** Only US Citizens please apply**

BITS is a growing software development company in Washington DC area. We provide project management, database solutions, application development, infrastructure supports, network engineering, and high-end computing using innovative technologies to the Federal agencies. We are looking for a Bioinformatics Analyst III for one of our FEDERAL projects.

Position Summary

The Bioinformatics Analyst III will serve as a key Subject Matter Expert (SME) supporting the FDA AI-Assisted Review of Clinical Trial Protocols program. This individual will provide advanced bioinformatics, clinical informatics, clinical data standards, and biomedical ontology expertise to support the development, validation, and refinement of AI-assisted methods for extracting, analyzing, comparing, and interpreting clinical trial protocol information.

The Bioinformatics Analyst III will work closely with the Project Manager, LLM AI Engineer, Data Standardization Specialist, Healthcare Ontologist, Data Modelers, Application Developers, Clinical SMEs, and Government SMEs to ensure that AI-enabled protocol review workflows are scientifically sound, clinically meaningful, standards-aligned, and suitable for FDA regulatory review use cases.

Key Responsibilities

· Serve as a senior bioinformatics and clinical informatics SME for AI-assisted analysis of clinical trial protocols, including structured ICH M11-compliant protocols and historical unstructured protocol documents.

· Support the development of generative AI queries to extract clinical, scientific, safety, study design, eligibility, endpoint, intervention, and regulatory information from clinical trial protocols.

· Assist in mapping protocol content to relevant clinical data standards, biomedical ontologies, controlled terminologies, conceptual information models, and FDA-recognized standards.

· Collaborate with Government SMEs to define clinically meaningful protocol data elements, extraction targets, comparison criteria, validation expectations, and reviewer-facing outputs.

· Support the design of methods to augment AI queries with domain-specific information, including therapeutic area knowledge, drug class information, study design concepts, safety considerations, and controlled terminology.

· Contribute to algorithms and analytical approaches for comparing newly submitted protocols against historical protocols by therapeutic area, indication, drug class, study design, endpoints, safety considerations, and other relevant protocol characteristics.

· Review AI-generated outputs for scientific accuracy, clinical relevance, completeness, consistency, and regulatory usefulness.

· Support quality control and validation activities, including the design of test cases, evaluation metrics, confidence scoring approaches, error analysis, and human-in-the-loop feedback processes.

· Work with the Healthcare Ontologist and Data Standardization Specialist to ensure consistent use of biomedical terminologies, data standards, protocol section mappings, and semantic relationships.

· Support the POC development team in defining data extraction logic, dashboard content, reviewer workflows, and protocol comparison use cases.

· Participate in working sessions with FDA reviewers and SMEs to understand protocol review pain points, validate AI-assisted outputs, and refine use case workflows.

· Document analytical methods, assumptions, data mappings, limitations, validation results, and recommendations for future expansion to other regulatory review areas.

· Ensure that all work involving FDA-furnished information, non-public information, and regulatory documents is performed in accordance with applicable FDA security, confidentiality, and data handling requirements.

Required Qualifications

· Bachelor’s degree in Bioinformatics, Biomedical Informatics, Computational Biology, Clinical Informatics, Life Sciences, Data Science, Public Health, or a related field.

· Minimum of 8 years of relevant experience in bioinformatics, clinical informatics, clinical data analysis, biomedical data standards, regulatory science, or AI-enabled biomedical information processing.

· Strong understanding of clinical trial protocol structure, clinical study design, endpoints, eligibility criteria, interventions, safety monitoring, and regulatory review considerations.

· Demonstrated experience working with clinical data standards, biomedical ontologies, controlled terminologies, and clinical information models.

· Experience supporting data extraction, information modeling, semantic mapping, or structured representation of biomedical or clinical research content.

· Working knowledge of ICH M11 structured protocol concepts and their relevance to clinical trial protocol standardization.

· Familiarity with FDA regulatory review processes, clinical protocol review workflows, and regulatory submission environments.

· Experience collaborating with cross-functional technical and scientific teams, including AI engineers, data modelers, application developers, clinical SMEs, and government stakeholders.

· Ability to assess AI-generated content for scientific accuracy, completeness, consistency, and regulatory relevance.

· Strong analytical, documentation, communication, and stakeholder engagement skills.

Preferred Qualifications

· Master’s degree or Ph.D. in Bioinformatics, Biomedical Informatics, Computational Biology, Clinical Informatics, Clinical Research, Life Sciences, or a related field.

· Experience with FDA, NIH, HHS, or other federal health or regulatory programs.

· Experience with clinical trial data standards and terminology resources such as CDISC, HL7 FHIR, MedDRA, SNOMED CT, RxNorm, LOINC, UMLS, or related standards.

· Experience supporting AI, machine learning, natural language processing, or generative AI applications in biomedical, clinical, or regulatory contexts.

· Familiarity with retrieval-augmented generation, prompt/query development, human-in-the-loop review, confidence scoring, and AI validation approaches.

· Experience working with historical clinical protocol documents, regulatory review comments, scientific literature, or structured/unstructured clinical documents.

· Understanding of therapeutic area classification, drug class mapping, indication-level analysis, and protocol similarity assessment.

Required Subject Matter Expertise

The Bioinformatics Analyst III shall bring demonstrated SME-level expertise in:

· Clinical trial protocol content and structure.

· Clinical data standards and regulatory data concepts.

· Biomedical ontologies and controlled terminologies.

· Clinical information modeling and semantic mapping.

· Protocol data extraction and comparison methods.

· Validation of AI-assisted scientific and regulatory outputs.

· Collaboration with clinical reviewers and government SMEs.

· Application of generative AI and agentic AI concepts to biomedical and regulatory review workflows.

Role in the FDA AI-Assisted Protocol Review Program

The Bioinformatics Analyst III will be essential to ensuring that the AI-assisted protocol review process is grounded in sound biomedical science, clinical trial methodology, regulatory expectations, and data standards. This role will help bridge the gap between FDA clinical review needs and technical AI implementation by translating complex protocol review requirements into structured, testable, and validated AI-assisted workflows.

The individual will help ensure that the program’s outputs support FDA reviewers in efficiently locating protocol information, comparing new and historical protocols, identifying relevant scientific and safety considerations, populating reviewer dashboards, and improving the consistency and efficiency of clinical trial protocol review.

Key Deliverable Contributions

The Bioinformatics Analyst III will contribute to:

· Documented process for extracting information from new structured protocols.

· Documented process for extracting information from historical unstructured protocols.

· Documented algorithms for comparing new and historical protocols.

· Documented validation processes and metrics.

· Human-in-the-loop feedback and quality control processes.

· POC tool for protocol information extraction.

· POC dashboard content and reviewer workflow support.

· Documentation of challenges, limitations, recommendations, and future expansion opportunities.

· Draft and final project reports.

Collaboration Expectations

The Bioinformatics Analyst III will work collaboratively with Government SMEs and contractor team members to ensure alignment between scientific review needs, clinical protocol standards, AI-enabled extraction methods, validation expectations, and reviewer-facing outputs. This individual must be able to communicate effectively with both technical and non-technical stakeholders and translate FDA SME feedback into actionable analytical and technical requirements.

Experience Required : Minimum 10 years

Job Type: Full-time

Pay: $180,000.00 per year

Work Location: Remote