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Ionis Pharmaceuticals

Leidos QTC Health Services

Hybrid

Do you crave a career that truly makes an impact in people’s lives? Do you thrive on problem-solving and finding solutions? Join a dedicated, tight-knit team that creates an immediate and meaningful impact every day
Leidos QTC Health Services is seeking a mid‑to‑senior‑level AI Engineer who loves wrestling with large language models (LLMs) and building useful products. You will design and ship AI‑powered applications that leverage the latest LLMs while meeting the strict privacy and security requirements of the healthcare industry. 
Primary Responsibilities:   
<ul>
<li>Develop AI‑powered applications using state‑of‑the‑art LLMs. You will build and deploy applications for our internal customers, selecting the right models (e.g., GPT‑4o, Claude Sonnet 4, Gemini 2.5 or open‑source alternatives).</li>
<li>Implement retrieval‑augmented generation (RAG) pipelines and agents using LangChain, LangGraph, LlamaIndex, and other emerging frameworks.</li>
<li>Integrate ML models with front-end apps, REST APIs, and backend systems.</li>
<li>Design and build end-to-end AI systems—ranging from chatbots and recommendation engines to vision-based pipelines.</li>
<li>Build robust logic around ML models to address edge cases, failovers, and complex business rules.</li>
<li>Leverage prebuilt models or services (e.g., OpenAI API, Azure Cognitive Services, HuggingFace) to accelerate development cycles.</li>
<li>Fine‑tune and customize models using LoRA, prompt tuning, or RLHF techniques.</li>
<li>Occasionally perform custom model training—but more often fine-tune or adapt existing models to meet business needs.</li>
<li>Work with vector databases (e.g., Pinecone, Weaviate) and explore graph-based approaches (e.g., GraphRAG, Knowledge Graphs).</li>
<li>Ensure privacy and compliance with HIPAA, including encryption, PHI protection, and vendor due diligence.</li>
<li>Prototype multi‑agent systems using frameworks like CrewAI or Stands SDK and evaluate emerging agent orchestration solutions.</li>
<li>Collaborate cross-functionally with product managers, data scientists, and compliance teams.</li>
<li>Mentor junior engineers, lead innovation discussions, and continuously evaluate emerging LLM architectures.</li>
</ul>
Required Qualifications/Competencies:
<ul>
<li>Bachelor’s degree from an accredited college in Computer Science, Computer Engineering, Statistics, Data Science or another similar quantitative field. Additional experience in lieu of a degree may be considered.</li>
<li>9+ years in software engineering or machine learning, with 2+ years building production AI/ML systems.</li>
<li>Strong programming skills in Python and Typescript.</li>
<li>Experience with REST APIs and frameworks like Flask or FastAPI.</li>
<li>Familiarity with LangChain, LlamaIndex, HuggingFace Transformers, SGLang, and OpenAI API.</li>
<li>Experience with RAG architectures, including vector databases and GraphRAG approaches.</li>
<li>Experience deploying AI solutions using cloud platforms (AWS, Azure, or GCP).</li>
<li>Understanding of HIPAA compliance: handling PHI, encryption protocols, and vendor BAAs.</li>
<li>Experience in prompt engineering, prompt security, and evaluation strategies.</li>
<li>Familiarity with containerization, CI/CD, and MLOps pipelines</li>
</ul>
Preferred Qualifications:
<ul>
<li>Experience in healthcare, life sciences, or other regulated industries.</li>
<li>Background in autonomous agents and orchestration frameworks (e.g., CrewAI, Strands, OpenAI Agents SDK).</li>
<li>Exposure to multi-modal models (e.g., GPT‑4o, Pixtral Large).</li>
<li>Knowledge of chain-of-thought reasoning and RLHF workflows.</li>
<li>Additional languages like Rust or Go; experience with microservices or event-driven architecture.</li>
</ul>
About Leidos QTC Health Services
Leidos QTC Health Services collaborates closely with government and non-government customers to address current and future program needs within the health services domain. We specialize in disability-focused medical examinations, independent medical exams and review services, occupational health services, diagnostic testing, and case management solutions. As innovators, we focus on advancing technologies that improve service delivery, with a particular emphasis on enhancing accessibility for examinees in rural communities. With a proven track record of continuous improvement and steady growth, we now handle over 2 million appointments annually. Visit <a style="color: #000000;" href="http://www.qtcm.com/" target="_blank" rel="noopener">www.qtcm.com</a> for more information.
Compensation and Benefits
Pay and benefits are fundamental to any career decision. That's why we craft compensation packages that reflect the importance of the work we do for our customers. As a result, we offer meaningful and engaging careers to support you and your career goals, all while nurturing a healthy work-life balance. Employment benefits include competitive compensation, Health and Wellness programs, Income Protection, Paid Leave and Retirement. <a style="color: #000000;" href="https://www.qtcm.com/careers/" target="_blank" rel="noopener">More details are available here.</a>
This role may fall under the Service Contract Act (SCA), a federal law which provides for a U.S. Department of Labor-prescribed minimum prevailing rate of pay and certain benefit levels. Where appropriate, Company-provided benefit plans such as comprehensive leave, holiday, medical, dental, life, accident, disability coverages, retirement plan contributions, and other health and welfare benefits and payments are utilized to meet these obligations. 
Commitment to Non-Discrimination
All qualified applicants will receive consideration for employment without regard to sex, race, ethnicity, age, national origin, citizenship, religion, physical or mental disability, medical condition, genetic information, pregnancy, family structure, marital status, ancestry, domestic partner status, sexual orientation, gender identity or expression, veteran or military status, or any other basis prohibited by law. Leidos QTC Health Services will also consider for employment qualified applicants with criminal histories consistent with relevant laws.

