NOW RECRUITING: 2024-2025 NSF-funded UNDERGRADUATE STEM INTERN!
Grigore Boldirev February 05, 2024
NOW RECRUITING: 2024-2025 NSF-funded UNDERGRADUATE STEM INTERN!
We are actively accepting applications from current undergraduate STEM students to fill the position of an Undergraduate Researcher at the Mangul Lab for Summer 2024. The Mangul Lab is committed to ensuring an inclusive and supportive environment regardless of age, gender, sexual orientation, disability, race, ethnicity, religion, nationality, or socioeconomic background.
DEADLINE TO APPLY?
Monday, May 20, 2024 5:00pm Pacific Time (We will be interviewing candidates on a rolling basis, we encourage you to apply early)
WHO SHOULD APPLY?
Undergraduate students who are interested in computational bioscience research and have basic computational training are invited to join Mangul Lab from June 16th, 2024, to August 20, 2024 (dates can be changed if necessary). The intern will perform individual research projects, guided by Dr. Mangul, in collaboration with and assistance from our graduate students and postdoctoral scholars. Candidates must be eligible to work in the United States.
We strongly encourage applications from traditionally underrepresented students.
WHAT IS INVOLVED IN THE INTERNSHIP?
The intern will spend up to 40 hours each week working on their own bioinformatics project, which presents an excellent opportunity to develop competency in various aspects including designing a project, learning to work with Unix and Python scripts, implementing and debugging software packages, and pipelines, analyzing data obtained from statistical tests and data visualization, curating project materials for long-term storage on GitHub, and producing a scholarly scientific report consisting of aims, methods, results and interpretation. Interns will each be assigned their own desk for the duration of their internship in our computational lab located in the Center for the Health Professions Building (CHP) 236, on the USC Health Sciences Campus (HSC). Alternatively, if needed, interns will work in hybrid mode and all the resources can be accessed in remote settings. Due to the multidisciplinary nature of computational genomics and biomedical research, interns will collaborate with different faculty and researchers from different departments and universities.
STUDENT STIPEND
The successful applicant will be employed by USC and paid $3000 over the period of the internship.
PROJECT SUMMARY
Mangul Lab designs, develops, and applies novel data-driven, computational approaches that accelerate the diffusion of genomics and biomedical data into translational research and education. Mangul Lab undergraduate and graduate students, postdocs, and PI create novel bioinformatics methods and apply these tools to big omics data; perform benchmarking studies to assess omics methods and help researchers select the right tools for a project; and work to increase the installability and archival stability of bioinformatics software. Our primary goal is to equip the intern with practical, hands-on training in the use of computational genomics tools for analyzing big data and ensuring scientific replicability. Through this internship, the intern will gain a realistic and multidisciplinary research experience equivalent to that of a first-year graduate student. Our approach will be centered on providing the intern with ample opportunities to engage in meaningful research, learn new techniques, and develop key skills that will prepare them for a successful career in the field. Our team of experienced professionals will provide mentorship and guidance throughout the program, ensuring that the intern receives the support they need to thrive.
SAMPLE PROJECTS
We propose research projects that are well-suited to model for the URAP Fellow how scientific methods, data, and ideas translate in real time. Each benchmarking study will require the Fellow to select performance metrics relevant to their research questions; document their work as they install, run, and debug each computational tool; generate summary statistics using open-source genomics tools; interpret results in the context of major scientific questions; and present project materials on an open-source data-sharing platform.
(1) Benchmarking of computational genomics tools designed for read alignment, quantification, and detection of structural variants in genomic data, to assess their robustness and reproducibility.
(2) Benchmarking of computational methods developed to perform error correction on next-generation sequencing data. Errors present in genomic data may impact downstream analysis and limit the applicability of sequencing technologies in clinical tools.
(3) Benchmarking of gene expression deconvolution tools, which are designed to estimate cell type abundance using gene expression data.
(4) Develop robust and scalable methods to assemble V(D)J alleles from next-generation sequencing data and robust species- and strain-specific methods to assemble B and T cell receptor repertoire from next-generation sequencing data.
REQUIRED ACTIVITIES IN ADDITION TO RESEARCH
(1) Participate in the weekly lab meetings in CHP 236 or via teleconferencing means. The Fellow will be responsible for weekly presentations of results and issues encountered, as well as at least one formal oral presentation (with slides) per academic term.
(2) Write a two-page perspective paper, supported by five scholarly references, discussing the role of scientific reproducibility in research ethics.
(3) Create a formal poster presentation of project aims, methods, and results, to be presented at an end-of-the-year Mangul Lab social event. Our graduate students and postdoctoral scholars will guide the Interns in developing and presenting their posters. We will also encourage the Intern to submit their work to national conferences. The interns will be encouraged to, and supported in, preparing a manuscript for submission to a peer-reviewed journal, on successful completion of the project.
SELECTION CRITERIA
(1) Computational background (Experience in Python, Bash shell scripting, Jupyter Notebooks preferred but not required)
(2) Life science background
(3) Past academic performance
(4) Aptitude for completion of a research project
ABOUT PI MANGUL
Dr. Mangul is a highly experienced instructor with over a decade of expertise teaching BDAT and computational genomics techniques to researchers at various levels, including undergraduate students. During his postdoctoral fellowship at UCLA, he created a comprehensive “Intro to UNIX” workshop that he taught 15 times, reaching over 300 individuals between 2013 and 2019. In addition to his instructional roles, Dr. Mangul has mentored over 30 undergraduate students, 16 of whom were enrolled in the UCLA Bruins-in-Genomics (B.I.G.) Summer Undergraduate Research Program, and six of these students won the Best Poster Award. Six former mentees of Dr. Mangul are currently pursuing Ph.D. degrees in bioinformatics at esteemed institutions such as USC, UCLA, UC Davis, and George Washington University. Moreover, at least 20 of Dr. Mangul’s undergraduate mentees are contributing authors on peer-reviewed publications, with three of them as the first author. Furthermore, Dr. Mangul has recently mentored three undergraduate students under the USC URAP 2020-23 program, one of whom, Cecilia Liu, was accepted into the prestigious USC Quantitative and Computational Biology Ph.D. program.