4DN Summer Undergraduate Program for Excellence in Research
The Summer Undergraduate Program for Excellence in Research (SUPER) provides the opportunity for undergraduate students from US colleges and universities to receive mentorship and training from NIH 4D Nucleome (4DN) Program labs over the summer.
NIH encourages the participation of individuals from populations that are underrepresented in the biomedical, clinical, behavioral and social sciences. See the Notice of NIH’s Interest in Diversity.

Applications closed.

2024 Internship Information

Applications will be accepted from December 15, 2023 until February 16, 2024.

Internship experiences can be computational or experimental. The lab descriptions below identify which experiences will be computational and which will be experimental. Applicants can indicate their preference for computational or experimental internships on the application.

Preference will be given to students who do not have ready access to biomedical research opportunities in their home institutions.

Accepted students will receive a stipend of $9,000 to be used for lodging, food, and expenses. Additional funding to cover travel expenses will be determined on a lab by lab basis.

Questions? Email us at:

Important Dates

Applications Open: December 15, 2023

Applications Close: February 16, 2024

Acceptance Notifications: March 30, 2024

Performance Period: ~10-12 weeks between May – August, 2024. Specific start and end dates will be discussed with accepted students.

Eligibility Criteria

Eligible students will be:

  • Freshman through Senior undergraduate students attending a US institution at the time of application.
  • Majoring in any of the STEM fields with a minimum 2.8 grade point average.
  • A minimum of 18 years of age.

Successful applicants will have:

  • An interest in and passion for studying biological or computational sciences, or related STEM fields.
  • A demonstrated strong work ethic.
  • Some experience with lab work.

Preference will be given to students who do not have ready access to biomedical research opportunities in their home institutions.

Requirements and Expectations

Accepted students are required to:

  • Conduct your own small research project or work on part of an ongoing research project.
  • Participate in professional development opportunities available through the host institution.
  • Complete all Compliance Training, Conflict of Interest Forms and/or any other training deemed necessary for your internship as soon as it is received.
  • Report to work on time as designated by the mentor to work on assigned research project. Students are expected to work no more than 40 hours a week.
  • Present a summary about your summer research experience at the end of the project.

Application Process

Application: All applicants will be required to submit an application form, transcript, resume/CV, personal statement, and two letters of recommendation. All materials should be submitted via the application form by February 16, 2024.

Transcript: Unofficial transcripts are acceptable. Please submit transcripts as an attachment to your application form, as a PDF.

Personal Statement: Please submit a personal statement including the five required structured elements/questions listed in the application form. Please attach your personal statement in PDF format. Personal statements should be no longer than two pages single spaced, font size 11, Times New Roman.

Resume/CV: Please submit a resume or CV which includes descriptions of any leadership and/or extracurricular activities. NIH guidelines for constructing a resume/CV can be found here. Purdue University also has helpful guidelines here.

Letters of recommendation: Two letters of recommendation should be sent to the application committee from your references, by the application due date of February 16, 2024. These letters should include reference to the required criteria as listed on the application form. Letters of recommendation should be sent to

2024 Internship Opportunities

Internship opportunities for 2024 are listed below. Each entry indicates if the internship will be computational or experimental. Clicking on a lab name will expand the detailed information on that opportunity.

1. Memorial Sloan Kettering Cancer Center, Huangfu Lab (Computational and Experimental)

We are at Sloan Kettering Institute located in New York city (430 E 67th St., New York, NY 10065). Our 4DN project involves applying cutting-edge genomic approaches to capture the dynamic rewiring of 3D enhancer networks during human pluripotent stem cell (hPSC) differentiation, and conducting CRISPRi mediated perturbation screens to translate 3D genomics data into functional data with respect to gene expression in the context of human pancreas development and diabetes.


The intern is expected to work on validating findings from genomic assays and CRISPRi screens under the supervision of a PhD student or postdoctoral researcher. Practical laboratory experience in molecular biology is required. Experience with tissue culture and CRISPR is a plus.

2. Memorial Sloan Kettering Cancer Center, Leslie Lab (Computational)

Our lab is in the Computational and Systems Biology Program of the Sloan Kettering Institute, the basic science institute of Memorial Sloan Kettering Cancer Center in New York, NY. We develop computational methods including machine learning models to study the regulation of gene expression from a global and data-driven perspective perspective, with applications to basic and cancer immunology, cancer epigenetics, and stem cell biology and cellular differentiation. Within the 4DN consortium, we are studying 3D enhancer rewiring in pancreatic differentiation, developing novel statistical methods for the analysis of diverse chromosome conformation capture assays, and building machine learning models to predict the Hi-C contact map from bulk and single-cell epigenomic data and to predict gene expression from 1D and 3D genomic data.


Programming in R and other (Python), a solid mathematical foundation for data science (ideally: linear algebra, multivariate calculus, probability and statistics), exposure to basic concepts in molecular biology. Contribute to the computational analysis of a 3D genomics data set and/or to the development/testing of a new machine learning model. Any intern who is hosted in our lab could participate in events organized by the MSK Computational Biology Summer Program ( and therefore be part of a cohort of computational interns.

