Bioinformatics & AI Engineer

Career Category

Job Description

Bioinformatics & AI Engineer

Location: Amgen India office, Hyderabad
 Employment type: Full-time
 Department / Team: Computational Biology, Precision Medicine

Role summary

We are seeking a Bioinformatics & AI Engineer to build, evaluate, and deploy deep learning and foundation-model-enabled systems that accelerate biomarker discovery, translational research, and clinical development. This individual contributor role combines bioinformatics, machine learning, and software engineering to turn genomic, multi-omics, imaging, and clinical data into reliable, traceable scientific capabilities. The engineer will develop and evaluate biological foundation-model applications and supporting platforms, working closely with computational biologists, data engineers, translational scientists, and clinical teams.

Key responsibilities

• Design, develop, validate, and operate foundation-model-enabled applications for genomics, transcriptomics, single-cell and spatial omics, proteomics, imaging, and clinical data.
• Adapt and evaluate biological foundation models, protein and sequence models, multimodal models, and large language models for biomarker discovery, target identification, patient stratification, and scientific decision support.
• Build robust model development workflows spanning data curation, representation learning, fine-tuning or parameter-efficient adaptation, retrieval augmentation, evaluation, and monitored deployment.
• Engineer scalable, reproducible pipelines for preparing and harmonizing multi-omics and clinical datasets, with clear provenance, versioning, quality controls, and fit-for-purpose access controls.
• Develop agentic workflows that combine foundation models with validated bioinformatics tools, structured knowledge, and human review to support research planning, quality control, analysis execution, and result interpretation.
• Define rigorous benchmarking and validation strategies, including biological relevance, robustness, bias assessment, uncertainty, hallucination risk, and reproducibility for models and AI-enabled workflows.
• Partner on real world data projects and establish utility for precision medicine applications
• Partner with computational biology, wet-lab, clinical, data engineering, and product teams to translate scientific needs into usable, well-documented technical solutions.
• Develop production-ready services and interfaces using cloud and GPU infrastructure; optimize performance, cost, reliability, and observability for large-scale data and model workloads.
• Produce clear technical documentation, model cards, evaluation reports, and methods descriptions suitable for internal review, regulated development contexts, and scientific publication.
• Troubleshoot end-to-end platform and pipeline issues, promote engineering best practices, and contribute to a culture of scientific rigor and responsible AI use.

Required qualifications

Education & experience

• Master’s or PhD in Bioinformatics, Computational Biology, Computer Science, Machine Learning, Statistics, Genetics/Genomics, or a related discipline.
• 7+ years of hands-on experience building bioinformatics, machine learning, data science, or research software solutions; experience applying AI to biomedical or life-science data is strongly preferred.

Technical skills

• Strong programming skills in Python and practical experience with software engineering practices, including Git, testing, code review, CI/CD, and documentation.
• Hands-on expertise with deep learning and foundation models, including transformers, self-supervised learning, embedding models, fine-tuning or parameter-efficient adaptation, evaluation, and inference optimization.
• Experience using or adapting biological foundation models for sequence, protein, cellular, molecular, or multimodal biomedical data; familiarity with LLMs, retrieval-augmented generation, and tool-using agents.
• Experience with Hugging Face and AWS Sagemaker.
• Strong understanding of genomics, transcriptomics, single-cell or spatial omics, proteomics, imaging, or other biomedical data modalities and their analytical limitations.
• Experience designing reproducible data and analysis workflows using workflow engines such as Nextflow or Snakemake and containers such as Docker or Singularity.
• Experience with cloud and HPC environments, GPU compute, distributed training or inference, and scalable data processing frameworks.
• Working knowledge of biological data formats and standards, including FASTQ, BAM/CRAM, VCF/MAF, HDF5, AnnData, Seurat, and metadata best practices.
• Experience curating, integrating, and governing data from public biological and clinical resources such as TCGA, GTEx, GEO, SRA, dbGaP, cBioPortal, ClinVar, CellxGene, COSMIC, gnomAD, and UniProt.
• Ability to design scientifically meaningful benchmarks and communicate model performance, limitations, uncertainty, and responsible-use guidance to technical and scientific stakeholders.
• Strong statistical reasoning and experience applying quality control and appropriate evaluation methods to biological data and machine learning systems.
• Experience in a biomedical, pharmaceutical, or regulated research environment is preferred.