Postdoctoral Fellow/ Scientist I, Single-Cell Method Development

Biohub is the first large-scale initiative bringing frontier AI models, massive compute, and frontier experimental capabilities under one roof. We're building a general-purpose system to accelerate scientific discovery, integrating frontier AI models, biological foundation models, and lab capabilities, with the ultimate goal of curing disease. Our technology powers scientists around the world, translating AI capabilities into tools that accelerate research everywhere.

The Team

The Chan Zuckerberg Biohub New York (CZ Biohub NY, https://www.czbiohub.org/ny/) 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. CZ Biohub NY 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 CZ Biohub 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 inclusive organization where all colleagues feel inspired and know their work makes an important contribution.

The Laboratory of Immunogenomics at CZ 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 are seeking a highly motivated Postdoctoral Fellow/ Scientist I to lead the development of a high-throughput adaptation of a newly established single-cell nascent RNA sequencing method (scGRO-seq) and apply it to patient biopsies and organoid models. The role involves designing, optimizing, and benchmarking cutting-edge single-cell genomics workflows, integrating them with perturbation-based assays, and generating datasets that drive transformative insights into immune regulation.

This is a wetlab-based, hands-on position that specifically requires experience in method development and offers the opportunity to develop and implement the assay, conduct perturbation experiments, and oversee data generation. Once the workflow is established, this position will coordinate large-scale data acquisition and collaborate with computational biologists on downstream analyses to deliver actionable translational insights. This role is ideal for a recent PhD with a proven track record in single-cell biology who excels at the intersection of technological innovation and transcription regulation. You will join a highly collaborative team working toward a shared vision at the cutting-edge of single-cell immunogenomics.

What You'll Do

• Assay development: Design, optimize, and scale high-throughput single-cell/nuclei extraction, barcoding, and library preparation workflows for scGRO-seq.
• Perturbation integration: Combine scGRO-seq with CRISPR-based enhancer perturbation, drug treatments, and multi-omics profiling.
• Molecular biology techniques: Execute advanced methods including assay design, cell manipulation, RNA/DNA isolation, PCR/qPCR, NGS library construction, high-dimensional flow cytometry, and sequencing.
• Translational applications: Adapt and validate protocols in patient biopsies and 3D organoid models, with emphasis on reproducibility and sensitivity.
• Immune cell engineering: Isolate, culture, and reprogram hematopoietic stem/progenitor cells (HSPCs) and primary immune subsets.
• Data integration: Partner with computational biologists to process and interpret large-scale single-cell datasets (RNA, chromatin, proteomics).
• Collaboration & dissemination: Collaborate across disciplines to investigate regulatory genomics in immune dysfunction, tumor-infiltrating immune cells, and autoimmune disease variants. Contribute to publications, preprints, conference presentations, and grant proposals.

What You'll Bring

Essential: 

• PhD in Biomedical Engineering, Molecular Biology, Systems Biology, Genetics, or related field.
• 4+ years of experience working in genomics assay development or method optimization.
• 2+ years of experience working on single-cell transcriptomics, droplet chemistry, and microfluidics.
• Proven expertise and demonstrated success in bulk or single-cell method development.
• Experience designing and executing CRISPR screens and perturbation assays (genetic or chemical/drug).
• Strong problem-solving skills, independence, and the ability to troubleshoot complex workflows.
• Excellent communication skills and proven ability to work in collaborative, multidisciplinary teams.

Nice to have: 

• Experience and broad domain knowledge in microfluidic-based single-cell methods.
• Experience with hydrogel synthesis, single-cell barcoded bead generation, and aqueous droplets in oil emulsions.
• Experience with functional genomics in immune cells.
• Experience integrating multi-modal single-cell datasets (RNA, ATAC, proteomics).
• Working knowledge of Linux/HPC environments and single-cell analysis tools (e.g., Seurat, Scanpy).

Compensation

The New York, NY base pay for a new hire in this role is Postdoctoral Fellow = $93,000.00, Scientist I = $120,000 - $150,000. This position may be eligible to participate in Biohub's discretionary annual performance bonus program. Bonus eligibility and targets are determined in accordance with Biohub's total rewards philosophy and may vary by role.

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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