3. University of Massachusetts Chan Medical School, Dekker Lab (Computational and Experimental)

Our 4DN project is located at the University of Massachusetts Chan Medical School, in Worcester MA. It is part of the Department of Systems Biology. The focus of our 4DN site is to determine how the folding and function of the human genome (the 4D nucleome) develops during life span: from an immature state in embryonic stem cells, to a mature state during cell differentiation into hepatocytes, and then how the 4D nucleome changes again and deteriorates as cells (prematurely) age. The project involves a range of approaches such as genomic experimentation, microscopy, proteomics, computational analyses, polymer modeling, and software development.


Interns joining our project ideally would have some training in lab work and/or in computation, but no prior experience is required. Interns will be embedded in the existing summer intern program organized by our department of Systems Biology that provides weekly lectures by our faculty in areas of systems biology. The position will include housing. The intern(s) will be supervised by Dr. Johan Gibcus, the project leader of our 4D Nucleome Center, Dr. Liyan Yang, the lead genomic experimentalist in our Center, Dr. Sergey Venev, the lead computational biologist in our Center, and Dr. Job Dekker, Director of the Center.

4. University of Washington, Beliveau Lab (Computational and Experimental)

Dr. Brian Beliveau’s lab develops technologies for studying the organization and regulation of the genome. A 4DN-SUPER intern assigned to the Beliveau lab will work alongside a postdoc and research staff who are applying advanced molecular techniques to label specific cell types in the developing mouse embryo for imaging and sequencing based readouts. The goal of the project is to understand the connection between the spatial positioning of cell types within developing tissues and their chromatin and gene expression states.


The project offers both wet and dry lab activities; the intern may elect wet, dry, or both. For the wet lab activities, a basic understanding of designing and performing experiments (e.g., from an undergraduate-level biology or chemistry lab course) would be an important foundation. For the dry lab activities, familiarity with Python programming or an equivalent general purpose language (e.g. R, C, Java) is essential. The intern would work in the Foege Building, which houses the Department of Genome Sciences on the UW campus.

5. University of Washington, Disteche/Deng Labs (Computational and Experimental)

Dr. Christine Disteche’s lab studies the regulation and function of genes that are differentially expressed from the maternal and paternal chromosome copies using resources to identify alleles that differ by single nucleotide polymorphisms. Such genes, which include sex-linked genes and imprinted genes, play important roles in normal development and sex differences.


Dr. Xinxian Deng’s lab studies dosage regulation of the mammalian X chromosome and its role in normal development and sex differences. The project involves both wet lab and dry lab activities.


A 4DN-SUPER intern will be mentored under Drs. Deng and Disteche to work alongside research staff to follow allele-specific gene expression in specific cell types from mouse embryos. The project involves both wet lab and dry lab activities. The Disteche and Deng labs are located in the Health Sciences building on the University of Washington campus.

6. University of Washington, Duan Lab (Experimental)

The Duan lab is located on the 4th floor of the North Research Building on the UW Medicine South Lake Union campus. The intern assigned to the lab would be housed on the UW campus. The Duan lab, associated with the UW 4D GENOME Center, develops single-cell genomic technologies for studying genome structure and function, and aims to apply them to various biological contexts, such as human hematopoiesis and malignancies.


An ideal 4DN-SUPER intern would be with the basic knowledge of molecular biology, biochemistry and/or genome sciences. A 4DN-SUPER intern assigned to the lab will work on an ongoing project to develop a method for mapping promoter-enhancer loops and concurrently profiling gene expression in large numbers of single cells, under the supervision of Dr. Duan. The goal of this project is to provide the research communities with a single-cell technology for elucidating the connections between the three-dimensional nuclear organization of cis-regulatory elements and gene regulation at the single-cell level.

7. University of Washington, Fowler Lab (Computational and Experimental)

Dr. Doug Fowler’s lab develops experimental methods, including for linking cell morphology to cell internal state and behavior.


A 4DN-SUPER intern assigned to the Fowler lab will work closely with research staff and trainees to apply one such method, Visual Cell Sorting, to the developing mouse embryo. The goal of the project is to understand how changes in nuclear morphology during development are linked to and influenced by changes in gene expression and chromatin state. The project offers both wet and dry lab activities. The intern would work in the Foege Building, which houses the Department of Genome Sciences on the UW campus.

8. University of Washington, Noble Lab (Computational)

Dr. William Noble’s lab develops statistical and machine learning methods for interpreting genomic data. A 4DN-SUUPER intern assigned to the Noble Lab will work closely with a postdoctoral fellow on development of machine learning methods for analyzing time series single-cell Hi-C data and, potentially, for integrating that data with parallel single-cell measurements of gene expression and chromatin accessibility.


The student will meet weekly with Dr. Noble and the postdoc mentor, participate in one on-one meetings with their mentor, and also attend a weekly two-hour lab meeting. The goal will be to implement and validate a model for scHi-C time series analysis. This is a purely “dry lab” internship. As such, familiarity with Python programming is essential. Linux skills are also beneficial. The intern would work in the Foege Building, which houses the Department of Genome Sciences on the UW campus.

9. Duke University, Diao Lab (Computational & Experimental)

The Diao Lab is a functional genomics lab with strong interest in tissue regeneration. Our summer projects will allow the trainees to get hands on experience of conducting both bench work and learning bioinformatics skills to study the dynamics changes of transcriptome, chromatin accessibility, and 3D genome organization of human muscle stem cells undergoing proliferation and differentiation.

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