Bioinformatics Scientist

Amgen Inc. (IR); Hyderabad; On-site; INR 1,800,000 - 3,200,000; Full time

Job summary

Amgen Inc. (IR) seeks a Bioinformatics Scientist to design, automate, validate, and execute advanced analyses and reproducible pipelines for biomarker analysis, translational research and clinical development.

This individual contributor will combine expertise in NGS/omics, scRNA/spatial omics, data science and software engineering to deliver robust, scalable and well-documented results for computational biologists, translational scientists, data engineers and clinical teams.

Qualifications

• Master’s or PhD in Bioinformatics, Computational Biology, Genetics/Genomics, CS, Statistics or related.
• ~8+ years hands-on bioinformatics experience designing and delivering production or research pipelines for NGS/omics data.
• Strong programming and statistical analysis skills for multi-omics data.

Responsibilities

• Design, automate, validate and maintain end-to-end bioinformatics pipelines for genomics, transcriptomics, single-cell and multi-omics.
• Implement reproducible workflows with Nextflow/Snakemake and containerization; ensure provenance and CI/CD.
• Lead production-grade pipelines optimizing runtime, memory, scalability and cost.
• Develop multi-omics integration frameworks for biomarker discovery and patient stratification.
• Collaborate with labs, CROs, and clinical teams; produce documentation for reports and submissions.

Skills

Python

R

C/C++

Java

Git & CI/CD

ML/DL & LLMs

NGS/omics pipelines

Nextflow/Snakemake

Docker/Singularity

Cloud & HPC

Education

Master’s or PhD in Bioinformatics/Computational Biology

Tools

Nextflow

Snakemake

Docker

Singularity

AWS

Job description

Career Category Scientific Job Description Role summary

We are seeking a strong Bioinformatics Scientist to design, automate, implement, validate, and execute advanced bioinformatics analyses and reproducible pipelines that support biomarker analysis, translational research, and clinical development. This individual contributor role combines deep technical expertise in NGS/omics analyses, scRNA/spatial omics, data science, modern AI technologies and software engineering with strong scientific judgment to translate biological data into robust, reproducible results used by computational biologists, translational scientists, data engineers and clinical teams.

Key Responsibilities

• Design, develop, validate, automate and maintain end-to-end bioinformatics analysis pipelines and tools for genomics, transcriptomics, single-cell, spatial omics, proteomics, epigenomics, MRD, metabolomics, and related biomarker assays.
• Implement reproducible workflows using workflow engines (e.g., Nextflow, Snakemake) and containerization (e.g., Docker); ensure provenance, versioning and CI/CD for pipelines.
• Lead the design and optimization of production-grade bioinformatics pipelines and analytical workflows, driving improvements in runtime efficiency, memory footprint, scalability, reproducibility, and cost-effectiveness for large-scale genomic and multi-omics analyses.
• Design and implement scalable multi-omics integration frameworks that combine genomic, transcriptomic, proteomic, imaging, and clinical data to enable biomarker discovery, patient stratification, predictive modeling, and data-driven decision-making in drug development and clinical trials.
• Develop state-of-the art agentic workflows, build agents capable of QC, tool selection, execution optimization, and results interpretation Define and execute QC, benchmarking and validation strategies for pipelines and algorithms; perform evaluation and assessment of technical wetlab platforms through data; produce metrics and reports documenting performance and limitations.
• Collaborate with internal biomarker labs and CROs/vendors to onboard new assays; author and maintain data transfer specifications, interface control documents, and acceptance criteria.
• Ensure cross functional coordination and data integrity.
• Produce high-quality technical documentation, statistical methods descriptions, and contribute methods sections for reports, regulatory submissions and publications.
• Troubleshoot and resolve pipeline issues and collaborate with cross-functional teams to deliver timely results.

Required qualifications

• Education & experience Master’s or PhD in Bioinformatics, Computational Biology, Genetics/Genomics, Computer Science, Statistics or a related discipline.
• ~8+ years of relevant hands-on experience in bioinformatics or computational biology, including experience designing and delivering production or research pipelines for NGS/omics data.

Technical skills

• Strong programming skills in Python and R.
• Familiarity with other languages (C/C++, Java) is a plus.
• Deep understanding of biomarker assays and sequencing technologies (immunoassay, flow cytometry, immunohistochemistry, proteomics, whole genome sequencing, exome sequencing, targeted panel sequencing, bulk RNA-seq, methylation, metabolomics) Hands-on experience with NGS analysis workflows (alignment, variant calling, RNA-seq, single-cell, fusion detection, copy number, structural variants) and with downstream statistical methods for omics data (pathway annotation, GSVA/GSEA, DE analysis).
• Experience with single cell RNA-seq and spatial transcriptomics data is a plus.
• Practical experience with workflow engines (Nextflow, Snakemake) and containerization (Docker/Singularity).
• Experience with cloud (AWS) and HPC environments and scalable compute frameworks.
• Experience using GPU is a plus.
• Solid understanding of data formats and standards (FASTQ, BAM/CRAM, VCF/MAF, HDF5/AnnData/Seurat) and metadata best practices.
• Deep knowledge of public genomics, transcriptomics, proteomics, and clinical databases, including TCGA, GTEx, GEO, SRA, dbGaP, cBioPortal, ClinVar, COSMIC, gnomAD, and UniProt, to support biomarker discovery, genomic interpretation, and translational research.
• Experience and expertise with deep learning models, foundation models, large language models (LLMs), RAG, and agentic AI workflows is preferred.
• Familiarity with version control (Git), CI/CD, automated testing, and reproducible research practices.
• Strong statistical reasoning and experience applying appropriate models and QC for biological data.
• Experience with benchmarking and validation frameworks, unit/integration testing for pipelines.
• Prior experience in a biomedical/pharmaceutical environment .

Amgen is committed to unlocking the potential of biology for patients suffering from serious illnesses by discovering, developing, manufacturing and delivering innovative human therapeutics. This approach begins by using tools like advanced human genetics to unravel the complexities of disease and understand the fundamentals of human biology. Amgen focuses on areas of high unmet medical need and leverages its biologics manufacturing expertise to strive for solutions that improve health outcomes and dramatically improve people's lives. A biotechnology pioneer since 1980, Amgen has grown to be one of the world's leading independent biotechnology companies, has reached millions of patients around the world and is developing a pipeline of medicines with breakaway potential. For more information, visit www.amgen.com and follow us on www.twitter.com/amgen