Senior Scientist - NGS Bioinformatics (Data Standardization & Platform Integration)

Amgen; Hyderabad; On-site; INR 2,800,000 - 4,200,000; Full time

Job summary

Amgen seeks a Senior Scientist in NGS Bioinformatics to standardize, validate, and scale sequencing data workflows for enterprise reuse. The role focuses on reproducibility, efficiency, and integration of pipelines into existing data systems and analytics.

The candidate should have deep expertise in workflow optimization, data standardization, and collaboration with data scientists to model and organize scientific data for downstream use.

Qualifications

• Doctoral degree (PhD) or master’s degree with 8+ years of directly related experience, or bachelor’s degree with 10+ years of directly related experience.
• Strong background in workflow performance optimization, including runtime, memory efficiency, and operational stability.
• Familiarity with workflow management and orchestration tools such as Nextflow or Snakemake.
• Experience with structured NGS data capture in LIMS for downstream analytics and platform use.
• Experience integrating bioinformatics outputs into enterprise data platforms and structured repositories with emphasis on governance, traceability, lineage, and reproducibility.
• Experience working closely with data scientists to ensure scientific data is modeled, saved, and organized correctly for downstream use.
• Familiarity with containerization and cloud- or HPC-based execution environments.

Responsibilities

• Standardize, validate, and optimize NGS workflows to support reproducible and scalable sequencing analysis across research programs and data analysis pipelines.
• Improve pipeline performance, including runtime, memory efficiency, operational reliability, and consistency of outputs.
• Support development of NGS data models, metadata standards, and structured output formats for downstream use in enterprise platforms.
• Collaborate with bioinformatics scientists, data scientists, software engineers, and lab scientists to align workflow requirements and integrate sequencing data into enterprise platforms.
• Support validation, testing, and reproducibility practices to ensure sequencing workflows are reliable, traceable, and suitable for long‑term use.

Skills

Workflow optimization

Data standardization

Platform integration

NGS data modeling

LIMS data capture

Containerization

Education

PhD

Master's degree

Bachelor's degree

Tools

Nextflow

Snakemake

LIMS

Job description

Senior Scientist - NGS Bioinformatics (Data Standardization & Platform Integration)

What You Will Do

The Bioinformatician – NGS will support Large Molecule Discovery by standardizing, validating, and scaling NGS data workflows so sequencing outputs can be reliably reused across research programs and enterprise platforms. This role focuses on making NGS pipelines reproducible, efficient, and ready for integration into existing data systems and downstream analytics.

Core Responsibilities

• Standardize, validate, and optimize NGS workflows to support reproducible and scalable sequencing analysis across research programs and data analysis pipelines.
• Improve pipeline performance, including runtime, memory efficiency, operational reliability, and consistency of outputs.
• Support development of NGS data models, metadata standards, and structured output formats to ensure sequencing information is captured and stored appropriately for downstream use in the database/CDL and broader informatics ecosystem.
• Collaborate closely with bioinformatics scientists, data scientists, software engineers, and laboratory scientists to align workflow requirements and integrate sequencing data into enterprise platforms for analytics, reporting, and downstream reuse.
• Support validation, testing, and reproducibility practices that help ensure sequencing workflows are reliable, traceable, and suitable for long‑term operational use.

What We Expect Of You

We are looking for a subject matter expert who is a dynamic professional, enjoys building robust computational systems, and has deep expertise in workflow optimization, data standardization, and platform integration.

Basic Qualifications

• Doctoral degree (PhD) or master’s degree with 8+ years of directly related experience, or bachelor’s degree with 10+ years of directly related experience.

Preferred Qualifications

• PhD with 5+ years of experience standardizing, validating, and scaling NGS workflows for reproducible use across research programs or enterprise environments.
• Strong background in workflow performance optimization, including runtime, memory efficiency, and operational stability.
• Familiarity with workflow management and orchestration tools such as Nextflow or Snakemake.
• Experience with structured NGS data capture in LIMS for downstream analytics and platform use.
• Experience integrating bioinformatics outputs into enterprise data platforms and structured repositories with an emphasis on supporting data governance, traceability, lineage, and reproducibility for scientific datasets.
• Experience working closely with data scientists to ensure scientific data is modeled, saved, and organized correctly for downstream use.
• Familiarity with containerization and cloud- or HPC-based execution environments.

What You Can Expect Of Us

As we develop treatments that take care of others, we also care for our teammates’ professional and personal growth and well‑being.

Amgen is an Equal Opportunity employer and will consider you without regard to your race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status. We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation.