New generation of transcriptome analysis methods receives $625k in funding
Earning a National Science Foundation (NSF) Faculty Early Career Development (CAREER) award is a goal for many researchers and faculty. It is one of the most prestigious awards the National Science Foundation grants in support of “faculty who exemplify the role of teacher-scholars through research, education and the integration of education and research within the context of the mission of their organizations.”
The Department of Computer Science is proud to announce its second 2018 NSF CAREER awardee, Professor Robert Patro. In February 2018 Patro learned that he had received a 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.
Samir Das, chair of computer science at Stony Brook University, offered his congratulations to Patro and said, “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.”
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 $625k supports Patro’s involvement as well as 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 the Alan Alda Center for Communicating Science here at Stony Brook which will aid in developing media products that are comprehensible on all levels.
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.