters are located on the Torrey Pines Mesa, in La Jolla, California at the center of the biotech hub. Our Manufacturing facility is in Sorrento Valley.\nPosition Summary:\nAs a Senior Scientist on the Bioinformatics team, you will play a key role in expanding Singular Genomics' spatial biology platform and service offerings. This position sits at the intersection of computational biology, assay development, and hands-on scientific computing. You will report into the Bioinformatics functional group and, initially, be matrixed into the Panel Design team to focus on its most pressing needs. Your initial focus will be supporting the design and optimization of targeted in situ transcriptomics panels for tissue- and disease-specific applications. This includes selecting biologically informative genes for cell type identification, defining pathway-focused content that enables cell-state interpretation, and developing computational tools to automate and improve panel design. As the platform and services continue to evolve, you will contribute to the development of spatial bioinformatics workflows, analysis pipelines, and computational methods that enable customers to generate meaningful biological insight from spatial multiomics data. This is an ideal role for someone who enjoys applying computational approaches to challenging biological problems while building software that directly impacts cutting-edge products and services. This position can be remote or hybrid/on-site. If remote, travel to the headquarters in San Diego, CA will be required at least quarterly.\nResponsibilities:\nPrimary Responsibilities:\nSupport the computational design and optimization of targeted spatial transcriptomics panels for tissue- and disease-specific applications.\nDefine biologically relevant panel content by integrating current literature, public datasets, and pathway knowledge to support cell type annotation and cell state characterization.\nDevelop computational methods and software tools for automated panel design, probe evaluation, and panel optimization.\nCollaborate closely with molecular biology, chemistry, and assay development teams to iteratively improve probe performance and panel quality.\nEvaluate panel performance using internal datasets and external spatial and single-cell reference atlases.\nSpatial Bioinformatics\nDevelop and maintain analysis pipelines for spatial transcriptomics and spatial multiomics datasets.\nApply modern spatial bioinformatics methods to support sequencer / assay development and biological interpretation, including cell typing, differential expression, pathway analysis, spatial neighborhood analysis, and cell-state characterization.\nWork with scientists across R&D to develop new analysis capabilities that support expanding service offerings.\nStay current with advances in spatial biology, single-cell genomics, and computational biology, incorporating new approaches where appropriate.\nScientific Software & Automation\nWrite clear, workable code (primarily Python) to automate panel design, analysis, and other repetitive scientific tasks.\nBuild and maintain automated analysis workflows that make routine spatial and single-cell analyses repeatable and easy to run. \nQualifications:\nPhD in Bioinformatics, Computational Biology, Genomics, Computer Science, or a related discipline. Candidates with an MS plus industry experience will also be considered.\nExperience analyzing spatial transcriptomics, single-cell sequencing, or related genomics datasets.\nStrong understanding of tissue biology, cell type annotation, and pathway-based biological interpretation.\nProficiency writing analysis code in Python; able to produce clear, workable code without requiring production-software polish.\nExperience building automated analysis workflows or pipelines. • Working knowledge of Linux-based computational environments.\nExcellent written and verbal communication skills\nPreferred Qualifications:\nExperience designing targeted sequencing or hybridization-based panels.\nExperience with probe design, oligonucleotide design, or molecular assay development.\nExperience with single-cell analysis frameworks such as Scanpy, Squidpy, Seurat, or similar.\nKnowledge of cancer biology, immunology, or tissue-specific biology.\nExperience developing workflow pipelines using Nextflow.\nFamiliarity with containerization (e.g., Docker) and reproducible-environment tooling.\nSoftware-engineering rigor (testing, CI/CD, packaging) is welcome but not expected at this level.\nExperience with cloud computing environments (AWS preferred). • Familiarity with image-based spatial technologies or microscopy data.\nExperience with primary analysis methods such as image processing, feature detection, registration, or sequencing base calling is a plus but not required..\nThe estimated base salary range for this role based in the United States of America is: $131,600 - $154,800. Additionally, this role is eligible for to receive equity as part of the compensation package. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Should the level of the role change during the hiring process, the applicable salary range may be updated accordingly.\nSingular Genomics is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees.\nSingular Genomics is committed to working with and providing reasonable accommodations to job applicants with physical or mental disabilities. Applicants with a disability who require a reasonable accommodation for any part of the application or hiring process can provide their name and contact information to our Accommodations team at . Your request will be responded to as soon as possible.","description_format":"text","description_chars":7017,"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":["Equity"],"hiring_locations":[{"name":"United States","iso":"US","kind":"country"}],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics","Genomics & Genetic Testing","Laboratory Equipment"],"lifecycle":[{"event":"open","at":"2026-09-27T09:08:36Z"}],"visa":[{"country":"US","licensed_sponsor":true,"evidence":"green card filings: 1","filings_12m":0,"filings_prev_12m":1,"green_card_filings_12m":1,"median_offered_wage_usd":127500,"route":null,"cap_exempt":false,"checked_at":"2026-10-15T11:24:14+00:00","sources":["US Department of Labor: LCA disclosure data (H-1B, H-1B1, E-3)","US Department of Labor: PERM disclosure data (green cards)"],"filings_for_role_12m":0}],"liveness":{"score":11,"band":"cold","label":"Long shot","p_open":1,"p_active":0.389,"p_room":0.28,"age_days":64,"expected_fill_days":30,"reasons":["conf:1","win:tail","crowd:"],"computed_at":"2026-10-23T05:54:15Z"},"pay":{"stated_usd_annual":154800,"is_top_pay":false},"html_url":"https://alion.io/job/singular-genomics-systems-sr-bioinformatics-scientist","json_url":"https://alion.io/job/singular-genomics-systems-sr-bioinformatics-scientist.json","meta":{"generated_at":"2026-10-23T21:18:13Z","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":3216,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-10-24T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.02,"usd":0.002,"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":3782968},"rest":"https://alion.io/mcp/rest/get_company?id=3782968"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Fsingular-genomics-systems-sr-bioinformatics-scientist"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"live","price":{"credits":1,"usd":0.1},"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%2Fsingular-genomics-systems-sr-bioinformatics-scientist"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.02,"usd":0.002},"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%2Fsingular-genomics-systems-sr-bioinformatics-scientist"},{"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/singular-genomics-systems-sr-bioinformatics-scientist\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Fsingular-genomics-systems-sr-bioinformatics-scientist"}]}