Scientist​/Sr. Scientist - Bioinformatics Engineer

Scientist/Sr. Scientist - Bioinformatics Engineer

Cambridge, MA

Position Summary:

Join the City Therapeutics Data Science Team as a Scientist/Sr. Scientist, Bioinformatics Engineer, and help shape the future of drug discovery.

In this role, you will work cross‑functionally across Biology, Chemistry, and High‑Throughput Screening teams to gather use cases, requirements, and feedback to deploy tools addressing pain‑points in research informatics.

Key Responsibilities:

• Design and deploy custom computational tools and applications for siRNA compound design, protein structure prediction, novel sequence alignment approaches, bench‑to‑ELN integration, and data lake querying
• Establish and maintain workflows and databases for multi‑omics data integration and visualization to generate novel biological insights and inform lead drug candidate selection
• Build, optimize, and maintain bioinformatics pipelines to analyze and interpret transcriptomics data
• Execute a data curation strategy for large volumes of raw and processed data
• Maintain data in an ML‑ready state to support machine learning projects; oversee deployment and retention of machine‑learning models and artifacts
• Ensure high‑quality documentation of codebase, pipelines, and analyses for reproducibility and compliance

Qualifications:

• Advanced degree in Bioinformatics, Computational Biology, Computer Science or relevant discipline with industry/pharma experience (minimum 3+ years PhD, 6+ years MS)
• Experience working with next‑generation sequencing (NGS) data (e.g. RNA‑seq)
• Proficiency in Python and R for data visualization and analysis
• Strong knowledge of version control, the software development lifecycle framework, and reproducible code deployment (Git, Docker)
• Demonstrated experience in building and managing scalable automated bioinformatics workflows in Nextflow
• Experience operating and troubleshooting in AWS cloud compute environments
• Strong understanding of statistics fundamentals and data analysis methods
• Strong understanding of molecular biology, genetics, NGS technologies and related fields
• Ability to translate complex biological problems into reproducible and robust computational approaches
• Excellent problem‑solving abilities, attention to detail, strong communication skills and a track record of collaborating effectively in a team‑oriented, cross‑functional environment
• Please note this role is required to be on‑site 5 days a week at our offices in Cambridge, MA

Preferred Qualifications:

• Portfolio of diverse and impactful research informatics data products in an industry setting
• Experience with data visualization and application frameworks like R Shiny, Plotly, Dash, Flask, Streamlit, etc
• Experience with Benchling and Benchling‑SDK
• Experience in oligonucleotide therapeutics (RNAi, ASOs, etc) and/or gene editing fields
• Familiarity with data lakes and/or data warehouses
• Working knowledge of machine learning and its applications in genetics and drug discovery

Compensation: The base salary range provides an estimate of the compensation for this position. The actual base salary will be based on several factors, including relevant skills, experience, internal equity, relevant education or training and market dynamics. In addition, this role is eligible for an annual cash bonus and equity compensation. City Therapeutics offers a comprehensive and competitive benefits package including medical, dental, vision, life insurance, health and dependent care FSA accounts, HSA/HRA accounts with company contributions, in addition to a 401(k) with competitive company match.

Per Year Salary Range: $117,000 to $154,000.

City Therapeutics is accepting resumes/CVs from direct applicants only. Recruitment agency submissions will not be accepted at this time.

City Therapeutics is an Equal Opportunity and Affidavit Action employer committed to a culturally diverse workforce. All qualified applicants will receive consideration for employment without regard to race, color, creed, religion, national origin, age, ancestry, nationality, marital, domestic partnership, or civil union status, sex, gender, gender identity or expression, affectional or sexual orientation, disability, veteran or military status, domestic violence victim status, atypical cellular or blood trait, genetic information (including the refusal to submit to genetic testing), or any other characteristic protected by law.