Top 70 bioinformatics scientist Jobs in boston, ma

Research Scientist, AI/ML Agentic Systems
Takeda Pharmaceutical —Boston, MA
- $116,000 - $182,270 a year
- Hybrid work
- Computer Science
- System design
- Databases
- Paid holidays
- Disability insurance
Bioinformatics Analyst
Dana-Farber Cancer Institute —Boston, MA
- $58,400 - $80,400 a year
- Full-time
- Hybrid work
- Computer Science
- Mid-level
- Java
Computational Biologist II
Dana-Farber Cancer Institute —Boston, MA
- $85,000 - $105,000 a year
- Full-time
- Hybrid work
- Computer Science
- Mid-level
- Master's degree
9d
Data Scientist
MIT Lincoln Laboratory —Lexington, MA
- $116,400 - $182,200 a year
- Mid-level
- 3 years
- Master's degree
- Health insurance
- Dental insurance
Computational Biologist - Marasco Lab
Dana-Farber Cancer Institute —Boston, MA
- $75,000 - $91,500 a year
- Full-time
- Computer science
- Computer Science
- Master's degree
Senior Bioinformatics Scientist
Boston Children's Hospital —Boston, MA
- $83,241.60 - $133,192.80 a year
- Full-time
- Bachelor's degree
- Doctor of Philosophy
- Training & development
Bioinformatics Engineer
Arrayo —Boston, MA
- Computer Science
- Office
- Master's degree
Sarcoma Computational Biologist
Dana-Farber Cancer Institute —Boston, MA
- $85,000 - $105,000 a year
- Full-time
- Computer Science
- Master's degree
- Analysis skills
Data Scientist in Bioinformatics and Neuroscience
Chen Lab @ Boston University —Boston, MA
- Email
- Computer Science
- Bachelor of Science
- Mid-level
14d
Associate Computational Biologist
Dana-Farber Cancer Institute —Boston, MA
- $60,000 - $67,466 a year
- Full-time
- Bachelor of Science
- No experience needed
- Mid-level
Staff Computational Biologist
Valo Health —Lexington, MA
- $165,750 - $230,100 a year
- Hybrid work
- Computer science
- Azure
- Computer Science
- Retirement plan
Computational Biomedical Research Scientist
Delta Search Labs —Cambridge, MA
- Email
- Computer science
- Computer Science
- Analysis skills
Scientist, Oncology Bioinformatics
Moderna, Inc. —Cambridge, MA
- $121,600 - $194,500 a year
- Full-time
- Office
- AWS
- Doctor of Philosophy
- Health insurance
- Paid time off
9d
Research Scientist 1
MIT —Cambridge, MA
- Weekends as needed
- Computer Science
- Mid-level
- Doctor of Philosophy
Computational Genomics Senior Research Scientist
Vertex Pharmaceuticals —Boston, MA
- $129,900 - $194,900 a year
- Full-time
- Hybrid work
- 3 years
- Master's degree
- Analysis skills
- Loan repayment program
- Health insurance
Bioinformatics Software Engineer
Harvard University —Boston, MA
- Full-time
- Hybrid work
- Analysis skills
- University
- Doctor of Philosophy
- Commuter assistance
- Health insurance
Applied AI Engineer, Clinical Informatics
Lilly —Boston, MA
- $181,500 - $283,800 a year
- Full-time
- Medicine
- Azure
- Computer Science
- Health insurance
- Dental insurance
14d
Principal Machine Learning Scientist
Bayer —Cambridge, MA
- $123,760 - $185,640 a year
- 5 years
- Analysis skills
- Doctor of Philosophy
- Health insurance
- Dental insurance
Scientist II, Bioinformatics
Cystic Fibrosis Foundation —Lexington, MA
- $126,200 - $157,600 a year
- Full-time
- Mid-level
- Master's degree
- Analysis skills
Post Doctoral Scientist- Human Genomics and Translational Data Science
Xenon7 —Boston, MA
- Contract
- Remote
- Analysis skills
- Doctor of Philosophy
- US work authorization
- Opportunities for advancement
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Research Scientist, AI/ML Agentic Systems

Takeda Pharmaceutical -
Boston, MA

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Job Details

$116,000 - $182,270 a year

Benefits

Paid holidays
Disability insurance
Health insurance
Dental insurance
Tuition reimbursement
Paid time off
Vision insurance
401(k) matching
Volunteer time off
Life insurance

Qualifications

AI models
Generative models
AI platforms (beyond public GPTs)
Computational framework
Drug discovery
Doctor of Philosophy
Developing large-scale AI models
Machine learning frameworks
Python
Generative AI

Full Job Description

By clicking the “Apply” button, I understand that my employment application process with Takeda will commence and that the information I provide in my application will be processed in line with Takeda’s Privacy Notice and Terms of Use. I further attest that all information I submit in my employment application is true to the best of my knowledge.

