New

Bioinformatician I

Massachusetts General Hospital
United States, Massachusetts, Boston
149 13th Street (Show on map)
Dec 25, 2025
SUMMARY: We are seeking a highly motivated Bioinformatics Specialist to join our research team. This position will focus on implementing and maintaining the hardware and software infrastructure for deep leaning, high-dimensional image analysis using proteomic, genomic and transcriptomic data analysis, and data management/husbandry. The successful candidate will work closely with biologists, computational scientists, and clinicians to extract meaningful insights from multimodal datasets. KEY RESPONSIBILITIES: 1. Data Management & Computational Infrastructure Develop and maintain data pipelines for large-scale imaging and sequencing datasets. Set up and maintain multi-user GPU/HPC infrastructure for large-scale multi-omics analysis and deep learning model training/inference. Manage data storage, versioning, and retrieval in compliance with FAIR data principles. Maintain documentation and reproducible workflows using Snakemake, Nextflow, or WDL. 2. Multiplex Immunofluorescence Image Analysis & Spatial Biology Develop and implement workflows for Lunaphore COMET and Singular Genomics G4X multiplexed immunofluorescence image analysis. Process and analyze high-dimensional imaging datasets using QuPath, ImageJ, Cellpose, and other computational tools. Integrate spatial biology data with transcriptomic/genomic data for multimodal analysis. 3. Genomic & Transcriptomic Data Analysis Develop and implement workflows for bulk RNA-seq, single-cell RNA-seq (scRNA-seq), and spatial transcriptomics data analysis. Conduct Next-Generation Sequencing (NGS) analysis, including variant calling, gene expression analysis, and pathway enrichment studies. Utilize bioinformatics pipelines (e.g., STAR, Cell Ranger, Seurat, DESeq2, Monocle, Scanpy) for data processing. Work with long-read sequencing (PacBio, Oxford Nanopore) and epigenomics as needed. Required Skills & Qualifications* MSc or PhD (or BSc with equivalent experience)inBioinformatics, Computational Biology, Biostatistics, or related field. Proficiency inPython, R, Java/Groovy and Bash scripting. Familiarity with containerized environments (e.g. Docker, Apptainer). Familiarity withmachine learning / AI for image and genomic data analysis. Experience working inUnix/Linux environmentsand usingHPC/cloud-based pipelines. Strong organizational skills for handlinglarge and complex datasets. Ability to collaborate effectively in amultidisciplinary research team. The General Hospital Corporation is an Equal Opportunity Employer. By embracing diverse skills, perspectives and ideas, we choose to lead. All qualified applicants will receive consideration for employment without regard to race, color, religious creed, national origin, sex, age, gender identity, disability, sexual orientation, military service, genetic information, and/or other status protected under law. We will ensure that all individuals with a disability are provided a 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.