U

University of Washington

Public research university in Seattle, WA

Research Scientist/Engineer 1

Full-Time
$65k - $70k/yr
Junior
Bachelor's
Seattle, WA, USA
In Person
Academic & Institutional ResearchLife Sciences Research
H1B Sponsorship Available

About the job

Requirements
  • A bachelor's degree in Computer Science, Applied Mathematics, Bioinformatics, Computational Biology, Electrical and Computer Engineering, or an equivalent combination of education and experience, plus one year of relevant computational biology or bioinformatics experience.
  • Proficiency with Python, including NumPy and pandas; basic R, including Seurat and tidyverse; Bash; Git; and Linux.
  • Experience with next-generation sequencing data processing, including BCL-to-FASTQ demultiplexing, adapter and quality trimming, unique molecular identifier handling, MultiQC quality control, and alignment and quantification to a reference.
  • Knowledge of Pixel-seq barcode-to-coordinate mapping and creation of spatially annotated AnnData or Seurat objects.
  • Practical experience with Cellpose, FICTURE, or similar segmentation tools and basic image quality control.
  • Knowledge of normalization, clustering, label transfer, and spatial neighborhood or domain analyses using tools such as Squidpy or Giotto.
  • Experience with Snakemake or Nextflow, Apptainer or Docker containerization, documentation, and basic SLURM job submission.
  • Ability to write clear READMEs, short analysis memos, and figure captions for collaboration with biologists and clinicians.
  • Experience using Linux and high-performance computing environments, including SLURM job submission, resource requests, and environment management.
Responsibilities
  • Process sequencing data end to end from BCL or FASTQ files through quality control and count generation.
  • Demultiplex sequencing data, perform adapter and quality trimming, handle unique molecular identifiers, align and quantify reads, and generate MultiQC reports and run manifests.
  • Build and validate Pixel-seq barcode-to-coordinate maps, perform error correction, join gene and protein counts to spatial coordinates, and assess mapping rates.
  • Apply and benchmark nuclei or whole-cell segmentation, maintain curated masks, and produce quality-control thumbnails.
  • Create annotated single-cell and spatial data objects, perform normalization, clustering, label transfer, spatial neighborhood and domain analysis, and RNA-plus-protein multi-omic modeling where applicable.
  • Implement and maintain Snakemake or Nextflow workflows with containers, continuous integration tests, and clear documentation.
  • Prepare figures and tables, write concise analysis memos, and contribute to methods sections.
  • Build and update containerized analysis environments and maintain conda or uv environments.
  • Maintain analysis environments and containers, write basic SLURM job scripts, and coordinate with information technology on storage and backup hygiene.
Desired Qualifications
  • Experience with scVI, scANVI, or totalVI for RNA and RNA-plus-protein integration.
  • GPU experience with PyTorch and CUDA for segmentation or model inference.
  • Experience with DVC or equivalent data versioning and basic Prometheus or Grafana dashboarding and monitoring.
  • Prior coursework or research in biochemistry or genetics, or interest in medical or MD-PhD pathways.
  • Experience with GitHub Actions continuous integration, environment pinning, reproducible reference bundles, and runbooks.
  • Experience assisting with server upgrades in collaboration with information technology, including CUDA/cuDNN and GPU driver stacks, SLURM client updates, and module systems.
  • Familiarity with configuration and monitoring for research workflows, including basic Ansible and Prometheus or Grafana dashboards, under information technology guidance.
  • Awareness of storage and input/output considerations for high-throughput data, including scratch NVMe versus bulk storage and pipeline performance troubleshooting.

About the company

U

University of Washington

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The University of Washington is a public research university founded in 1861, with campuses in Seattle, Bothell, and Tacoma. It provides undergraduate, graduate, and professional education alongside research and public service.

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