Research Scientist​/Engineer

Job Title

Field of Research:
Computational biology/bioinformatics with emphasis on spatial transcriptomics, proteomics, and immunosequencing using Pixel-seq and an immune receptor-focused multimodal expansion (Immuno Pixel-seq). Work includes NGS data processing, spatial barcode mapping, single-cell & spatial analysis, and cell segmentation in brain, tumor, and other tissues.

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).

• 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/Star Dist/SAM); maintain curated masks and QC thumbnails.
• Downstream single-cell & spatial analysis – 20%
• Create annotated data objects (e.g., Ann Data/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 (Dev Ops-lite) — 5% Build and update containerized analysis environments, maintain conda/uv environments. Dev Ops-lite & data stewardship – 3% Maintain analysis environments/containers; basic SLURM job scripts; coordinate with IT on storage/backup hygiene.

This position is eligible for H-1B sponsorship.

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.

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 (Ann Data/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.

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. Dev Ops-lite:
Git Hub 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…