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.
Meet the SUPER interns
Isabel Watson
Isabel Watson is an incoming second-year Microbiology, Immunology, and Molecular Genetics major at UCLA. Her internship was at the Disteche Lab at the University of Washington, where she helped the lab study the role of the mammalian X chromosome in development and sex differences by performing staging, DNA isolation, PCR, and gel electrophoresis. After graduation, Isabel plans on going to graduate school and researching ways of using gene editing to possibly cure and prevent genetic disorders, which have plagued her dad’s side of the family. Her experience has been immeasurably valuable, as it strengthened her resume and provided her with skills applicable to other molecular and cell biology labs.
Abel Tesfaye
Abel Tesfaye was involved in the work focused on mouse embryonic development. This significantly increased his understanding and passion for computational biology and computational analysis. By studying the temporal expression patterns of genes in the mouse embryo, Abel gained valuable knowledge of the complexities of gene regulation during critical stages of the mouse embryo development. This research has not only enhanced his biological knowledge but also developed his skills in programming and data analysis using R and Python. This experience where he applied computational tools to real-world biological data has increased his ability to bridge the gap between theoretical knowledge and practical application. By analyzing complex datasets and visualizing gene expression dynamics, Abel developed a strong foundation in bioinformatics that will help him tackle real-world challenges, such as understanding human diseases. This project has empowered Abel as a researcher, by equipping him with the tools and confidence needed to contribute meaningfully to the field of computational biology.
Damisi Kayode
Damisi Kayode had the privilege of working in the Dekker Lab this summer where she learned how to perform basic research techniques to better understand the structure of human chromosomes. Damisi was able to successfully prematurely condense human chromosomes in the G1 phase, allowing researchers to eliminate the confusion of sister chromatids during Hi-C analysis. This experience allowed Damisi to hone her laboratory skills, enhance her analytical thinking, and deepen her understanding of molecular biology—all critical areas relevant to medicine. Collaborating with a diverse team of scientists also refined her communication and teamwork abilities. This internship has been invaluable in affirming her aspiration to pursue medical school, as it has provided insight into the importance of research in advancing medical knowledge and improving patient care.
Walid Ichcho
Walid Ichcho is a rising sophomore at Brandeis University, with a double major in Biology and Neuroscience. This summer, Walid had the opportunity to be an intern at the Duan Lab at the University of Washington, where he contributed to advanced genomic research, including mapping promoter-enhancer loops, performing Hi-C protocols, and working on tasks such as PCR, gels, and cell tissue culturing. His experience helped deepen his understanding of the intricate relationship between genome architecture and gene expression, which is essential for his aspirations in neuroscience. Walid’s passion for immunology and neuroscience continues to drive his ambition to become a neuroscientist or neurosurgeon.
Mansi Sharma
Frema Owusu-Ansah
Frema Owusu-Ansah is a fourth-year student at the University of Georgia, where she is pursuing a double major in Biology and Applied Biotechnology with a focus on Biomedical Science. This summer, Frem was an intern in the Diao Lab at Duke University. Her project was titled “Right place, Right time, Right amount: Developing Novel Cell-type Specific Tools to Study Human Heart Development”. Frema and her team focused on designing an inducible iPSCs cell line that could be used to understand the role and mechanisms of the non-coding DNA and cis-regulatory elements on congenital heart diseases via CRISPRi and CRISPRa dCas9 system.
As an aspiring physician-scientist, this internship has been instrumental in solidifying Frema’s career aspirations and planning her future steps. Frema gained exposure to a variety of new techniques and, under excellent mentorship, developed valuable skills in cell culturing, plasmid cloning, PCR and primer design, bacterial transformation, and plasmid preparation. After graduation, Frema intends to further hone these skills in a post-baccalaureate research program before applying to an MD/PhD program to advance her education and career.
Alex Belov
Alex Belov is a rising senior at Emory University studying Math & Computer Science and Biology from Wyckoff, NJ. He was an intern at the Leslie Lab at Memorial Sloan Kettering Cancer Center in New York City where his research focused on using machine-learning models to predict the Hi-C contact map from epigenomic data. Alex will continue working with the Leslie Lab as he pursues his honors thesis. The 4DN program sparked his passion for computational biology and genomic research through his exciting research project and the weekly lectures both at his host institution and through 4DN!
Jaden Mattison
Jaden Mattison is a rising junior at the University of Hawaii at Manoa studying biochemistry. This summer, Jaden was an intern at the Beliveau Lab at the University of Washington. His research involved using the RNA fluorescence in situ hybridization (RNA-FISH) technique to identify cell types within mouse embryo tissue sections. His internship has allowed him to experience the workflow of how research is conducted in an academic setting. After graduation, Jaden would like to enroll in pharmacy school to become a clinical pharmacist in a hospital setting.
Application 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: oh@4dnucleome.org
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 oh@4dnucleome.org.
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 (https://www.mskcc.org/education-training/high-school-college/computational-biology-summer-program-cbsp) 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.