Machine Learning Scientist / Senior Machine Learning Scientist

Calico Life Sciences; South San Francisco (CA); On-site; USD 170,000 - 233,000; Full time

Benefits offered by this job

Two annual cash bonuses

Job summary

Calico Life Sciences in South San Francisco is seeking a Machine Learning Scientist to investigate gene regulation through computational models. The role requires a PhD in a relevant field and offers a competitive salary range of $170,000 - $233,000, along with eligibility for two annual cash bonuses. Candidates should have deep expertise in machine learning, experience with genomic data, and a strong publication record. The position involves collaboration with experimental scientists and a significant focus on innovative biological insights.

Qualifications

• PhD required, with 0-5 years for Scientist level or 5+ years for Senior Scientist level.
• Strong publication record needed.
• Deep expertise in machine learning and solid grounding in algorithms.

Responsibilities

• Design and train deep learning models for biological sequence analysis.
• Partner with experimental scientists to connect model predictions to biological mechanisms.
• Communicate research through publications and public-facing tools.

Skills

Machine learning expertise

Genomic data analysis

Collaboration

Statistical analysis

Fluency with AI tools

Education

PhD in computational biology, bioinformatics, or related field

Tools

Deep learning frameworks

Genomic data analysis tools

Job description

Who We Are

Calico (Calico Life Sciences LLC) is an Alphabet‑founded research and development company whose mission is to harness advanced technologies and model systems to increase our understanding of the biology that controls human aging. Calico will use that knowledge to devise interventions that enable people to lead longer and healthier lives. Calico’s highly innovative technology labs, its commitment to curiosity‑driven discovery science and, with academic and industry partners, its vibrant drug‑development pipeline, together create an inspiring and exciting place to catalyze and enable medical breakthroughs.

Position Description

Calico is seeking a machine learning scientist to join a research group investigating how genome sequence determines regulatory function and how dysregulation of these programs drives aging. We develop sequence‑based deep learning models that predict gene expression, chromatin accessibility, and other functional readouts directly from DNA. We use these models to interpret human genetic variation, map causal regulatory mechanisms, and identify promising intervention points.

This work builds on a sustained research program at the intersection of deep learning and regulatory genomics, including:

• Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long‑range interactions. Nat Methods 18, 1196–1203 (2021).
• Yuan, H. & Kelley, D. R. scBasset: sequence‑based modeling of single‑cell ATAC‑seq using convolutional neural networks. Nat Methods 19, 1088–1096 (2022).
• Linder, J., Srivastava, D., Yuan, H., Agarwal, V. & Kelley, D. R. Predicting RNA‑seq coverage from DNA sequence as a unifying model of gene regulation. Nature Genetics (2025).

Position Responsibilities

• Design and train deep learning models for biological sequence analysis, with emphasis on gene regulation, single‑cell genomics, and variant interpretation
• Partner with experimental scientists to connect model predictions to biological mechanisms — designing validation experiments, analyzing large‑scale genomics data, and translating computational findings into actionable biological insights
• Communicate research through publications, open‑source software, and public‑facing tools

Position Requirements

PhD in computational biology, bioinformatics, computer science, or a related field, and 0-5 years (for Scientist level) or 5+ years (for Senior Scientist level) of additional training in an industry or academic setting, with a strong publication record.

• Deep expertise in machine learning with solid grounding in algorithms, data structures, and statistics
• Substantive knowledge of molecular biology and genetics; familiarity with genomic data types and public data resources
• Hands‑on experience analyzing genomics sequencing data, ideally including single‑cell assays
• Fluency with modern AI‑assisted development and research tools (e.g., LLM‑based coding assistants, literature synthesis), with a habit of proactively integrating new tools to accelerate scientific workflows
• A collaborative disposition, strong follow‑through, and comfort working at the interface of computation and experiment
• Must be willing to work onsite at least four days per week

The estimated base salary range for this role is $170,000 - $233,000. Actual pay will be based on a number of factors including experience and qualifications. This position is also eligible for two annual cash bonuses.