• Research Scientist/Engineer 1

    University of Washington (Seattle, WA)


    Job Description

    Field of Research:

    Computational biology/bioinformatics with emphasis on spatial transcriptomics, proteomics, and immunosequencing using Pixel‑seq and an immune receptor‑focused multimodal expansion (“ImmunoPixel‑seq”). Work includes NGS data processing, spatial barcode mapping, single‑cell & 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 high‑quality, spatially resolved single‑cell datasets; to deliver disease‑focused analyses that advance mechanistic discovery and translational hypotheses (e.g., tumor microenvironment, neuroanatomical circuits).

    Duties and 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.

     

    Visa Eligibility

     

    This position is eligible for H-1B sponsorship.

    Minimum Requirements:

    Bachelor's 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: BCL→FASTQ demultiplexing; adapter/quality trimming; UMI handling; QC with MultiQC; alignment/quantification to reference.

    3. Spatial omics: Pixel‑seq barcode→(x,y) mapping concepts; creation of spatially annotated objects (AnnData/Seurat).

    4. Segmentation: Practical use of Cellpose/FICTURE (or similar); basic image QC.

    5. Single‑cell & 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 RNA+protein 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/MD‑PhD pathways.

    5. DevOps‑lite: 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 high‑throughput data (scratch NVMe vs. bulk); performance troubleshooting for pipelines.

     

    Compensation, Benefits and Position Details

    Pay Range Minimum:

    $65,004.00 annual

    Pay Range Maximum:

    $70,008.00 annual

    Other Compensation:

    -

    Benefits:

    For information about benefits for this position, visit https://www.washington.edu/jobs/benefits-for-uw-staff/

    Shift:

    First Shift (United States of America)

     

    Temporary or Regular?

     

    This is a regular position

    FTE (Full-Time Equivalent):

    100.00%

    Union/Bargaining Unit:

    UAW Research

     

    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 world. In 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 (https://policy.uw.edu/directory/po/executive-orders/eo-81-prohibiting-discrimination-harassment-and-sexual-misconduct/) .

     

    To request disability accommodation in the application process, contact the Disability Services Office at 206-543-6450 or [email protected] .

     

    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 (https://app.leg.wa.gov/RCW/default.aspx?cite=28B.112.080) .

     

    University of Washington is an affirmative action and equal opportunity employer. All qualified applicants will receive consideration for employment without regard to, among other things, race, religion, color, national origin, sexual orientation, gender identity, sex, age, protected veteran or disabled status, or genetic information.