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Functional interpretation of genomes using human cell-type-specific biological networks adsa


Term:

Summer

Department:

BI: Broad Institute

Faculty Supervisor:

Guopin Feng / Kasper Lage

Faculty email:

fengg@mit.edu

Apply by:

June 1st

Contact:

lage.kasper@mgh.harvard.edu

Project Description

The rapid improvements in our ability to interrogate genomes for variation associated with diseases, has lead to an explosion in genomic data. Systematically assigning function to genetic variants in these large datasets, and understanding how variation in different genes converge on functional molecular networks, remains a major challenge. This limits our progress towards biological insight and therapeutic intervention. The specific goal of this UROP project is to contribute to data analytics in a cross-disciplinary team that develops large-scale computational and experimental methods to functionally interpret genomic data using biological networks. These networks are generated from human cell-type-specific protein-protein interactions and RNA sequencing datasets we produce at the Broad Institute. Moreover, he/she will incorporate these networks into a computational pipeline being built at the Broad Institute of MIT and Harvard for genome interpretation. The student will also be involved in testing the pipeline and running analyses on new genomic datasets. A pilot version of the pipeline is already being used widely in the genomics community and the student will have the opportunity to interact with computer scientists, computational biologists, experimentalists, software developers and researchers in areas such as type-2-diabetes, cardiovascular diseases and psychiatric disorders where the pipeline is being implemented. The student will become a full member of the Lage Lab at the Broad Institute and MGH and we expect that that she or he will fully engage and participate in lab activities full time over the summer and longer if there is mutual interest. The work will be carried out remotely at least until June 28th and perhaps further if the Broad Institute remains closed. The lab currently interacts per Slack, Google Hangouts, and Zoom and is in constant communication despite the pandemic. We expect the student to join virtual lab meetings and present their work on these meetings. In the past, UROP students in the lab have been highly successful and presented their work at the Broad Retreat, the Annual Meeting of the American Society of Human Genetics, the annual joint meeting of the Executive Committee and the Scientific Advisory Board of the Stanley Center for psychiatric Research at the Broad Institute. A majority of UROP students in the lab have also been first or coauthors on manuscripts that are either published in peer-reviewed journals or currently in review while posted as preprints on bioRxiv. Several have gone on to receive full MD/PhD or PhD scholarships at Harvard, Oxford, and Johns Hopkins Universities after their undergraduate research in the lab. The project will be mainly supervised by Kasper Lage (Associate Professor, Massachusetts General Hospital and Harvard Medical School and Group Leader and member of the Leadership Group of the Stanley Center for Psychiatric Research at the Broad Institute of MIT and Harvard); and co-supervised by Guoping Feng (the Poitras Professor of Neuroscience at the McGovern Institute for Brain Research in the Department of Brain and Cognitive Sciences at MIT and member of the Stanley Center for Psychiatric Research at Broad Institute. Contact: Please send your application to lage.kasper@mgh.harvard.edu. The application should contain a CV, your availability schedule over the summer, and a brief paragraph on your interests and expectation of the project.

Pre-requisites

- Highly motivated student in computer science, bioinformatics, computational biology or the likes. - Good collaboration and communication skills. - Fully dedicated to joining the lab and becoming a fully-fledged lab member. - An interest in the genetics of common disorders and cancers. - Strong computational skills in R, Perl, C++, Python or Java. - The ability and will to work in cross-disciplinary teams and learn about other fields. - Knowledge about biology and genetics is a plus, but not a must. Contact: Please send your application to lage.kasper@mgh.harvard.edu. The application should contain a CV, your availability schedule over the summer, and a brief paragraph on your interests and expectation of the project.