SENIOR DATA SCIENTIST - Python

Job description

Job Description: Lead Bioinformatics Engineer (Multi-Omics & AI Platform) ? C3/C4 • Role Summary We are hiring a Lead Bioinformatics Engineer to drive architecture and engineering for an enterprise-scale Multi-Omics & AI platform. This is a systems and platform-building role, focused a production-grade data harmonization engine that transforms fragmented omics data into ML-ready feature stores. • Key Responsibilities 1. Multi-Omics Data Platform Architecture • Building automated harmonization engine for multi-modal data (genomics, transcriptomics, proteomics, metabolomics) • Develop scalable ETL pipelines to ingest and standardize formats (FASTQ, BAM, VCF, H5AD, MTX, GCT) • Architect ML-ready feature stores using optimized formats (Zarr, Apache Arrow, TileDB) • Define 3-tier data models (Dataset, Sample, Feature) linking clinical and molecular data • Implement ontology mapping using standards (Ensembl, HUGO, NCBI) • Embed batch correction & normalization (e.g., ComBat, Harmony) 2. Pipeline Engineering & MLOps • Build production-grade pipelines for RNA-seq, WGS, and proteomics • Scale data processing on cloud (AWS preferred: S3, EC2, Batch, Athena) • Implement reproducible workflows using Nextflow / Snakemake + Docker/Singularity • Design high-performance APIs (Python/R) for data access and model consumption • Leverage data lake/lakehouse architectures (Iceberg, Delta Lake) 3. AI & Data Governance Leadership • Translate biological problems into ML-ready datasets and features • Define data validation, contracts, and quality checks • Implement CI/CD and data quality frameworks (Great Expectations, Pydantic) • Ensure data integrity and prevention of bias/data leakage in AI models Required Qualifications 1. Experience • Master?s/PhD in Bioinformatics, Computational Biology, Computer Science, or related field • 5+ years? experience in bioinformatics data engineering or platform development • Proven experience building production-grade data platforms / data lakes for ML • Hands-on experience with multi-omics integration (=3 modalities) • Exposure to AI/ML pipelines (deep learning, embeddings, LLMs in biology) 1. Technical Skills • Strong expertise in NGS data processing (WGS, WES, RNA-seq, single-cell etc) using tools like GATK, BWA, SAMtools, STAR, Kallisto and frameworks such as Scanpy, Seurat, Bioconductor, AnnData etc • Deep understanding of variant calling, gene expression analysis, pathway analysis, and single-cell data workflows etc • Proven experience in bioinformatics ETL, data harmonization, and processing large-scale multi-format omics datasets • Hands-on with optimized data structures like AnnData/H5AD, Zarr, Apache Arrow, TileDB, including sparse matrix handling • Experience building scalable scientific data platforms/data lakes on AWS (S3, EC2, Batch, Athena) with Delta Lake / Iceberg • Strong in workflow orchestration (Nextflow/Snakemake), containerization (Docker/Kubernetes/Singularity), and CI/CD automation • Proficient in Python (Pandas, NumPy, Scikit-learn) with exposure to PyTorch/TensorFlow for ML integration • Experience in creating ML-ready datasets, feature engineering pipelines, and ensuring data validation (bias, leakage, quality checks)