Bioinformatics Specialist I

Massachusetts General Hospital
United States, Massachusetts, Boston
149 13th Street (Show on map)
Mar 25, 2025
We are seeking a highly motivated Bioinformatics Specialist to join our research team. This position will focus on high-dimensional image analysis using Lunaphore, 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. Lunaphore Image Analysis & Spatial Biology Develop and implement workflows forLunaphore COMETmultiplexed immunofluorescence image analysis. Process and analyze high-dimensional imaging datasets usingQuPath, ImageJ, Cellpose, and other computational tools. Integrate spatial biology data with transcriptomic/genomic data for multimodal analysis. 2. Genomic & Transcriptomic Data Analysis Performbulk RNA-seq, single-cell RNA-seq (scRNA-seq), and spatial transcriptomicsdata analysis. ConductNext-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 and interpretation. Work withlong-read sequencing (PacBio, Oxford Nanopore) and epigenomicsas needed. 3. Data Management & Computational Infrastructure Develop and maintaindata pipelinesfor large-scale imaging and sequencing datasets. Manage data storage, versioning, and retrieval in compliance withFAIR data principles. Maintain documentation and reproducible workflows usingSnakemake, Nextflow, or WDL. Required Skills & Qualifications PhD (or MSc with equivalent experience)inBioinformatics, Computational Biology, Biostatistics, or related field. Strong proficiency inPython, R, and Bash scripting. Experience withspatial biology tools(e.g., QuPath, Cellpose, Napari, Halo, or Fiji/ImageJ). Expertise inNGS data processing and analysis, including RNA-seq, scRNA-seq, and variant analysis. 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. *PLEASE READ THE REQUIREMENTS THOROUGHLY AND ONLY APPLY IF YOU QUALIFY* 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.