Computational Scientist, Lung Transplant Immunology Full-time

Computational Scientist, Lung Transplant Immunology

The UCSF Lung Transplant Research Laboratory (PI's Calabrese and Greenland) is recruiting a computational scientist who is excited to address fundamental, mechanistic questions in transplant immunology and airway biology, with clear paths to clinical translation. Lung transplantation creates a uniquely informative human setting because of the defined mismatch between host and donor genetics, predictable peri-operative injury, and reproducible immune perturbations. Outcomes from lung transplantation lag behind other solid organs, amplifying the potential for high-impact discovery with immediate consequences for patient outcomes. We are looking for a scientist who will own the analysis from question to inference.

The lung transplant research group is well established and funded through a balanced portfolio of federal, VA, foundation, and industry mechanisms. The lab studies innate immune inflammation, NK cell biology, airway epithelial responses, and chronic tissue remodeling across primary graft dysfunction (PGD), acute and chronic lung allograft dysfunction (ALAD/CLAD), antibody-mediated rejection, and parallel injury phenotypes in cystic fibrosis and ARDS. The successful candidate will be embedded in one of the largest lung-transplant biorepositories in the country and in the UCSF immunology ecosystem (Department of Medicine, Department of Microbiology and Immunology, ImmunoX, CoLabs, Bakar ImmunoX Initiative), a uniquely deep environment for immune-focused discovery.

Ongoing projects and datasets you would work on:

• Longitudinal single-cell (Chromium 5′/3′, CITE-seq, TCR/BCR) atlases of bronchoalveolar lavage and small-airway brushings
• Spatial transcriptomics (Visium HD, Xenium/CosMx) of lung tissue
• Bulk transcriptomes and metagenomes linked to detailed clinical phenotypes
• Mechanistic mouse model data
• Primary human airway epithelial cells differentiated at air–liquid interface data
• Integration of these data with multimodal flow cytometry, microbiome, plasma proteomics, EHR-derived outcomes, and increasingly with ML approaches

Primary responsibilities:

• Lead end-to-end analysis of multimodal genomic datasets, from raw data through biological interpretation, with ownership of methodology.
• Define and pursue scientific questions: shape hypotheses with the PI and collaborators, design analyses, and translate findings into figures, talks, and manuscripts.
• Build durable, reproducible pipelines that can be re-run by the next trainee and published as part of our methods.
• Co-design experiments with wet-lab bench scientists to ensure data are statistically defensible and biologically interpretable.
• Contribute to grant aims and resubmissions, including writing analytic sections and generating preliminary data.
• Mentor graduate students, postdocs on computational best practices; lead lab-meeting
• Represent the lab at national and international conferences

Required qualifications:

• Specialists appointed at the junior rank must possess (or in process of obtaining) a baccalaureate degree (or equivalent degree) or at least four years of research experience (e.g., with instrumentation and research equipment, social science research methods, or creative activities).
• Specialists appointed at the Assistant rank must possess (or in process of obtaining) a master's degree (or equivalent degree) or a baccalaureate degree with 3 or more years of research experience.
• Specialists appointed at the Associate rank must possess (or in process of obtaining) a master's degree (or equivalent degree) or five to ten years of experience in the relevant specialization.
• Specialists appointed at the full rank must possess (or in process of obtaining) a terminal degree (or equivalent degree) or ten or more years of experience in the relevant specialization.
• First-author or major-contribution publication(s) using bulk RNA-seq, scRNA-seq, or comparable high-dimensional modality.
• Strong working proficiency in R (Bioconductor, Seurat or equivalent) and Python (scanpy, anndata, scikit-learn, pandas).
• Expertise in Linux-based high performance computational environments (eg. SLURM).
• Demonstrated reproducible-analysis practice: Git/GitHub, environment management (conda/mamba/renv), and workflow tooling (Nextflow or Snakemake).
• Statistical fluency: Dimensionality reduction, GLMs, mixed-effects models, multiple-testing, and survival analysis, longitudinal modeling, and causal inference.
• Vibe Coding for efficiency (Visual Studio)
• Excellent scientific writing and communication; ability to explain methods to clinicians and biology to engineers.
• Commitment to working with IRB-governed human samples and clinical metadata with the rigor and discretion that requires.

Preferred qualifications:

• Hands-on experience with one or more of: single-cell multi-omics integration (CITE-seq, scATAC), spatial transcriptomics (Visium/Xenium/CosMx/MERFISH), TCR/BCR repertoire analysis
• Bioinformatics neural network (AI) expertise
• Experience with cloud (AWS/GCP) and academic HPC (UCSF Wynton, AWS HealthOmics) at production scale.
• Familiarity with modern ML for genomics
• Prior work in immunology, transplantation, pulmonary medicine, fibrosis, or related translational settings.
• Experience analyzing paired mouse & human studies.
• Track record contributing to grants, public data deposition or open-source software.

Scientific traits and collaborative qualities we look for:

• Curiosity about the underlying biology
• Comfort with ambiguity.
• Rigor and humility about negative results, batch effects, confounders, and reproducibility.
• Generosity as a collaborator
• Strong written and verbal communication, including the ability to explain a method to a clinician at the bedside and a biological inference to a statistician.

Appointment level, compensation, and location:

Title and step will be calibrated to the candidate's training and experience within the UCSF Specialist series (Assistant, Associate, or Full Specialist). The position is based in San Francisco at UCSF Parnassus and the San Francisco VA Medical Center.

Salary range for this position is $63,500-$194,800.