AI/ML Engineer

9+ years software/ML experience; 2+ years in production AI; Python and Typescript; REST APIs; LangChain, LlamaIndex, HuggingFace; OpenAI API; ML model deployment and RAG architectures.

Headquartered in Carlsbad, California, and with offices in Boston, Massachusetts, and Dublin, Ireland, Ionis has been at work for more than three decades discovering medical breakthroughs that have redefined life for people with serious diseases. We’re pioneers in RNA-targeted medicines, and our platform continues to revolutionize drug discovery and transform lives for patients with unmet needs.  With multiple marketed medicines and a leading pipeline in neurology, cardiology and select areas of high patient needs, we continue to drive innovation in RNA therapies in addition to advancing new approaches in gene editing to provide greater value to patients and are well positioned financially to deliver on our strategic goals.
At Ionis, we pride ourselves on cultivating a challenging, motivating and rewarding environment that fosters innovation and scientific excellence. We know that our success is a direct result of the exceptional talents and dedication of our employees. 
With an unprecedented opportunity to change the course of human health, we look to add diverse individuals, skill sets and perspectives to our exceptional team. We continue to invest time, money and energy into making our onsite, hybrid and remote work environments a place where solid and lasting relationships are built and where our culture and employees can thrive. 
We’re building on our rich history, and we believe our greatest achievements are ahead of us. If you’re passionate about the opportunity to have meaningful impact on patients in need, we invite you to apply and join us. Experience and contribute to our unique culture while you develop and expand your career!
 
