Position Description

The Koo Lab at the Simons Center for Quantitative Biology (SCQB) at Cold Spring Harbor Laboratory (CSHL) is seeking a highly motivated and self-directed postdoctoral fellow to work at the intersection of machine learning and genomics.

This position focuses on developing large language models (LLMs) and diffusion models to study gene regulation using high-throughput functional genomics data. The work will emphasize applying state-of-the-art machine learning techniques to uncover the mechanisms of cis-regulatory elements and sequence motifs that coordinate gene expression.

Key Features of the SCQB:

The SCQB is building a cutting-edge experimental core dedicated to generating large-scale perturbation datasets for training and validating ML models. This integration of experimental and computational efforts ensures the maximum impact of research by directly linking model development to high-quality data.

Position Responsibilities

• Develop and implement advanced machine learning models, with a focus on LLMs and diffusion models, for genomic data analysis.
• Design and improve core ML algorithms to address challenges in genomics.
• Collaborate with experimental biologists to validate computational predictions and integrate multiomics data.
• Publish high-impact research in top-tier journals and conferences.

Position Requirements

PhD in a computation

• PhD in machine learning, computer science, or a quantitative discipline.
• Proven expertise in developing core ML algorithms, with a strong track record of publications in major venues (e.g., NeurIPS, ICML, ICLR).
• Proficiency in deep learning frameworks (e.g., PyTorch, TensorFlow).
• Strong programming skills in Python or similar languages.
• Self-driven with excellent problem-solving and communication skills.
• Preferred but not required: Prior experience or interest in genomics and gene regulation.

Supplemental Information

To apply: Interested candidates should email Peter Koo (koo@cshl.edu) with a cover letter, CV and contact information for two individuals who can provide letters of reference upon request. In addition, please apply via the CSHL careers website at 

Post Doc Computational - Koo Lab | Job Details tab | Career Pages

Position ID: 1290

Candidates from non-traditional and/or underrepresented backgrounds, broadly defined, are strongly encouraged to apply. 

About the Koo Lab:

The Koo Lab develops machine learning solutions to study gene regulation, focusing on interpreting deep learning models to reveal biological mechanisms underlying sequence-function relationships. The lab’s overarching goal is to advance precision medicine, with applications in complex diseases such as cancer. For more information, visit http://koolab.cshl.edu/.

Environment:

Cold Spring Harbor Laboratory is a world-renowned research and educational institution located on Long Island, NY, with easy access to New York City. The Simons Center for Quantitative Biology is a collaborative research environment dedicated to tackling complex biological questions using quantitative approaches. The SCQB’s experimental core is a unique initiative that enables tight integration between ML model development and experimental data generation, ensuring models are both robust and biologically validated.It has shaped contemporary biomedical research and is the home of eight Nobel Prize laureates. Cold Spring Harbor Laboratory provides a highly dynamic and interactive research environment and also a unique opportunity of timely exposure to advances in various biomedical research fields and of interaction with a broad range of researchers from all over the world through its renowned Meetings and Courses program. We believe that science is for everyone and our researchers have a wide variety of backgrounds.  

Compensation & Benefits

Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, paid time off, and a range of recognition and wellness programs. Visit our CSHL Benefits , Postdoctoral Landing & Postdoctoral Fellow Stipend Schedule (Download PDF reader) (Download PDF reader) (Download PDF reader)  sites to learn more. The salary for this role is $76,440.00 per annum. The salary range or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a base salary and/or rate, several factors may be considered as applicable (e.g., years of relevant experience, education, credentials, and internal equity).

CSHL is an EO Employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or protected veteran status. VEVRAA Federal Contractor

About Cold Spring Harbor Labora

Since 1890, Cold Spring Harbor Laboratory (CSHL) has been a global leader in research and education. The international scientific community at CSHL provides a unique and stimulating atmosphere for doctoral research?an environment where students, postdoctoral fellows, and faculty work side-by-side. The Watson School of Biological Sciences (WSBS) was founded on the belief that with well thought-out mechanisms, enthusiastic involvement of faculty, and highly motivated students, an innovative curriculum could be provided that would allow students to earn a doctoral degree in a shorter time than in traditional programs without compromising the quality of their training. The curriculum is designed to train students to become scholars and independent thinkers.

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