Computational Scientist / Senior Computational Scientist

Switchpoint Bio; Boston (MA); Hybrid; USD 140,000 - 200,000; Full time

Benefits offered by this job

Health insurance

Dental insurance

401k with matching

Generous paid time off

Disability insurance

Job summary

Switchpoint Bio is building computational pipelines to integrate genomics, epigenomics, transcriptomics, and proteomics with biobank cohorts and exposure data to uncover disease mechanisms and guide drug discovery. You will lead biological interpretation, design robust analyses, and work closely with ML scientists to turn molecular signals into actionable evidence.

You will collaborate with wet-lab and clinical teams, shape study design, and drive the translation of high-dimensional data into

Qualifications

• PhD in genomics, epigenomics, or a related field with a strong publication record.
• Hands-on multiomics data experience including single-cell or biobank-scale data.
• Ability to design and interpret integrative analyses across data modalities.
• Strong quantitative skills and proficiency in Python or R.
• Excellent cross-disciplinary communication in English.

Responsibilities

• Design and lead multimodal data integration analyses combining genomics, epigenomics, transcriptomics, and proteomics with cohorts and exposure data.
• Provide biological interpretation and validation to connect signals to mechanisms and disease pathways.
• Collaborate with ML scientists to translate scientific questions into models and evaluative metrics.
• Shape study design, ground truth, and validation to ensure biologically meaningful results.
• Partner with wet-lab and clinical collaborators to ensure data is analyzable and relevant to questions.

Skills

Multiomics

Data integration

Independent scientific judgment

Python or R

Clear communication

English fluency

Collaborative work

Education

PhD in relevant field

Tools

Python

R

Bioconductor

Job description

Switchpoint Bio is decoding the molecular switchpoints that drive human health and disease. The choices our cells make — which genes to activate, how to respond to environment and exposure, when to mount immune defenses — are governed by epigenetic mechanisms. We bring together genomics, epigenomics, and AI to turn epigenetic biology into decision-grade evidence for drug discovery and clinical decision-making.

The opportunity. Epigenetics is how cells record genetics, aging, environment, and exposure across a lifetime — and it shapes nearly every major area of human disease. Our flagship programs focus on autoimmune conditions and cancer today, but the same mechanisms underlie cardiovascular, metabolic, and neurodegenerative disease. Together, these touch billions of lives — yet most treatments are still chosen by trial and error. We're building the platform that makes these mechanisms visible — and the evidence base that turns it into better drugs, earlier diagnoses, and treatments matched to the person, not the population.

Founded by pioneers in single-cell biology, epigenetics, and genomics, we operate across Helsinki and Boston. We're a small founding team in the earliest days — building not just a platform, but a company and a culture from scratch.

We hire builders. People who take ownership, move fast, and thrive when the problem is bigger than the playbook. If you want to join the first wave of hires at a company tackling some of the biggest open questions in human biology — and shape what it becomes — this is that moment. We're AI-native from day one, and we hire people who already work that way.

The role

We have an established team building machine learning models and infrastructure. For this role, we're looking for the scientist who brings the deep domain knowledge to point these tools towards new biological opportunities.

As a Computational Scientist you'll be the biological and analytical lead on our multiomic data: designing how we integrate genomics, epigenomics, transcriptomics, and proteomics with biobank cohorts, health registries, and exposure data, and interpreting what it means for disease mechanism and drug discovery. You'll work closely with our ML scientists — you shape the scientific questions, the study design, the ground truth, and the biological validation; together you turn high-dimensional molecular data into evidence the company can act on.

What you'll work on

• Lead the design and analysis of multimodal data integration — combining molecular data (genomics, epigenomics, transcriptomics, proteomics), single-cell and biobank-scale cohorts, health registries, and lifestyle/exposure data into coherent, interpretable analyses.
• Bring domain judgment to modeling: define the biological questions, choose the right cohorts and comparisons, engineer biologically meaningful features, and decide what "good" looks like for immune cell-type identification, disease classification, and treatment-response prediction.
• Own biological interpretation and validation — connect molecular signals to mechanisms (immune regulation, epigenetic control, disease pathways), and separate real biology from batch effects, technical artifacts, and confounding.
• Read the frontier of the genomics, epigenomics and immunology literature independently, judge what's credible, and recommend what we should build or adopt next.
• Partner with the ML scientist to turn scientific questions into models and evals, and translate model output back into decision-grade biological evidence.
• Work with wet-lab and clinical collaborators to shape assay and study design so the resulting data is analyzable, well-controlled, and answers the question we actually care about.

