Postdoctoral Associate | Vertebrate Genome Laboratory

Rockefeller University

New York, New York

JOB DETAILS
SALARY
LOCATION
New York, New York
POSTED
30+ days ago
Organization Overview: The Vertebrate Genome Laboratory (VGL) at The Rockefeller University leads international efforts in vertebrate genome sequencing, assembly, annotation, and evolutionary analysis. As a core laboratory of the Vertebrate Genomes Project and a major hub of the Earth BioGenome Project, VGL is at the forefront of generating high-quality, telomere-to-telomere genome assemblies across vertebrate diversity.The laboratory provides an end-to-end genomics platform spanning sample processing, sequencing, genome assembly, and downstream data analytics. It specializes in high-molecular weight DNA extraction and long-read genomic technologies, offering integrated library preparation and sequencing services for high–molecular weight genomic DNA, long amplicons, and full-length transcriptome sequencing (Iso-Seq). These capabilities are tightly coupled with in-house computational expertise for genome assembly, curation, annotation, and comparative genomics, and are supported by state-of-the-art platforms including PacBio and ONT. Overview:

We seek a Postdoctoral Associate with AI engineering skills to work as part of our new GAIA (Genomic Artificial Intelligence Applications) collaboration, between The Rockefeller University, Revive & Restore, Cornell University, and partners including Google AI Genomics, funded by the Bezos Earth Fund and Google.org. The project aims to develop next-generation AI systems that scale genome assembly and enable genome-driven conservation.

Two central goals of GAIA are: 

  1. to build an AI Genome Curation Assistant (Jarvis): an AI system that combines modern machine learning approaches with large-scale biological data to automate genome curation by detecting, interpreting, and correcting structural errors, reducing manual effort from weeks to minutes thus that allowing to scale up to thousands of species per year;
  2. To build Genera, a multimodal, agentic AI system that integrates genomic and ecological data to assess extinction risk and generate actionable genetic rescue strategies for conservation practitioners.

This role blends research and engineering, with an emphasis on building deployable AI systems while contributing to scientific publications. The successful Postdoc will focus on the development of Jarvis and will also have the opportunity to contribute to the development of Genera.

The core technical challenge is to translate expert-driven genome curation workflows into learnable AI systems. This involves combining:

  • Pattern recognition
  • DNA sequence-level reasoning
  • Iterative decision-making across multi-step pipelines

 

The successful candidate will design and implement end-to-end AI pipelines integrating:

  • Transformer-based models for DNA sequence reasoning
  • Computer vision approaches for genomic data representations
  • Graph-aware or structured prediction methods for genome assembly

 

You will work across modeling, data, and systems integration to build a unified platform for AI-assisted genome assembly and curation, in close collaboration with VGL bioinformatics teams, genome curators, and the Rockefeller Data Science Platform, a resource center with AI developers. The role includes access to substantial compute resources and collaboration with leading AI partners.

Responsibilities:

Responsibilities include, but are not limited to:

  • Design and implement AI models for genome assembly tasks, including: 
  • Chromosome assignment and ordering
  • Detection of structural errors from Hi-C/contact maps
  • Suggestion of corrections using sequence-aware models
  • Develop multi-stage inference and decision pipelines integrating detection, reasoning, and correction
  • Build and optimize models combining multiple data modalities (sequence, Hi-C, annotations, assembly graphs) 
  • Engineer training datasets and features from large curated genome collections (~3,000 species) 
  • Develop scalable, production-quality pipelines and contribute to system architecture 
  • Collaborate with domain experts to formalize and automate genome curation strategies 
  • Contribute to scientific publications, software releases, and collaborative research
Qualifications:

REQUIRED QUALIFICATIONS:

 

  • Ph.D. (or equivalent) in machine learning, computer science, computational biology, or a related field
  • Strong experience in machine learning and deep learning, including transformer-based or related architectures 
  • Proven ability to build end-to-end AI systems, from modeling to integration
  • Proficiency in Python and ML frameworks (e.g., PyTorch, JAX, TensorFlow)
  • Experience with HPC or cloud environments and distributed training
  • Strong software engineering skills (modular design, testing, version control) 
  • Ability to work effectively in interdisciplinary teams

 

PREFERRED QUALIFICATIONS:

 

  • Experience building multimodal models combining sequence, image, and structured data
  • Experience with computer vision or analysis of structured visual data
  • Familiarity with graph-based models or structured prediction methods
  • Experience with foundation models or large-scale pretraining
  • Familiarity with genomic data formats and pipelines (FASTA, BAM, Hi-C, assembly graphs)
  • Experience with MLOps/DevOps (Docker, Kubernetes, CI/CD)

 

The Rockefeller University is an equal opportunity employer – veterans/individuals with disabilities. Qualified applicants will receive consideration for employment without regard to characteristics protected by applicable local, state or federal law, including but not limited to disability and protected veteran status.

