Research Scholar, Engineering Non-Coding Genome in Immune Cells (Immunogenomics Group - Biohub NY)

The Team

CZ Biohub New York will first harness the natural capabilities of our immune cells to detect and fix abnormalities in our bodies at very early stages. It will then bioengineer immune cells to create new capabilities to detect and potentially treat events before they lead to untreatable disease.

CZ Biohub New York is part of the CZ Biohub Network, a group of nonprofit research institutes created and supported by the Chan Zuckerberg Initiative.

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 the CZ Biohub Network facilitate research by scientists and clinicians at our home institutions and beyond

Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network 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 Opportunity

The Laboratory of Immunogenomics at CZ Biohub NY 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.

We are seeking a highly motivated Research Scholar to lead pioneering research into the functional mapping and engineering of non-coding regulatory elements that govern immune cell gene expression. This role will focus on identifying and manipulating enhancers, silencers, and other cis-regulatory elements that control immune-modulating genes (cytokines, chemokines, checkpoint regulators) to reprogram immune responses in health and disease.

The successful candidate will integrate advanced functional genomics, single-cell multi-omics, and synthetic biology approaches to dissect immune regulatory circuits, engineer precise expression control in immune cell subsets, and apply these strategies in in vivo models and human-derived immune organoid systems. This is a unique opportunity to operate at the intersection of genomics, immunology, and bioengineering in a collaborative, multidisciplinary environment.

What You'Ll Do

Functional genomics & genome engineering:  Apply high-throughput CRISPR/Cas9 and CRISPRi/a screens, STARR-seq, and massively parallel reporter assays (MPRA) to functionally map immune-cell-specific enhancers, silencers, and boundary elements.

Single-cell & spatial genomics: Develop and optimize protocols for scRNA-seq, scATAC-seq, scCUT&Tag, spatial transcriptomics, and multimodal platforms (e.g., 10x Genomics Multiome, Visium).

Transcriptional regulation: Use scGRO-seq, SLAM-seq, and nascent RNA profiling to dissect transcriptional kinetics in engineered immune cells.Epigenome editing: Employ targeted histone modification and DNA methylation tools (e.g., dCas9-p300, dCas9-TET1) to modulate enhancer activity in immune contexts.

Immune Cell Engineering:

• Primary cell manipulation: Isolate, culture, and genetically reprogram primary human and murine immune cells, including T cells, B cells, NK cells, dendritic cells, macrophages, and HSPCs.
• Synthetic biology circuits: Design logic-gated circuits and inducible systems for spatially and temporally controlled gene expression.
• Ex vivo & organoid models: Engineer immune cells within human immune organoids, tumor–immune co-cultures, and 3D hydrogel scaffolds.
• In vivo translation: Apply engineered cells in syngeneic and patient-derived xenograft (PDX) mouse models.
• Apply machine learning and AI-based models to prioritize candidate regulatory elements for functional validation.
• Contribute to algorithm development for integrating RNA, chromatin accessibility, and protein expression data.
• Publish findings in preprints and peer-reviewed journals, and present at scientific conferences.
• Support grant development, technology transfer, and mentoring of graduate students and junior researchers.
• Nice to have - 
• Primary cell manipulation: Isolate, culture, and genetically reprogram primary human and murine immune cells, including T cells, B cells, NK cells, dendritic cells, macrophages, and HSPCs.
• Synthetic biology circuits: Design logic-gated circuits and inducible systems for spatially and temporally controlled gene expression.
• Ex vivo & organoid models: Engineer immune cells within human immune organoids, tumor–immune co-cultures, and 3D hydrogel scaffolds.
• In vivo translation: Apply engineered cells in syngeneic and patient-derived xenograft (PDX) mouse models.
• Apply machine learning and AI-based models to prioritize candidate regulatory elements for functional validation.
• Contribute to algorithm development for integrating RNA, chromatin accessibility, and protein expression data.
• Publish findings in preprints and peer-reviewed journals, and present at scientific conferences.
• Support grant development, technology transfer, and mentoring of graduate students and junior researchers.
• Nice to have - 
• In vivo translation: Apply engineered cells in syngeneic and patient-derived xenograft (PDX) mouse models.
• Apply machine learning and AI-based models to prioritize candidate regulatory elements for functional validation.
• Contribute to algorithm development for integrating RNA, chromatin accessibility, and protein expression data.
• Publish findings in preprints and peer-reviewed journals, and present at scientific conferences.
• Support grant development, technology transfer, and mentoring of graduate students and junior researchers.
• Nice to have - 

Data Integration & Computational Biology:

• Analyze large-scale multi-omic datasets with established and custom pipelines (e.g., STAR, Bowtie2, Cell Ranger, Seurat, Scanpy, ArchR).
• Analyze large-scale multi-omic datasets with established and custom pipelines (e.g., STAR, Bowtie2, Cell Ranger, Seurat, Scanpy, ArchR).

Collaboration & Dissemination:

• Partner with teams in immunology, cancer biology, and systems genomics.
• Partner with teams in immunology, cancer biology, and systems genomics.

What You'Ll Bring

Essential -

• A PhD in Molecular Biology, Genetics, Immunology, Bioengineering, or related field.
• Hands-on experience with CRISPR/Cas genome editing, perturbation screens, and enhancer assays.
• Familiarity with base and prime editing, and CRISPR off-target profiling.
• Expertise in immune cell biology, including isolation, culture, and functional assays for primary immune cells and/or HSPCs.
• Experience with multi-omic data analysis or working closely with computational biology teams.
• Proven ability to troubleshoot complex experimental workflows and work independently.
• Genetic payload delivery with optimized capsid biology or lipid nanoparticles.
• Experience with high-dimensional immune profiling (e.g., CyTOF, spectral flow cytometry).
• Track record in single-cell technology development and application.
• Proficiency in R/Python for omics data analysis.
• Prior work with 3D organoid systems or microfluidics for immune cell studies.
• Understanding of gene regulatory network modeling and enhancer-promoter interaction mapping (Hi-C, PLAC-seq, HiChIP).
• Experience in translational immunology or immuno-oncology models

Compensation

The New York, NY base pay range for a new hire in this role is $85,000.00. New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process. 

Benefits For The Whole You

We’re thankful to have an incredible team behind our work. To honor their commitment, we offer a wide range of benefits to support the people who make all we do possible. 

• 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

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

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