What you'll help build in your first 12 months

• Multiomic integration framework — establish how we bring molecular, cohort, registry, and exposure data together, with the QC, harmonization, and confounder handling that make cross-cohort analysis trustworthy.
• Immune cell-type and disease signatures — define and validate the biological ground truth behind our immune cell-type identification and disease classifiers, so the models the team ships reflect real biology.
• Mechanistic evidence for programs — deliver analyses that link epigenetic and molecular signals to disease mechanisms in autoimmune conditions and cancer, feeding target and biomarker decisions.
• Clinical and translational read-outs — help build predictors of health outcomes and treatment response from high-dimensional molecular profiles, and own the question of whether they generalize across populations.
• A shared scientific workflow — with the ML scientist and agentic tooling, shape how analyses, hypotheses, and literature synthesis flow through the team so science moves faster without losing rigor.

What we're looking for

Must-have

• Multiomics domain expertise — you've worked hands-on with omics data (e.g. genomics, epigenomics, transcriptomics, methylation, proteomics) and understand the biology behind it, not just the matrices. Single-cell and/or biobank-scale experience is strongly preferred.
• Multimodal / health data integration — you've integrated and analyzed heterogeneous biological and health data, and you know how to make signals from different modalities and cohorts comparable.
• Independent scientific judgment — you read cutting-edge papers in genomics/genetics/epigenomics, assess what holds up, and recommend concrete solutions.
• Quantitative and computational rigor — solid statistics and hands-on Python (or R) for real analysis; you don't need to be an ML infrastructure engineer, but you collaborate fluently with one.
• Fluency with how naive analysis fails on molecular data — batch effects, technical artifacts, ascertainment, population structure, and confounding; you anticipate them and design around them.
• Clear cross-disciplinary communication — you translate between biology and ML/engineering, explain your reasoning, and write and speak fluent English.
• High-impact published science — a track record of strong, high-impact publications is especially favored.
• PhD in relevant field

Nice to have

• Domain depth in immunology, or autoimmune disease biology.
• Experience with epigenomic assays and data (ATAC-seq, DNA methylation, single-cell multiomics).
• Familiarity with genomic/epigenomic foundation models (e.g., AlphaGenome, Evo, Nucleotide Transformer, scGPT, Geneformer) and how to use them for real biological questions.
• Experience with causal inference, Mendelian randomization, or QTL integration for target and biomarker validation.
• Prior work in startups, frontier labs, or research environments where you owned problems end-to-end.
• Be the scientific voice that decides what we model and whether it's real — at the frontier of genomics, epigenetics, and human health.
• Own the biology end-to-end, from study design and integration to interpretation and translational impact.
• Work in a true complementary pair with a strong ML scientist, supported by experienced computational scientists, rather than doing everything alone.
• Help build a company, platform, and culture from the ground up, with high ownership and real influence from day one.
• Collaborate with globally recognized scientists across Helsinki and Boston.
• Solve meaningful problems with real-world clinical impact, on a lean team that moves fast and builds ambitiously.

Details

• Location: Cambridge, MA, USA, hybrid 2-3 days/week at a company office
• Relocation: We offer relocation support for strong candidates moving to Boston.
• Travel: Occasional — primarily to our Helsinki hub, plus the occasional conference. Expect a handful of trips per year, not a monthly thing.
• Reports to: Chief Scientific Officer
• Compensation: $140,000–200,000/year depending on the qualifications + meaningful option package. As a first-wave hire, your option package reflects the impact you'll have on what we build.
• Generous paid time off
• Health and Dental insurance
• 401k with matching
• life and short/long-term disability insurance

How we work

We believe great work and a good life outside work belong together. We value trust, autonomy, flexibility, low hierarchy, transparency, and sustainable ways of working. We focus on what you accomplish and the quality of your thinking rather than the hours you spend at your desk.

We want Switchpoint Bio to be a place where exceptional people can do some of the best work of their careers while still having the time and energy for life outside of work.

Switchpoint Bio is an equal opportunity employer. We welcome qualified applicants from all backgrounds and make employment decisions based on qualifications, merit, and business needs.