Postdoctoral Fellow, Non-Coding Genomics of Autoimmune Diseases

Biohub • New York, NY

3d • $93,000 • Onsite

About The Position

Biohub is a 501(c)(3) biomedical research organization building the first large-scale scientific initiative combining frontier AI with frontier biology to solve disease. We build the technology to help scientists around the world use AI-powered biology to study how cells operate, organize, and work as part of systems to understand why disease happens and how to correct it. With our compute capacity, AI research and engineering, and state-of-the-art technology for measuring, imaging, and programming biology, we are enabling scientists worldwide to use AI-powered biology to advance our understanding of human health.
The Team
The Biohub in New York is an independent nonprofit research institute that brings together three powerhouse universities - Columbia University, The Rockefeller University, and Yale University - into a single collaborative technology and discovery engine. Biohub itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.
Our Vision
We pursue large scientific challenges that cannot be pursued in conventional environments
We enable individual investigators to pursue their riskiest and most innovative ideas
The technologies developed at Biohub facilitate research by scientists and clinicians at our home institutions and beyond
Diversity of thought, ideas, and perspectives are at the heart of Biohub and enable disruptive innovation and scholarly excellence. We are committed to cultivating an organization where all colleagues feel inspired and know their work makes an important contribution.
The Laboratory of Immunogenomics at biohub NY (www.mahatlab.com) studies the non-coding regulatory genome to understand and address immune dysfunction in diseases like cancer, autoimmune disorders, and aging. We focus on enhancers—non-coding, highly cell-type-specific transcriptional regulatory elements—and their role in shaping immune responses.
We develop and utilize genomic technologies, including bulk and single-cell nascent RNA sequencing, genome editing, immune engineering, and CRISPR-based functional screens in patient biopsies, organoid systems, and mouse models. Through computational analysis integrating machine learning and AI, we map enhancer–gene networks and identify disease-driving elements. Our goal is to advance enhancer-guided precision genomic medicine for diseases involving immune dysfunction.
The Opportunity
We seek a Postdoctoral Fellow to dissect the non-coding genomic mechanisms underlying common autoimmune diseases (e.g., Type 1 Diabetes, Systemic Lupus Erythematosus, Celiac Disease, etc.). Over 80% of autoimmune disease-associated variants map to non-coding regions across numerous susceptibility loci, yet their target genes, relevant cell types, and molecular mechanisms remain largely unknown. This project aims to identify causal regulatory variants, map their cell-type-specific effects, and link genetic variation to immune dysfunction and disease phenotypes.

Requirements

• PhD in Genetics or Genomics with a dissertation focused on autoimmune or inflammatory diseases.
• Direct experience in systemic or organ-specific autoimmune diseases (e.g., SLE, T1D, systemic sclerosis), or related B/T cell-mediated disorders.
• Hands-on expertise with at least two: eQTL mapping, nascent RNA sequencing, MPRA/reporter assays, CRISPR editing in primary cells.
• Proficiency in isolating and culturing primary human B cells, T cells, or myeloid/target-tissue cells.
• Publication record demonstrating variant-to-function work or autoimmune disease mechanisms.

Nice To Haves

• Experience with GWAS fine-mapping tools and integrating genetic with epigenomic datasets.
• Single-cell multiomics: scRNA-seq, scATAC-seq, or CITE-seq with analysis pipelines.
• CRISPR-based editing or prime editing in hard-to-transfect primary immune cells.
• Knowledge of core immune cell biology (e.g., T/B cell activation, germinal center reactions, autoantibody production) and key signaling pathways (e.g., type I interferon biology, JAK-STAT signaling).

Responsibilities

• Variant Prioritization and Fine-Mapping
• Apply Bayesian fine-mapping (FINEMAP, SuSiE) to GWAS loci, integrating multi-ancestry data.
• Overlay variants with nascent RNA sequencing, open chromatin regions, histone modifications, and transcription factor motifs across relevant immune and target cell types.
• Cell-Type-Specific Mechanism Mapping
• Perform single-cell eQTL analysis in disease-relevant cell types (e.g., T cell subsets, B cell subsets, monocytes, or target-tissue cells) from patients.
• Map stimulus-dependent effects under key inflammatory or activating conditions (e.g., IFN, TLR agonists, TCR/BCR stimulation).
• Use promoter-capture Hi-C or similar methods to identify variant target genes through long-range chromatin interactions.
• Functional Validation
• Execute MPRAs (Massively Parallel Reporter Assays) testing allele-specific enhancer activity for prioritized variants.
• Deploy CRISPR base editing to introduce risk alleles into relevant cell lines and primary cells.
• Run CRISPRi/a screens targeting regulatory elements, measuring effects on core disease-driving pathways.
• Pathway Integration and Target Identification
• Map variant-regulated genes to core disease pathways.
• Build regulatory networks connecting variants to key disease-associated transcription factors and downstream immune programs.
• Identify druggable targets within variant-affected pathways for therapeutic development.
• Patient-Derived Studies
• Isolate and functionally test primary immune or target cells from patients carrying specific risk haplotypes.
• Develop polygenic risk scores stratifying patients by pathway involvement.
• Correlate variant effects with clinical subtypes (e.g., disease-specific organ involvement or systemic manifestations).

Benefits

• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice.
• Funding for select family-forming benefits.
• Relocation support for employees who need assistance moving

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: Ph.D. or professional degree