DIRECTOR, COMPUTATIONAL BIOLOGY
 
SUMMARY:
We are seeking an exceptional computational biologist to lead target identification and multi-omics research efforts. In this role, you will drive the use of high-throughput, transcriptomics, epigenomics, proteomics, and functional genomics data to identify and prioritize novel therapeutic targets. You will bring a strategic, industry-wide perspective on the field — staying ahead of where it is moving and translating that into a differentiated approach which will align with Ionis's RNA-targeting and oligonucleotide platforms. You will lead a team of computational biologists, shape analytical strategy, and partner tightly with biology, human genetics, and drug discovery colleagues to bring forward the next wave of therapeutic targets.
RESPONSIBILITIES: 
<ul>
<li>Lead the development of a target identification and prioritization pipeline using multi-omics data (transcriptomics, proteomics, metabolomics, chromatin conformation, and functional genomics – e.g. CRISPR screens).</li>
<li>Define internal standards for validation of target discovery methods, including benchmarking against orthogonal datasets.</li>
<li>Apply rigorous model-to-human translation, evaluating cross-species conservation, model fidelity, and translational risk when nominating and de-risking targets.</li>
<li>Partner with the Human Genetics group to integrate genetic evidence into target identification and prioritization.</li>
<li>Propose targets with clear mechanistic hypotheses, building evidence packages that draw on orthogonal data and analyses.</li>
<li>Assess data quality, batch effects, and biological confounders throughout the analytical cycle – statistical rigor and reproducibility are paramount.</li>
<li>Develop and maintain scalable, reproducible analytical pipelines, including human-in-the-loop-AI workflow as required. Use best practices in software engineering and ensure appropriate data governance and infrastructure for large-scale omics data.</li>
<li>Lead or contribute to cross-functional target assessment documents and portfolio decision-making meetings with clear, evidence-based scientific recommendations.</li>
<li>Lead a team of computational biologists fostering a culture of scientific rigor, reproducibility, and continuous learning.</li>
<li>Maintain working knowledge of the current literature on computational biology and stay current with novel methodologies, including applicable advances in AI.</li>
</ul>
REQUIREMENTS: 
<ul>
<li>PhD in computational biology, bioinformatics, genomics, systems biology, or a closely related quantitative field and 8+ years of relevant experience required.</li>
<li>Proven experience in target identification and validation using multi-omics approaches in a pharma or biotech.</li>
<li>Experience in multi-omics analyses and integration (including RNA-seq, ATAC-seq – bulk, single cell – spatial transcriptomics, proteomics, metabolomics, ChIP-seq and similar, long read RNA-seq, small RNA-seq, and functional genomics perturbation screens).</li>
<li>Methodological breadth across comp-bio modeling spectrum – classical and hierarchical statistics, causal inference, Bayesian modeling, network-based and mechanistic approaches, and modern deep learning – with hands-on depth in biological foundation models (fine-tuning, interpretability, efficient deployment) and the judgment to match method to biological question and data.</li>
<li>Proficiency in Python and/or R, plus working knowledge of Bash and Docker is required, proficiency or familiarity with Nextflow workflows and AWS cloud stack strongly preferred.</li>
<li>Knowledge of human genetic analyses methods (e.g. GWAS, rare variant analyses, QTL colocalization etc.) is preferred.</li>
<li>Experience directly managing PhD-level scientists is required.</li>
<li>Excellent communication skills across audiences, with a track record of influencing cross-functional teams (including non-computational partners) and translating complex computational findings into clear, actionable recommendations that inform senior leadership on portfolio and target decisions.</li>
</ul>
 
 
Please visit our website, <a href="http://www.ionis.com" target="_blank" rel="noopener">http://www.ionis.com</a> for more information about Ionis and to apply for this position; reference requisition # IONIS004015
Ionis offers an excellent benefits package! Follow this link for more details: <a href="https://ionis.com/careers#:~:text=Highly%20competitive%20benefits" target="_blank" rel="noopener">Ionis Benefits</a>
Full Benefits Link: <a href="https://ionis.com/careers#:~:text=Highly%20competitive%20benefits" target="_blank" rel="noopener">https://ionis.com/careers#:~:text=Highly%20competitive%20benefits</a>
The pay scale for this position is $200,385 to $250,332
NO PHONE CALLS PLEASE. PRINCIPALS ONLY.
Ionis Pharmaceuticals, Inc. and all its subsidiaries are proud to be EEO employers.

Director, Computational Biology

PhD in computational biology or related field; 8+ years experience; leadership experience; multi-omics expertise; strong programming.

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