In the summer of 2022, the Human BioMolecular Atlas Program (HuBMAP) launched its second iteration of the Undergraduate Student Internship Program which enables undergraduate students to work with HuBMAP researchers for the summer to learn cutting-edge single-cell technologies, 3D model making, and software building. Thirteen students were chosen by HuBMAP researchers at ten institutions to work in their labs over the summer to learn these technologies. At the end of the internship, each student gave a presentation about their experience. See below to learn more about their exciting work!
HuBMAP Researcher: Alison Pouch, Ph.D. and James Gee, Ph.D, Ph.D. at the University of Pennsylvania
Intern project: Karli Prather worked at the Penn Image Computer and Science (PICSL) Labto develop an interactive and customizable digital representation of the ovary. She built a computer model of the pelvis to give users a point of reference for where the ovary is situated in the body.
Watch the presentation - here.
HuBMAP Researcher: Ljiljana Paša-Tolić, Ph.D. at Pacific Northwest National Laboratory (PNNL)
Intern project: Camryn Pettenger-Willey worked at PNNL to optimize a protocol for imaging different versions of proteins within tissues.
Watch the presentation - here.
HuBMAP Researcher: Kate O'Neill, MD, MTR at the University of Pennsylvania
Intern project: Marielena Grijalva optimized the protocol for isolating nuclei from uterine tissue for Singulator, a machine that dissociates tissue into single-cell or nuclei suspensions.
Watch the presentation - here.
HuBMAP Researcher: Liming Pei, Ph.D. at the Children’s Hospital of Philadelphia
Intern project: Anusha Thaniana performed single-cell RNA-sequencing to determine the activity levels of genes within the heart to study Fontan Associated Liver Disease.
Watch the presentation - here.
HuBMAP Researcher: Brian Gregory, Ph.D. at the University of Pennsylvania
Intern project: Mohamed El-Sadec optimized the High-throughput Analysis of Modified Ribonucleoties (HAMR) software which makes notes of nucleotides in RNA sequencing data that have been modified after transcription.
Watch the presentation - here.
HuBMAP Researcher: Jeff Spraggins, Ph.D. at Vanderbilt University
Intern project: Lin Xu helped to develop a program that automatically adds different colors to images of tissue slices. By colorizing these images, people are more easily able to understand the structure of the cells and tissues that they see.
Watch the presentation - here.
HuBMAP Researcher: Huiping Liu, Ph.D. at Northwestern University
Intern project: Genna Mahabeer mapped proteins within the red and white pulp regions of the spleen.
Watch the presentation - here.
HuBMAP Researcher: Katy Börner, Ph.D. at Indiana University
Intern project: Sangmyung (Sam) Lee compared Tabula sapiens to HuBMAP’s Human Reference Atlas (HRA). Tabula sapiens is a molecular reference atlas for more than 400 cell types of the human body, and ASCT+B tables are a data framework built by HuBMAP researchers to capture naming terms for anatomical human body parts and spatial reference objects. By comparing the two, the HRA can determine what’s missing, and what needs to be added to improve.
Watch the presentation - here.
HuBMAP Researcher: James Hagood, MD at the University of North Carolina
Intern project: M.J. Hopkins determined the optimal concentration of antibodies necessary to characterize the cells from the airway in single-cell techniques.
Watch the presentation - here.
HuBMAP Researcher: Phil Blood, Ph.D.( at the Pittsburgh Supercomputing Center (PSC)
Intern project: Fransiskus Agapa developed a computer program that automatically extracted, prepared, and submitted data and metadata from HuBMAP and the NIH database of Genotypes and Phenotypes (dbGap) to be ingested by the Common Fund Data Ecosystem (CFDE).
Watch the presentation - here.
HuBMAP Researcher: Kate O'Neill, MD, MTR at the University of Pennsylvania
Intern project: Gabrielle LeNoir analyzed specific cell populations in the female reproductive system to better understand the stages of the menstrual cycle.
Watch the presentation - here.
HuBMAP Researcher: Nils Gehlenborg, Ph.D. at Harvard University
Intern project: Tram Nguyen worked on the user interface for the HuBMAP Data Portal by making graphs of existing metadata using the R programming language.
Watch the presentation - here.
HuBMAP Researcher: Rahul Satija, Ph.D. at the New York Genome Center (NYGC)
Intern project: Lesley Aguilar-Salceda used single-cell RNA sequencing to study different cell types in the motor cortex of the brain in mice, ferrets, and pigs to find genes that have been conserved throughout evolution.
Watch the presentation - here.
If you would like to see more about the work of the these talented students, or the HuBMAP Consortium itself, please go to the HuBMAP YouTube channel or visit us at HuBMAP Consortium or NIH Common Fund HuBMAP.
HuBMAP Undergraduate Student Internship Program was funded by 1OT2OD026675-01.
