Professor Robert Patro of the Department of Computer Science has received a 2018 National Science Foundation (NSF) CAREER award for his research proposal, A Comprehensive and Lightweight Framework for Transcriptome Analysis.
In layman’s terms, this project focuses on the field of RNA (ribonucleic acid) research and how to analyze sequencing data pertaining to it. In addition to performing various other functions in the cell, RNA acts as a messenger molecule, carrying instructions from DNA and acting as a template for protein synthesis.
“As a researcher at an institution focused on developing engineering-driven solutions in medical research, his proposed project supports not only the mission of the Department of Computer Science but also the University as a whole,” said Samir Das, chair of computer science at Stony Brook.
As Patro’s project proposal explains, the goal is “to develop a new generation of accurate, lightweight methods for the analysis of both bulk and single-cell transcriptomic data.” Patro says the project should “push forward the state-of-the-art in terms of both the accuracy and fundamental capabilities of lightweight transcriptome analysis methods.” He hopes the final outcome of the project will provide a new generation of accurate and lightweight transcriptome analysis tools and methods. These advancements in method and software should ultimately reduce costs, enable new analyses, and help contribute to discoveries in future RNA research.
The NSF CAREER funding in the amount of $625,000 supports Patro’s involvement as well as that of several grad and PhD students working in his research lab. The education plan detailed in the CAREER proposal involves working with both students and the campus community and incorporates creating a series of educationally-driven podcasts and videos. He believes that in using a variety of educational methods to accompany his CAREER research he will reach people of both technical and non-technical backgrounds as well as people from diverse communities. In conjunction, Professor Patro also has the support of Stony Brook’s Alan Alda Center for Communicating Science.
Robert Patro is an assistant professor of computer science in the College of Engineering and Applied Sciences at Stony Brook University since 2014. He earned a PhD and BS in computer science from the University of Maryland-College Park. Prior to joining Stony Brook, he was a visiting scholar as well as a Postdoctoral Research Associate at Carnegie Mellon University. Patro’s main academic interests are in the design of algorithms and data structures for processing, organizing, indexing and querying high-throughput genomics data. He is also interested in the intersection between efficient algorithms and statistical inference. Previous to this NSF CAREER award, Patro was the Stony Brook PI on an NSF award shared with Cambridge University entitled Data-driven hierarchical analysis of de novo transcriptomes. Patro and his students develop, maintain and contribute to a number of different open-source bioinformatics software tools.