Computational Science Developer - Koo Lab

The Koo Lab at the Simons Center for Quantitative Biology (SCQB) at Cold Spring Harbor Laboratory (CSHL) is seeking a Computational Science Developer to support large-scale biological data processing for machine learning (ML) projects. This role is essential for harmonizing and curating functional genomics datasets, building robust pipelines, and enabling cutting-edge AI research in genomics.

* Develop and maintain pipelines for processing functional genomics data, including ChIP-seq, ATAC-seq, RNA-seq, and perturbation datasets such as MPRAs.
* Harmonize data across multiple sources to ensure consistency and scalability for AI model training.
* Collaborate with interdisciplinary teams to support diverse ML projects by preparing datasets and optimizing ML software.
* Optimize and refactor lab-developed ML code for improved performance and scalability.
* Maintain and manage computational resources, including servers and databases, for the lab's research activities.

Education: Bachelor's degree in a quantitative field (e.g., bioinformatics, computer science, physics, or mathematics). Exceptional candidates with advanced degrees will be considered for an advanced role.

Skills and Experience: *Experience with Functional Genomics Data: Proven ability to process and analyze large-scale genomics datasets such as ChIP-seq, ATAC-seq, RNA-seq, and MPRA data. * Data Harmonization: Experience with normalizing and integrating multi-omics datasets from diverse sources for downstream analysis and AI applications. * Knowledge of Genomic Formats and Tools: Familiarity with common genomics data formats (e.g., BAM, BED, FASTQ, VCF) and tools (e.g., SAMtools, BEDTools, STAR, HISAT2, MACS2). * Strong coding background: Proficiency in Python and bash in the context of bioinformatics. Working knowledge of TensorFlow and/or PyTorch is a plus. * Scalable data analysis: Experience with sharding large datasets, dataloader optimization, scalable data storage is a plus. * Familiarity with source code management systems (e.g., Git) and software development best practices.

Join us in shaping the future of AI-driven biology and be part of a groundbreaking initiative that bridges the experimental and computational worlds at Cold Spring Harbor Laboratory! Please submit an online application here: Computational Science Developer- Koo lab Position 1490. We look forward to reviewing your application. 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 biomedical research institution in New York. 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. We have had researchers with a variety of backgrounds and believe in the importance of diversity, equity, and inclusion.

Compensation and Benefits Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our CSHL Benefits sites to learn more. The salary range for this role is $64,350- 67,599. The salary range and/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/AA 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