Internship Program Description

NYGC’s Summer Internship Program is designed to provide students hands-on mentorship from an assigned mentor. You will gain exposure to Laboratory Automation, working in a Next Generation Sequencing wet lab , and the research that we do, as well as have the opportunity to interact with top genomic researchers. In addition, NYGC interns will be able to attend and participate in a wide variety of other events scheduled specially for our Summer Intern group, including weekly workshops, presentations, career panels, social events (optional) and much more. The expected duration of the internship is June 2nd, 2025 – July 25th, 2025.

The program will support 2 summer interns, one for each of the following programs:

The Production Lab Intern: The Production Lab supports NYGC’s disease-research areas with the use of cutting-edge next generation sequencing technology. Using automated platforms and instruments we process a high throughput of samples from nucleic acid extractions through to sequencing. Within the Production Lab the Automation Engineering team ensures these automated platforms and instruments are running smoothly, develops new workflows and onboards new instruments.

The Production Lab intern will design and test an Automated Liquid Handler program. This position will involve hands-on bench work, working with manual pipettes. The intern will develop and write improvements to the automated liquid handler program, test the improvements in the laboratory, and record and document their results. The intern will learn about commonly used laboratory instruments and learn the parts of an Automated Liquid Handler program used in the lab. They will receive general laboratory training, an understanding of best practices in the lab, and will be trained in the use of pipettes. They will gain a general knowledge of how a high throughput lab operates, a detailed introduction to various automation and laboratory equipment, an understanding of basic software development methodology and knowledge of experimental design and documentation.

Computational Biology Intern: Single-cell RNA sequencing (scRNA-seq) provides a high-resolution view of gene expression at the individual cell level, enabling the study of cellular diversity, heterogeneity, and rare cell populations—insights that bulk RNA sequencing cannot achieve. Three critical steps in scRNA-seq analysis, quality control (QC) filtering, cell clustering, and cell annotation, collectively inform downstream analyses.

Recent advancements in QC best practices and the emergence of large language model (LLM)-based tools, such as Geneformer, scGPT, have introduced innovative methods for improving cell clustering and annotation. This project will assess these developments to enhance understanding of their impact on scRNA-seq workflows.

Project Aim:

Compare LLM-Based and Traditional Cell Annotation Tools:

• Apply LLM-based tools (e.g., Geneformer, scGPT, scBERT, scFoundation) for cell annotation.
• Compare their results to those from traditional annotation tools (e.g. SingleR, Symphony, scVI), to identify limitations or biases of these methods, particularly across diverse cell and tissue types.
• Implement quality control (QC) procedures on datasets using QC metrics that reference large-scale databases such as CELLxGENE Discover Census.

Responsibilities:

1. Install new software, including Python and R packages if necessary, with assistance from the sys admin team as needed, and follow the documentation to test the software on internal and external (published, downloaded) datasets.
2. Calculate and compile standard single-cell QC metrics using tools in R and/or Python
3. Data visualization of QC metrics and cluster and cell type labels using computational tools of choice.
4. Prepare detailed reports and deliver both poster and oral presentations to share project findings at the conclusion of the program.

About the New York Genome Center

The New York Genome Center (NYGC) is an independent, nonprofit, academic research organization dedicated to advancing genomic research. NYGC scientists and staff are furthering new approaches to diagnosing and treating neurological diseases and cancer through their unique capabilities in whole genome sequencing, RNA sequencing, state-of-the art analytics, and the development of genomic tools. NYGC concentrates specifically on disease-based research in the following areas: neuropsychiatric disease (autism, schizophrenia, bipolar); neurodegenerative disease (ALS, Alzheimer’s, Parkinson’s, Huntington’s), and cancer.

Located in Lower Manhattan, the New York Genome Center was founded by and remains closely affiliated with the leading academic medical centers and research universities in the New York region, engaging in research projects with and for these institutions. Essential to our collaborative work is an outstanding faculty, whose members typically hold a joint appointment at NYGC and a partner university. They support our scientific mission by conducting independent research in areas of mutual interest to us and the wider scientific community.