University of Washington · 23 hours ago
Research Scientist/Engineer 1
Seattle, WA
Full-time
Onsite
Entry Level
$65K/yr - $70K/yr
1+ years expThe University of Washington is a leading institution dedicated to fostering an inclusive environment and advancing research. They are seeking a Research Scientist/Engineer 1 to contribute to computational biology projects, focusing on developing pipelines for spatial transcriptomics and related analyses.
EducationHigher EducationUniversities
Responsibilities
End‑to‑end data processing (BCL/FASTQ → QC → counts) – 20%
Demultiplexing, adapter/quality trimming, UMI handling, alignment/quantification; generation of MultiQC reports and run manifests
Spatial barcode mapping & registration – 15%
Build/validate barcode→(x,y) maps for Pixel‑seq; error correction; join gene/protein counts to spatial coordinates; QA of mapping rates
Segmentation & QC – 20%
Apply/benchmark nuclei or whole‑cell segmentation (e.g., Cellpose/StarDist/SAM); maintain curated masks and QC thumbnails
Downstream single‑cell & spatial analysis – 20%
Create annotated data objects (e.g., AnnData/Seurat); normalization, clustering, label transfer; spatial neighborhood/domain analysis; multi‑omic modeling for RNA+protein where applicable
Pipeline automation & reproducibility – 10%
Implement/maintain Snakemake/Nextflow workflows with containers (Apptainer/Docker), CI tests, and clear documentation
Project support, collaboration & reporting – 7%
Prepare figures/tables; concise analysis memos; contribute to methods sections
Light server/environment maintenance & upgrades (DevOps‑lite) — 5%
Build and update containerized analysis environments, maintain conda/uv environments
DevOps‑lite & data stewardship – 3%
Maintain analysis environments/containers; basic SLURM job scripts; coordinate with IT on storage/backup hygiene
Qualification
Required
Bachelor's Degree in CS, Applied Math, Bioinformatics, Computational Biology, ECE and one year of relevant experience with Computational biology/bioinformatics
Programming & data: Python (numpy/pandas), basic R (Seurat/tidyverse), bash; Git; Linux
NGS data processing: BCL→FASTQ demultiplexing; adapter/quality trimming; UMI handling; QC with MultiQC; alignment/quantification to reference
Spatial omics: Pixel‑seq barcode→(x,y) mapping concepts; creation of spatially annotated objects (AnnData/Seurat)
Segmentation: Practical use of Cellpose/FICTURE (or similar); basic image QC
Single‑cell & spatial analysis: Normalization, clustering, label transfer; spatial neighborhood/domain analyses (e.g., with Squidpy/Giotto)
Reproducibility & automation: Snakemake or Nextflow; containerization (Apptainer/Docker); clean documentation; basic SLURM job submission
Communication: Clear writing of READMEs, short analysis memos, and figure captions for collaboration with biologists/clinicians
Linux/HPC usage; Slurm job submission, resource requests, and environment management
Preferred
Probabilistic modeling: scVI/scANVI/totalVI for RNA and RNA+protein integration
GPU experience: PyTorch/CUDA for segmentation/model inference
Data stewardship: DVC or equivalent data versioning; basic dashboarding/monitoring (Prometheus/Grafana)
Domain breadth: Prior coursework/research in biochemistry or genetics; interest in medical/MD‑PhD pathways
DevOps‑lite: GitHub Actions CI, environment pinning, reproducible reference bundles, and runbooks
Experience assisting with server upgrades in collaboration with IT (CUDA/cuDNN & GPU driver stacks, Slurm client updates, module systems)
Basic familiarity with configuration/monitoring for research workflows (e.g., Ansible basics, Prometheus/Grafana dashboards) under IT guidance
Storage and I/O awareness for high‑throughput data (scratch NVMe vs. bulk); performance troubleshooting for pipelines
Benefits
For information about benefits for this position, visit https://www.washington.edu/jobs/benefits-for-uw-staff/
Company
University of Washington
University of Washington is an educational institution that provides undergraduate, graduate, and research programs.
10001+ employees
H1B Sponsorship
University of Washington has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (249)
2024 (211)
2023 (159)
2022 (171)
2021 (169)
2020 (154)
Funding
Current Stage
Late StageTotal Funding
$205.35MKey Investors
Avista foundationNational Institute of Allergy and Infectious DiseasesAdvanced Research Projects Agency for Health
2025-04-21Grant· $0.01M
2024-09-13Grant
2024-08-13Grant· $21.1M
Leadership Team
Andrew S Allen
Adjunct Professor
Arthur Denny
Founder
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