Former CBCB Graduate Student Receives Larry S. Davis Doctoral Dissertation Award
A former graduate student in the Center for Bioinformatics and Computational Biology (CBCB) has been recognized for the excellence of her academic work on developing practical and efficient solutions to index large collections of genomes.
Fatemeh Almodaresi, who graduated with a Ph.D. in computer science in Summer 2020, is one of two students to receive the Larry S. Davis Doctoral Dissertation Award this year.
The annual award recognizes outstanding doctoral dissertations in the Department of Computer Science that convey excellence in their technical depth, significance, potential impact and presentation quality.
The award is named for Larry Davis, a Distinguished University Professor of computer science who served as chair of the department from 1999–2012. Davis was also the founding director of the University of Maryland Institute for Advanced Computer Studies (UMIACS), providing leadership for the institute from 1985–1994.
Her UMD dissertation, “Algorithms and Data Structures Indexing, Querying, and Analyzing Large Collections of Sequencing Data in the Presence or Absence of a Reference,” covers the development of new data structures as well as innovative, practical and efficient solutions to indexing large collections of genomes.
“Fatemeh demonstrates both technical brilliance and the ability to come up with ideas that are theoretically interesting and of tremendous practical impact,” says Rob Patro, an associate professor of computer science who advised Almodaresi during her doctoral studies.
In recommending her for the Davis dissertation award, Patro noted Almodaresi’s design of a new compacted version of a De Bruijn graph, a data structure that is used in bioinformatics to assemble and analyze genomes. Although similar structures have previously been proposed, Almodaresi’s work greatly improved the practicality and efficiency in important ways, Patro explains.
In recommending her for the dissertation award, Patro noted Almodaresi’s design of a new compacted version of a De Bruijn graph, a data structure that is used in bioinformatics to assemble and analyze genomes. Although similar structures have previously been proposed, Almodaresi’s work greatly improved the practicality and efficiency in important ways, Patro explains.
Almodaresi also built a tool using her new data structure for the taxonomic assignment of metagenomic read data, a well-studied problem in the field of computational biology. The taxonomic classifier she designed is both more accurate and more efficient—requiring less memory while operating at a similar speed—than two popular tools that are widely-used to accomplish the same task, Patro says.
One major goal in the field is to build practical indexes on the hundreds of thousands of sequencing samples available in public data repositories. In pursuit of this idea, Almodaresi developed new methods and solutions to perform large-scale search of raw sequencing data using a system called Mantis. Her methods allow the index to be iteratively updated–a crucial feature as the amount of genomic data to be indexed continues to grow.
“I anticipate that much of the theory and methodology Fatemeh develops will have a far-reaching impact both within and beyond the field of genomics,” says Patro. “She is a truly expectational researcher—displaying an intelligence, commitment and real passion at a level that I find to be rare, even among top Ph.D. students.”
—Story by Maria Herd