Chan Zuckerberg Biohub Network
Research Scholar, Engineering Non-Coding Genome in Immune Cells (Immunogenomics
Chan Zuckerberg Biohub Network, New York, New York, us, 10261
Overview
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, 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 with the goal of advancing enhancer-guided precision genomic medicine for immune-related diseases. 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 focuses 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 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 collaborative, multidisciplinary opportunity at the intersection of genomics, immunology, and bioengineering. What You'll Do
Functional genomics & genome engineering:
Apply high-throughput CRISPR/Cas9 and CRISPRi/a screens, STARR-seq, and 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 (isolation, culture, and genetic reprogramming of human and murine immune cells); design of synthetic biology circuits; ex vivo & organoid models; in vivo translation using mouse models. Data Integration & Computational Biology:
Analyze multi-omic datasets with pipelines (STAR, Bowtie2, Cell Ranger, Seurat, Scanpy, ArchR); apply ML/AI to prioritize regulatory elements; contribute to integrative algorithms. Collaboration & Dissemination:
Partner with immunology, cancer biology, and systems genomics teams; publish in preprints and peer-reviewed venues; support grants, tech transfer, and mentoring of students and junior researchers. 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 with computational biology teams. Proven ability to troubleshoot complex experimental workflows and work independently. Nice to have 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 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 placed in the lower portion of the range with growth over time; actual placement is based on job-related skills and experience. Benefits
Generous employer match on 401(k) contributions. Paid time off to volunteer. Funding for select family-forming benefits. Relocation support for employees needing assistance moving. If your experience doesn’t perfectly align with every qualification, you are encouraged to apply as you may be a great fit for this or other roles.
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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, 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 with the goal of advancing enhancer-guided precision genomic medicine for immune-related diseases. 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 focuses 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 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 collaborative, multidisciplinary opportunity at the intersection of genomics, immunology, and bioengineering. What You'll Do
Functional genomics & genome engineering:
Apply high-throughput CRISPR/Cas9 and CRISPRi/a screens, STARR-seq, and 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 (isolation, culture, and genetic reprogramming of human and murine immune cells); design of synthetic biology circuits; ex vivo & organoid models; in vivo translation using mouse models. Data Integration & Computational Biology:
Analyze multi-omic datasets with pipelines (STAR, Bowtie2, Cell Ranger, Seurat, Scanpy, ArchR); apply ML/AI to prioritize regulatory elements; contribute to integrative algorithms. Collaboration & Dissemination:
Partner with immunology, cancer biology, and systems genomics teams; publish in preprints and peer-reviewed venues; support grants, tech transfer, and mentoring of students and junior researchers. 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 with computational biology teams. Proven ability to troubleshoot complex experimental workflows and work independently. Nice to have 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 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 placed in the lower portion of the range with growth over time; actual placement is based on job-related skills and experience. Benefits
Generous employer match on 401(k) contributions. Paid time off to volunteer. Funding for select family-forming benefits. Relocation support for employees needing assistance moving. If your experience doesn’t perfectly align with every qualification, you are encouraged to apply as you may be a great fit for this or other roles.
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