 

The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting.

Compensation Range: Min: USD $72,100.00/Yr. Compensation Range: Max: USD $72,100.00/Yr.

About the Company

R

Rockefeller University

Founded by John D. Rockefeller, the Rockefeller Institute for Medical Research was incorporated on June 14, 1901. It was the first institution in the United States devoted solely to biomedical research--to understanding the underlying causes of disease.

Today, renamed Rockefeller University, it is one of the foremost research centers in the world, contributing to 23 Nobel Prizes as well as numerous other awards.

Rockefeller University Community
  • 71 heads of laboratories
  • 200 research and clinical scientists
  • 350 postdoctoral investigators
  • 1,050 support staff
  • 150 Ph.D. students
  • 50 M.D.-Ph.D. students
  • 887 alumni
Areas of basic interdisciplinary research
  • biochemistry, structural biology and chemistry
  • molecular, cell and developmental biology
  • immunology, virology and microbiology
  • medical sciences and human genetics
  • neuroscience
  • physics and mathematical biology
Revolutionary accomplishments

Rockefeller University researchers achieved many of the last century's seminal advances in the biomedical sciences, including:
  • Discovering that DNA is the basic material of heredity (1944)
  • Determining that cancer can be caused by a virus (1911)
  • Confirming the connection between cholesterol and heart disease (1950s)
  • Developing methadone maintenance for people addicted to heroin (1960s)
  • Developing the AIDS "cocktail" drug therapy (1990s)
Seventy-four laboratories form the university's core
The university's laboratory-based organizational structure "without walls" and pared-down layers of administration do away with the schools and academic departments that too often separate scientists. "This approach fosters a tremendously rich soup of interdisciplinary research and collaboration," says Rockefeller professor and Nobel laureate Günter Blobel.

Acclaimed scientists
In its history, Rockefeller has been associated with 23 Nobel laureates and 19 Lasker Award recipients. Five faculty members have been named MacArthur Fellows and 12 have garnered the National Medal of Science, the highest science award given by the United States. And, 33 Rockefeller faculty are elected members of the National Academy of Sciences.

Partnerships with other leading institutions
Rockefeller has close ties with neighboring Weill Medical College of Cornell University, New York-Presbyterian Hospital and Memorial Sloan-Kettering Cancer Center. Additional academic partnerships with the Courant Institute of New York University and Bard College provide students with a rich array of training opportunities. Rockefeller forges collaborations with biotech and pharmaceutical companies as needed to speed research findings into development to improve patient care.

Clinical research hospital
In 1910, Rockefeller scientists founded the nation's first hospital devoted exclusively to experimental medicine. The Rockefeller University Hospital's only patients are participants in clinical trials building on basic research findings from Rockefeller labs. This "allows the university to maintain an unbroken spectrum of research, from basic to clinical," says Joshua Lederberg, Nobel laureate and Rockefeller president emeritus. Unburdened by constraints of standard patient care, the hospital is a vital component of Rockefeller's commitment to accelerating basic research findings on their route from bench to bedside for the diagnosis, treatment and prevention of disease. Studies are under way on AIDS/ HIV, obesity, hepatitis C and addictive diseases.

More than science
Artistic and intellectual activity flourishes on Rockefeller's campus. The verdant grounds, situated on Manhattan's Upper East Side, boast a world-class art collection. The university regularly hosts events designed to explore the intuitive connection between science and the arts.Weekly and monthly recital series grace the university's spectacular auditorium, and a variety of exhibits regularly take shape on campus -currently including sculpture on temporary exhibition from New York's Museum of Modern Art.

Select graduate student body
A class of Ph.D. and M.D.-Ph.D. students from across the United States and the world works closely with international faculty in a rigorous, highly personalized program of graduate study and research. The university offers graduate students access and opportunities to work with leading scientists, as well as full financial support and affordable on- and off-campus housing.

University budget
Funding the research studies of The Rockefeller University's scientists are the National Institutes of Health and other government agencies, Howard Hughes Medical Institute, private gifts and endowment income.

COMPANY SIZE
2,500 to 4,999 employees
INDUSTRY
Education
FOUNDED
1901
WEBSITE
http://www.rockefeller.edu/