Research ScientistEngineer 1

Job Description

Field of Research:

Computational biology/bioinformatics with emphasis on spatial transcriptomics proteomics and immunosequencing using Pixelseq and an immune receptorfocused multimodal expansion (ImmunoPixelseq). Work includes NGS data processing spatial barcode mapping singlecell & spatial analysis and cell segmentation in brain tumor and other tissues.

Purpose of the Research project(s):

To build and operate robust reproducible pipelines that transform raw sequencing barcode map into highquality spatially resolved singlecell datasets; to deliver diseasefocused analyses that advance mechanistic discovery and translational hypotheses (e.g. tumor microenvironment neuroanatomical circuits).

Duties and Responsibilities:

Endtoend 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(xy) maps for Pixelseq; error correction; join gene/protein counts to spatial coordinates; QA of mapping rates.

Segmentation & QC 20%
Apply/benchmark nuclei or wholecell segmentation (e.g. Cellpose/StarDist/SAM); maintain curated masks and QC thumbnails.

Downstream singlecell & spatial analysis 20%
Create annotated data objects (e.g. AnnData/Seurat); normalization clustering label transfer; spatial neighborhood/domain analysis; multiomic modeling for RNAprotein 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 (DevOpslite) 5%
Build and update containerized analysis environments maintain conda/uv environments.

DevOpslite & data stewardship 3%
Maintain analysis environments/containers; basic SLURM job scripts; coordinate with IT on storage/backup hygiene.

Visa Eligibility

This position is eligible for H-1B sponsorship.

Minimum Requirements:

Bachelors Degree in CS Applied Math Bioinformatics Computational Biology ECE and one year of relevant experience with Computational biology/bioinformatics.

Equivalent education and/or experience may substitute for minimum qualifications except when there are legal requirements such as a license certification and/or registration.

Additional Requirements:

1. Programming & data: Python (numpy/pandas) basic R (Seurat/tidyverse) bash; Git; Linux.
2. NGS data processing: BCLFASTQ demultiplexing; adapter/quality trimming; UMI handling; QC with MultiQC; alignment/quantification to reference.
3. Spatial omics: Pixelseq barcode(xy) mapping concepts; creation of spatially annotated objects (AnnData/Seurat).
4. Segmentation: Practical use of Cellpose/FICTURE (or similar); basic image QC.
5. Singlecell & spatial analysis: Normalization clustering label transfer; spatial neighborhood/domain analyses (e.g. with Squidpy/Giotto).
6. Reproducibility & automation: Snakemake or Nextflow; containerization (Apptainer/Docker); clean documentation; basic SLURM job submission.
7. Communication: Clear writing of READMEs short analysis memos and figure captions for collaboration with biologists/clinicians.
8. Linux/HPC usage; Slurm job submission resource requests and environment management.

Desired Requirements:

1. Probabilistic modeling: scVI/scANVI/totalVI for RNA and RNAprotein integration.
2. GPU experience: PyTorch/CUDA for segmentation/model inference.
3. Data stewardship: DVC or equivalent data versioning; basic dashboarding/monitoring (Prometheus/Grafana).
4. Domain breadth: Prior coursework/research in biochemistry or genetics; interest in medical/MDPhD pathways.
5. DevOpslite: GitHub Actions CI environment pinning reproducible reference bundles and runbooks.
6. Experience assisting with server upgrades in collaboration with IT (CUDA/cuDNN & GPU driver stacks Slurm client updates module systems).
7. Basic familiarity with configuration/monitoring for research workflows (e.g. Ansible basics Prometheus/Grafana dashboards) under IT guidance.
8. Storage and I/O awareness for highthroughput data (scratch NVMe vs. bulk); performance troubleshooting for pipelines.

Compensation Benefits and Position Details

Pay Range Minimum:

Pay Range Maximum:

Other Compensation:

Benefits:

Temporary or Regular

FTE (Full-Time Equivalent):

Union/Bargaining Unit:

About the UW

Working at the University of Washington provides a unique opportunity to change lives on our campuses in our state and around the world.

UW employees bring their boundless energy creative problem-solving skills and dedication to building stronger minds and a healthier return they enjoy outstanding benefits opportunities for professional growth and the chance to work in an environment known for its diversity intellectual excitement artistic pursuits and natural beauty.

Our Commitment

The University of Washington is committed to fostering an inclusive respectful and welcoming community for all. As an equal opportunity employer the University considers applicants for employment without regard to race color creed religion national origin citizenship sex pregnancy age marital status sexual orientation gender identity or expression genetic information disability or veteran status consistent with UW Executive Order No. 81.

To request disability accommodation in the application process contact the Disability Services Office at or .

Applicants considered for this position will be required to disclose if they are the subject of any substantiated findings or current investigations related to sexual misconduct at their current employment and past employment. Disclosure is required under Washington state law.