Associate Director, Bioinformatics

Rhythm Pharmaceuticals, Inc; Boston (MA); Hybrid; USD 180,000 - 240,000; Full time

Job summary

Rhythm Pharmaceuticals, Inc. seeks an Associate Director of Data Science to advance AI-driven phenotyping and integrative analyses across obesity and metabolic diseases. You will lead multi‑modal data workflows, including EMR, genomics, and biomarker data, and build scalable analysis pipelines.

The role emphasizes production‑quality data products, coordination with Genetics‑led programs, and contributing to a fast‑paced research environment in a hybrid work model based in Boston or remote.

Qualifications

• Ph.D. in Biostatistics, Computational Biology, Genetics, Data Science, or related field.
• ~5+ years in biotechnology, pharmaceuticals, or healthcare analytics.
• Experience with neuroendocrine, obesity/metabolic biology and datasets.
• Experience applying ML/AI models to real-world and clinical data, including production deployment.
• Experience developing/using AI-driven agents/workflows for data tasks.
• Strong SQL, Python, and R with production-quality data pipelines.
• Cloud experience (AWS, GCP, Snowflake).
• Experience with variant calling pipelines and ACMG rare variant classification.
• EMR/EHR and real-world data analysis including cohorts and longitudinal modeling.
• Proficiency with ICD, CPT, SNOMED coding and clinical ontologies.

Responsibilities

• Design and deploy AI-driven phenotyping pipelines using EMR/EHR and real-world data.
• Develop scalable cohort identification, feature extraction, and phenotype validation.
• Maintain high-throughput rare variant curation and classification models.
• Design and deploy data analysis pipelines, statistical models, and predictive tools.
• Lead integration of clinical, EMR, genomics, and biomarker datasets.
• Build reproducible workflows for data ingestion, harmonization, QC, and analysis (SQL, Python, R).
• Apply statistical genetics to link phenotypes with genetic signals.
• Drive data infrastructure improvements and phenotyping framework expansion.

Skills

Biostatistics

Computational Biology

Data Science

SQL

Python

R

Machine Learning

Cloud Computing

Genomics data

Education

Ph.D. in Biostatistics

Tools

SQL

Python

R

AWS

GCP

Snowflake

Job description

Company Overview

Rhythm is a global, commercial‑stage biopharmaceutical company committed to transforming the lives of patients living with rare neuroendocrine diseases. We develop medicines for previously untreatable or undertreated diseases. We recognize the courage it takes for patients and their caregivers to begin their journey of advocacy to find the answers they need. Their courage inspires us to challenge convention, ask bold questions and seek answers for them. Every day, we strive for excellence through our willingness to adapt, learn, and our tenacity to overcome barriers, together.

Opportunity Overview

We are seeking a highly motivated Associate Director of Data Science within Rhythm's Research group and the Data Sciences Team in support of our clinical, regulatory, and scientific objectives in the rare neuroendocrine/obesity/metabolic disease. The successful candidate will have a strong background in biostatistics, genetics, and data analytics, and will be responsible for implementing advanced AI data models, predictive tools, and integrative analyses across the obesity and metabolic disease therapeutic areas. A core focus of this position will be the development and implementation of algorithmic phenotyping approaches using electronic medical records (EMR) and real‑world datasets, enabling robust patient stratification, cohort definition, and integration with genomics and biomarker data. This position is ideal for a technically strong investigator who thrives in a fast‑paced environment and is motivated to apply and scale high‑impact data science infrastructure alongside a growing team.

Responsibilities and Duties

• Design and deploy AI-driven, agent-based phenotyping pipelines that leverage EMR/EHR and real‑world data to define disease cohorts, endpoints, and longitudinal outcomes.
• Develop scalable approaches for cohort identification, feature extraction, and phenotype validation, including rule‑based and machine learning methods.
• Maintain high-throughput rare variant curation and classification models.
• Execute the design, development, and deployment of data analysis pipelines, statistical models, and predictive tools to support Genetics‑led programs.
• Lead hands‑on integration of clinical, EMR, genomics, and biomarker datasets, enabling multi‑modal analyses.
• Build and maintain reproducible workflows for data ingestion, harmonization (e.g., coding systems, ontologies), QC, and analysis (SQL, Python, R).
• Apply statistical genetics and advanced analytics to link phenotypic definitions with genetic signals, including rare variant analyses.
• Drive improvements in data infrastructure and phenotyping frameworks to support team expansion and increased dataset complexity.

Qualifications and Skills

• Ph.D. in Biostatistics, Computational Biology, Genetics, Data Science, or related quantitative field.
• ~5+ years of relevant experience in biotechnology, pharmaceuticals, or healthcare analytics.
• Experience with neuroendocrine, obesity/metabolic‑related biology and datasets.
• Experience applying machine learning and AI models to real‑world and clinical datasets, including model development, evaluation, and deployment in production or near‑production settings.
• Experience developing or utilizing AI‑driven agents/workflows to automate data extraction, phenotyping, analysis, or knowledge generation tasks.
• Strong hands‑on expertise in SQL, Python, and R, with experience building production‑quality data pipelines.
• Experience with cloud computing and storage environments including AWS, GCP, Snowflake.
• Demonstrated experience with variant calling pipelines, variant interpretation and ACMG rare variant classification.
• Demonstrated experience in EMR/EHR and real‑world data analysis (e.g., UK Biobank, All of Us) including cohort building and longitudinal data modeling.
• Proven track record in algorithmic phenotyping, including use of coding systems (ICD, CPT, SNOMED), clinical ontologies, and feature engineering.
• Familiarity with broader bioinformatics/multi‑omics methodologies including RNA‑seq, methylation analysis, long‑read sequencing would be advantageous.
• Strong problem‑solving skills and ability to operate independently in a fast‑paced, execution‑focused environment.
• Excellent communication skills with the ability to clearly present complex analytical outputs to technical stakeholders.

Important Details

This role can be remote or based out of our corporate office in Boston, Massachusetts. Rhythm operates in a hybrid‑work model. Candidates applying must be willing and able to be in the Boston office in coordination with their department and business needs. This role may involve some travel.

More About Rhythm

We are a dynamic and growing global team spanning more than a dozen countries. At Rhythm we are dedicated to transforming the lives of patients living with rare neuroendocrine diseases by rapidly advancing care and precision medicines that address the root cause. Our team is passionate about expanding access to reach more patients and developing novel therapies for other rare neuroendocrine diseases, including congenital hyperinsulinism.

Core Values

• We are committed to advancing scientific understanding to improve patients’ lives
• We are inspired to tackle tough challenges and have the courage to ask bold questions
• We are eager to learn and adapt
• We believe collaboration and ownership are foundational for our success
• We value the unique contribution each individual brings to furthering our mission

Ethics and Inclusion

Inherent in our core values is the commitment to act ethically and with integrity in all we do.

Rhythm is an equal employment opportunity employer and does not discriminate against any applicant because of race, creed, color, age, national origin, ancestry, religion, gender, sexual orientation, disability, genetic information, veteran status, military status, application for military service, or any other class protected by state or federal law.

Headquartered in Boston, Rhythm is proud to have been named one of the Top Places to Work in Massachusetts.