Now recruiting: 2024-2025 USC URAP Fellow!
We are actively accepting applications from current USC undergraduate students to fill the position for the USC Undergraduate Research Associates Program in Mangul Lab for Summer 2024, Fall 2024 and Spring 2025. The theme of our URAP fellowship for 2024-2025 is “Robustness and reproducibility of computational genomic tools.” Please review the details below for additional information. 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?
Deadline is rolling.
WHO SHOULD APPLY?
USC undergraduate students who are interested in computational bioscience research and have basic computational training are invited to join Mangul Lab from May 20th, 2024, to April 30, 2025 (Summer 2024 or Fall/Spring 2024-2025). Fellows will assume the role of undergraduate student researcher and perform individual research projects, guided by Dr. Mangul, in collaboration with and assistance from our graduate students and postdoctoral scholars.
WHAT IS INVOLVED IN THE FELLOWSHIP?
Fellows will spend approximately 10-12 hours each week working on their own robustness and reproducibility 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. Fellows 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, Fellows will work remotely and all the resources can be accessed in remote settings. Due to the multidisciplinary nature of computational genomics and biomedical research, Fellows will also work with faculty in the Keck School of Medicine, and Dept. of Computational Biology.
STUDENT STIPEND
The successful applicant will be paid the standard stipend per academic semester ($1,500 for Fall or Spring, $3,000 for Summer) for an average of ten hours of research per week during the Fall and Spring, and full-time during Summer. Stipends will be disbursed as merit-based financial aid through the Office of Undergraduate Programs. Please contact your financial aid counselor for any questions regarding eligibility or potential impacts to existing financial aid.
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 data; perform benchmarking studies to assess genomics methods and help researchers select the right tools for a project; and work to increase the installability and archival stability of bioinformatics software.
We will provide the URAP Fellow with hands-on training, with our main aim being - gaining competency in using computational genomics tools for big data analytic techniques (BDAT) and scientific replicability, and a realistic multidisciplinary research experience at the level of a typical first-year graduate student. With our guidance, the Fellow will leverage his/her acquired skills to conduct a project that assesses the robustness and reproducibility of computational tools developed for the analysis of biomedical data.
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.
REQUIRED ACTIVITIES IN ADDITION TO RESEARCH
(1) Create an Individual Development Plan to identify goals for the nine-month internship, hands-on training in computational tools and BDAT.
(2) 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.
(3) Complete online Responsible Conduct of Research (RCR) training (available free of charge to USC students; 2-4 hours). Mangul Lab research activities do not involve human subjects nor HIPAA-protected data; however, big data analysis presents unique ethical issues.
(4) Write a two-page perspective paper, supported by five scholarly references, discussing the role of scientific reproducibility in research ethics.
(5) Create a formal poster presentation of project aims, methods, and results, to be presented at an end-of-the-year Mangul Lab social event in CHP 236. Our graduate students and postdoctoral scholars will guide the Fellows in developing and presenting their posters.
(6) Develop lay-friendly scientific communication materials; a five-minute video summarizing their work for the lab YouTube channel, a one-page, lay-friendly summary for the lab blog, and a promotional tweet of their work for the lab Twitter account.
We will also encourage the Fellow to submit their work to the annual USC Undergraduate Symposium for Scholarly & Creative Work and national conferences; and to apply for USC UGP Conference Travel Grants when appropriate. URAP Fellows 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;
(2) Life science background;
(3) Past academic performance;
(4) Aptitude for completion of a research project.
Application form
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.
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