Senior Machine Learning Engineer
QIAGEN
Senior Machine Learning Engineer
QIAGEN
Molecular testing consumables, instruments, software
Overview
At QIAGEN, we are driven by a simple but powerful vision: making improvements in life possible.
We’re dedicated to revolutionizing science and healthcare for the better. From our entrepreneurial roots to our current global presence, we've grown into a force for positive change. With thousands of employees across six continents, collaboration is our greatest strength. We’re always striving to identify talented individuals to join our exceptional teams.
We have played a pivotal role in shaping modern science and healthcare, and we're just getting started. If you're someone who thrives on new challenges, values diversity and wants to make a tangible difference in people's lives, then QIAGEN is the place for you.
At QIAGEN, every day is an opportunity to make a real-life impact.
Join us, grow with us, and together, let's shape the future of biological discovery.
About the opportunity
QIAGEN Digital Insights (QDI) is a leading provider of bioinformatics software and knowledge bases used by life scientists to gain insight from the molecular information in their biological samples. We have developed industry-leading software tools for analysis and reporting of biological data. We are passionate about our users, products, and our vision, and are seeking smart, motivated engineers and scientists who are eager to join our team in creating software that actually helps improve people's lives.
As a Senior Engineer, you will be part of a growing NLP team collaborating with a cross-functional team of scientists, bioinformaticians, knowledge engineers, and software engineers building powerful tools to gain biological insight into gene expression, variant association, and molecular interaction data. This is a dynamic opportunity for you to develop cutting edge methods, explore new technologies, and help us overcome novel technical challenges. You will apply expertise in NLP, ML, and software systems to design production services that scale across QIAGEN's product portfolio.
Your tasks:
Develop, deploy, and maintain production LLM-integrated microservices using FastAPI
Integrate LLM APIs (OpenAI, Claude) with prompt engineering and RAG patterns
Balance accuracy, throughput, and operational cost by designing multi-model workflows and applying fit-for-purpose reasoning levels for different task complexities
Build robust data transformations and ETL layers across heterogeneous biomedical data models
Improve existing NLP pipelines for content acquisition (entity recognition, relationship extraction)
Develop and validate machine learning models for biological literature processing
Contribute to quality control, reliability, and observability for production systems
Your profile:
Proficiency in Python, including asynchronous patterns
Hands-on experience integrating LLM APIs (OpenAI, Claude, HuggingFace) into production systems
RAG (Retrieval-Augmented Generation) and vector embeddings
Data API integration: REST, custom authentication patterns
Testing practices: unit tests, integration tests, error handling
3+ years of professional software engineering experience
Understanding of NLP concepts: tokenization, POS tagging, semantic/syntactic parsing
Building and deploying production microservices: FastAPI, Docker, async/await, understanding of token management and costs
Nice to Have:
MCP (Model Context Protocol) server development, or other protocol-driven system design
Familiarity with embeddings (Cross-Encoder, Bi-Encoder, sentence-transformers)
Experience with Named Entity Recognition (NER), Entity Linking, and Relation Extraction for biomedical concepts
Experience with biomedical language models (bi-encoders as well as cross-encoders) such as SapBERT, BioBERT, PubMedBERT, or SciBERT
What we offer
Bonus/Commission
Local benefits
Referral Program
Volunteer Day
Internal Academy (QIALearn)
Employee Assistance Program
Hybrid work (conditional to your role)
Our people are the heartbeat of everything we do. Passion drives us as we push boundaries to innovate and evolve. We inspire with our leadership and make an impact with our actions. We cultivate a collaborative, supportive environment where each individual and team can flourish. We champion accountability and encourage entrepreneurial thinking.
QIAGEN is committed to creating a diverse environment and is proud to be an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, sex, age, national origin, religion, sexual orientation, gender identity, status as a veteran, or disability.
QIAGEN provides molecular testing solutions for DNA, RNA, and proteins used by researchers and clinicians in life sciences and diagnostics. Its products support the full workflow from sample preparation to data interpretation through a portfolio of sample technologies, assay technologies, and bioinformatics software, including QIAseq UPXome RNA Library Kits, QIAstat Dx Viral Vesicular Panel, and the QIAstat Dx Analyzer. The company differentiates itself with an integrated end-to-end ecosystem that combines hardware, reagents, and software to streamline workflows and data analysis. Its goal is to help researchers and clinicians obtain fast, reliable molecular insights to support scientific discovery, diagnostics, and patient care.
Explore more opportunities at QIAGEN