# Scientist

**Company:** [Astera](https://hotfix.jobs/companies/astera)
**Location:** Emeryville, CA
**Role:** ML Engineering
**Salary:** $100k – $180k/yr
**Skills:** Bioinformatics, Computational Biology, Machine Learning, Protein Structure, Bioinformatic Pipelines, High-Dimensional Datasets, Transformer Models, Protein Language Models, Esm, Alphafold, Llm Embeddings
**Posted:** 2026-07-07

> Scientist building ensemble-aware protein representations and ML models that integrate dynamic structural data with PLMs, ligands, and functional info to advance dynamic structural biology. Requires PhD and experience with large bioinformatic pipelines.

## Job Description

## Key Responsibilities
- Build ensemble-aware protein representations that integrate PLM and LLM embeddings with experimentally derived structural heterogeneity for functional prediction.
- Design, develop, and maintain large-scale bioinformatic pipelines capable of processing and managing complex, high-dimensional datasets.
- Fine-tune or architect ML models to capture sequence-structure-function relationships, with a focus on dynamic and conformational features.
- Synthesize diverse data sources spanning evolutionary history, binding affinity, allostery, and functional annotations to improve model performance and biological relevance.
- Collaborate closely with experimental partners to ground computational representations in real biological measurements and ensure models are continuously refined against experimental ground truth.
- Contribute to the broader diffUSE infrastructure, helping establish community-wide standards and tools for dynamic structural biology.

## Required Skills and Qualifications
- PhD in bioinformatics, computational biology, machine learning, or a related field.
- Strong understanding of protein structure and function.
- Demonstrated experience building large bioinformatic pipelines and managing high-dimensional datasets.
- Proficiency in fine-tuning or modifying ML models (e.g., transformer-based architectures).
- Familiarity with protein language models (ESM, AlphaFold, etc.) is a plus.
- Collaborative, team-oriented mindset with the ability to drive research questions from conception to execution.

## Similar roles

- [General DiffUSE Job Application](https://hotfix.jobs/jobs/6676763d-f0db-437a-b47b-09135360f2b3) - Astera - Emeryville, CA - $100k – $300k/yr
- [Model Behavior Engineer](https://hotfix.jobs/jobs/26d5a619-a0c7-4356-b422-eb5c88496464) - Notion - New York, NY - $98k – $140k/yr
- [AI Engineer](https://hotfix.jobs/jobs/78689d2f-baeb-4f39-9fb1-c9122eef3363) - GitLab - Remote - $108k – $130k/yr
- [Software Engineer, Generative AI](https://hotfix.jobs/jobs/5ccef877-0805-4fed-a8ae-ee43ec3dd0c5) - Writer - San Francisco, CA - $112k – $304k/yr
- [AI/ML Scientist/Developer](https://hotfix.jobs/jobs/84e165ef-2ec6-4560-852d-37e2c1b7973f) - Axle - Frederick, MD - $115k – $130k/yr

**Apply:** https://hotfix.jobs/jobs/fd1ba51c-2efc-465f-9891-a43db9ef7bcb
**Canonical:** https://hotfix.jobs/jobs/fd1ba51c-2efc-465f-9891-a43db9ef7bcb