Research Scientist​/Engineer

Position: Research Scientist/Engineer 1
** 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 (“Immuno Pixel‑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).
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* Duties and Responsibilities:

** End‑to‑end data processing (BCL/FASTQ → QC → counts) – 20%  Demultiplexing, adapter/quality trimming, UMI handling, alignment/quantification; generation of Multi

QC 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.
** 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.
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* 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 Multi

QC; 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.
** Desired Requirements:
** 1. Probabilistic modeling: scVI/scANVI/total

VI 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…