Now recruiting: 2020-2021 USC URAP Undergraduate Fellow!
We are actively accepting applications from current USC undergraduate students to fill one position for the USC Undergraduate Research Associates Program in Mangul Lab for Fall 2020 and Spring 2021. The theme of our URAP internship for 2020-2021 is “Big Data Analysis Techniques (BDAT) for Scientific Reproducibility.” 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?
Saturday, August 25, 2020 at 5:00pm Pacific Standard Time
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 September 1, 2020, to April 30, 2021 (nine months, full academic year). Fellows will assume the role of a trainee researcher and perform individual research projects, guided by PI Mangul, in collaboration with our team of graduate students and postdoctoral scholars.
WHAT IS INVOLVED IN THE FELLOWSHIP?
Fellows will spend approximately 10 hours per week working start-to-finish on their own benchmarking study, which represents an excellent opportunity to develop competency in designing a project, using Unix commands, running Python scripts, installing and debugging software packages, generating and shaping data, producing statistical results and data visualizations, curating project materials for long-term storage on GitHub, and producing a scholarly report of aims, methods, and results. 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). Due to the multidisciplinary nature of computational genomics and biomedical research, Fellows will work with faculty in the Keck School of Medicine, and Dept. of Computational Biology.
Note regarding the COVID-19 pandemic: the 2020-2021 URAP Fellow hosted by Mangul Lab will perform work remotely. We are prepared to accommodate a student who works remotely from different time zones.
The successful applicant will be paid the standard stipend per academic semester ($1,500) for an average ten hours of research per week during the academic terms. 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.
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 for the 2020-2021 URAP Fellow hands-on training with the aim of gaining competency in using computational 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 acquired skills to conduct a benchmarking project that assesses the accuracy and usability of computational tools developed for genomics and biomedical data.
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 tools for BDAT; interpret results in the context of major scientific questions; and present project materials on an open-source data sharing platform.
(1) Benchmarking of Structural Variant (SV) callers, computational tools designed to detect SVs in genomic data. SV are genomic regions that have an altered DNA sequence due to deletion, duplication, insertion, or inversion, and some SVs may indicate disease status.
(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) Attend weekly lab meetings in CHP 236. 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. The Fellow will be encouraged to, and supported in, preparing a manuscript for submission to a peer-reviewed journal.
Note regarding the COVID-19 pandemic: all lab activities will be conducted via Zoom.
(1) Computational background;
(2) Life science background;
(3) Past academic performance;
(4) Aptitude to complete a research project.
ABOUT PI MANGUL
PI Mangul has over six years of experience teaching BDAT to researchers of all levels, including undergraduates. While a postdoctoral scholar at UCLA, PI Mangul developed a three-day “Intro to UNIX” workshop that he taught 15 times to over 300 individuals (2013 to 2019). PI Mangul has mentored 27 undergraduates, including 16 students enrolled in the UCLA Bruins-in-Genomics (B.I.G.) Summer Undergraduate Research Program; he supervised six students who won a Best Poster Award. Three of PI Mangul’s former mentees are now PhD students in bioinformatics at UCLA. At least 20 of his undergraduate mentees are contributing authors on peer-reviewed publications; one mentee as first author. During Fall 2019, Mangul Lab at USC hosted one undergraduate intern from Rensselaer Polytechnic Institute.