Job Description

Title: Research Scientist, AI/ML – Agentic Systems

Position Overview

We are seeking a Research Scientist to develop agentic AI systems that transform how drug discovery research is conducted. As part of the AI/ML Foundation team, you will build autonomous AI agents capable of reasoning, planning, and executing complex scientific workflows—from literature synthesis and target identification to experimental design and data analysis. This role requires a unique combination of expertise in large language models, agentic frameworks, and understanding of drug discovery processes. You will translate standard research workflows into agentic frameworks, develop new agent skills, and deploy systems that augment scientist productivity across Computational Sciences and Global Research.

Key Responsibilities

Develop agentic AI systems for drug discovery applications including target-disease association, automated literature search and synthesis, hypothesis generation, and intelligent design of experiments.
Translate standard research workflows into agentic frameworks—decomposing complex scientific processes into autonomous agent tasks that can reason, plan, execute tools, and iterate based on results.
Design and implement new agent skills (tools, functions, APIs) that extend agentic capabilities to specialized scientific domains including molecular design, property prediction, assay planning, and data analysis.
Build agentic systems that integrate with foundation models and external knowledge sources for autonomous hypothesis generation, evidence retrieval, and scientific reasoning.
Develop retrieval-augmented generation (RAG) pipelines connecting agents to internal and external scientific literature, databases, and experimental results.
Partner with research scientists to understand workflow needs, validate agent outputs, and iterate on system design to ensure scientific rigor and utility.
Stay current with advances in agentic AI, LLM applications, and scientific automation; contribute to internal knowledge sharing and external publications.

Qualifications

Required:

PhD in Computer Science, Computational Biology, Bioinformatics, or related field
Experience with large language models (GPT, Claude, Llama) and their application to complex reasoning tasks.
Proficiency in Python and experience with agentic AI frameworks (LangChain, AutoGen, CrewAI, or similar).
Experience building RAG systems including vector databases, embedding models, and retrieval pipelines.
Understanding of drug discovery processes and scientific research workflows.
Strong problem-solving skills and ability to translate complex scientific processes into computational workflows.

Preferred:

Experience in pharmaceutical or biotech R&D environments.
Background in biology, chemistry, or disease biology.
Experience with reinforcement learning or planning algorithms for agent decision-making.
Familiarity with scientific databases (PubMed, UniProt, ChEMBL) and APIs.
Experience deploying AI systems in production environments.
Track record of publications or presentations on LLM ap

ADDITIONAL INFORMATION

The position will be based in Cambridge, MA. This position is currently classified as “hybrid” by Takeda’s Hybrid Work policy

Takeda Compensation and Benefits Summary

We understand compensation is an important factor as you consider the next step in your career. We are committed to equitable pay for all employees, and we strive to be more transparent with our pay practices.

For Location:

Boston, MA

U.S. Base Salary Range:

$116,000.00 - $182,270.00

The estimated salary range reflects an anticipated range for this position. The actual base salary offered may depend on a variety of factors, including the qualifications of the individual applicant for the position, years of relevant experience, specific and unique skills, level of education attained, certifications or other professional licenses held, and the location in which the applicant lives and/or from which they will be performing the job. The actual base salary offered will be in accordance with state or local minimum wage requirements for the job location.

U.S. based employees may be eligible for short-term and/ or long-term incentives. U.S. based employees may be eligible to participate in medical, dental, vision insurance, a 401(k) plan and company match, short-term and long-term disability coverage, basic life insurance, a tuition reimbursement program, paid volunteer time off, company holidays, and well-being benefits, among others. U.S. based employees are also eligible to receive, per calendar year, up to 80 hours of sick time, and new hires are eligible to accrue up to 120 hours of paid vacation.

EEO Statement

Takeda is proud in its commitment to creating a diverse workforce and providing equal employment opportunities to all employees and applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, gender expression, parental status, national origin, age, disability, citizenship status, genetic information or characteristics, marital status, status as a Vietnam era veteran, special disabled veteran, or other protected veteran in accordance with applicable federal, state and local laws, and any other characteristic protected by law.

Locations

Boston, MA

Worker Type

Employee

Worker Sub-Type

Regular

Time Type

Job Exempt

Yes

It is unlawful in Massachusetts to require or administer a lie detector test as a condition of employment or continued employment. An employer who violates this law shall be subject to criminal penalties and civil liability.

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Refine Your Search

bioinformatics scientist jobs in boston, ma

Research Scientist, AI/ML Agentic Systems

Bioinformatics Analyst

Computational Biologist II

Data Scientist

Computational Biologist - Marasco Lab

Senior Bioinformatics Scientist

Bioinformatics Engineer

Sarcoma Computational Biologist

Data Scientist in Bioinformatics and Neuroscience

Associate Computational Biologist

Staff Computational Biologist

Computational Biomedical Research Scientist

Scientist, Oncology Bioinformatics

Research Scientist 1

Computational Genomics Senior Research Scientist

Bioinformatics Software Engineer

Applied AI Engineer, Clinical Informatics

Principal Machine Learning Scientist

Scientist II, Bioinformatics

Post Doctoral Scientist- Human Genomics and Translational Data Science

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