The Waldron Lab in the Department of Epidemiology and Biostatistics at the CUNY Graduate School of Public Health and Health Policy (Harlem, New York City) seeks a postdoctoral research associate. The lab develops open-source software, curated databases, and statistical methods for cancer genomics and the human microbiome. We are core contributors to Bioconductor, the open-source R ecosystem of more than 2,200 packages for genomic data analysis. We maintain widely used resources including curatedMetagenomicData, BugSigDB, MultiAssayExperiment, and curatedTCGAData.

The postdoc will work across two NIH-funded projects:

• Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor (NCI U24CA289073). This project expands Bioconductor infrastructure for multimodal and spatial omics. It connects R/Bioconductor with histopathology image analysis, for example foundation-model embeddings of TCGA whole-slide images. It also builds federated, language-agnostic systems for sharing curated data, and new training resources, including AI-assisted tools.
• Exploiting Public Metagenomic Data (NCI R01CA230551). This project builds the next generation of curatedMetagenomicData and BugSigDB. That includes ontology-based curation, scalable metagenomic profiling of public sequencing data, enrichment analysis of microbial signatures, and meta-analyses of cancer-microbiome relationships.

The postdoc will lead original research and first-author publications drawing on these resources. They will also contribute to software and data infrastructure that thousands of researchers use. The balance between the two projects can be shaped around the candidate’s interests.

Responsibilities

• Design and carry out analyses integrating microbiome, multi-omic, and imaging data in cancer, and lead resulting publications
• Develop and maintain R/Bioconductor packages and data resources, following open-source best practices: version control, testing, documentation, and code review
• Contribute to curation workflows and pipelines for large public datasets, such as NCBI SRA and TCGA
• Collaborate with lab members, Bioconductor core developers, and national and international partners
• Mentor graduate students and data curators, and help teach workshops and training materials
• Present work at conferences, including the annual Bioconductor conference
• Submit articles to peer-reviewed journals
• Performs related duties as assigned

Work Arrangement

• Hybrid, with a flexible schedule. The position is based at 55 West 125th Street, New York, NY, and requires living within commuting distance.
• Appointment: full-time, one year, renewable based on performance and funding
• Start date: flexible
• Visa sponsorship is available for qualified international candidates (typically J-1).
• No bargaining unit

Qualifications

• PhD (completed, or completed before the start date) in biostatistics, bioinformatics, computational biology, statistics, computer science, epidemiology, or a related field
• Strong programming skills in R, Python, or both, with experience analyzing high-dimensional biological data
• Evidence of independent research, such as first-author publications or preprints
• Clear written and spoken communication, and the ability to work collaboratively

Preferred Qualifications

• Experience developing R packages, especially for Bioconductor
• Experience with metagenomic or microbiome data, cancer genomics, spatial or single-cell omics, or histopathology images
• Experience with workflow systems (Nextflow, Snakemake), containers, cloud or HPC computing, or databases
• Interest in data curation, FAIR data, ontologies, or AI-assisted research tools
• A public portfolio of code (GitHub or similar)

CUNY Title Overview

• Conducts research activities with the mentorship of a CUNY faculty member.
• Collaborates with internal and external researchers
• Adheres to relevant regulations and ethical conduct standards pertinent to the conduct of their research.
• Performs related duties as assigned

Pay Range

Minimum – Maximum: $60,000 – $85,000

RFCUNY Benefits

RFCUNY Employee Benefits and Accruals

Equal Employment Opportunity Statement

The Research Foundation of the City University of New York is an Equal Opportunity/Affirmative Action/Americans with Disabilities Act/E-Verify Employer. It is the policy of the Research Foundation of CUNY to provide equal employment opportunities free of discrimination based on race, color, age, religion, sex, pregnancy, childbirth, national origin, disability, marital status, veteran status, sexual orientation, gender identity, genetic information, marital status, domestic violence victim status, arrest record, criminal conviction history, or any other protected characteristic under applicable law.