On the Distribution of Lexical Features at Multiple Levels of Analysis. - Fatemeh Almodaresi; Lyle H. Ungar; Vivek Kulkarni; Mohsen Zakeri; Salvatore Giorgi; H. Andrew Schwartz (ACL (2), 2017)

Rainbowfish: A Succinct Colored de Bruijn Graph Representation. - Fatemeh Almodaresi; Prashant Pandey 001; Rob Patro (WABI, 2017)

Improved data-driven likelihood factorizations for transcript abundance estimation. - Mohsen Zakeri; Avi Srivastava; Fatemeh Almodaresi; Rob Patro (Bioinform., 2017)

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. - Prashant Pandey 001; Fatemeh Almodaresi; Michael A. Bender; Michael Ferdman; Rob Johnson 001; Rob Patro (RECOMB, 2018)

A space and time-efficient index for the compacted colored de Bruijn graph. - Fatemeh Almodaresi; Hirak Sarkar; Avi Srivastava; Rob Patro (Bioinform., 2018)

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. - Laraib Malik; Fatemeh Almodaresi; Rob Patro (Bioinform., 2018)

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. - Fatemeh Almodaresi; Prashant Pandey 001; Michael Ferdman; Rob Johnson 001; Rob Patro (RECOMB, 2019)

An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. - Fatemeh Almodaresi; Prashant Pandey 001; Michael Ferdman; Rob Johnson 001; Rob Patro (J. Comput. Biol., 2020)

Algorithms and Data Structures for Indexing, Querying, and Analyzing Large Collections of sequencing Data in the presence or Absence of a Reference. - Fatemeh Almodaresi (2020)

PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. - Fatemeh Almodaresi; Mohsen Zakeri; Rob Patro (Bioinform., 2021)

An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. - Fatemeh Almodaresi; Jamshed Khan; Sergey Madaminov; Michael Ferdman; Rob Johnson 001; Prashant Pandey 001; Rob Patro (Bioinform., 2022)